Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
$
A
- a - Variable in class javajs.util.Matrix
- a - Variable in class org.jmol.g3d.PrecisionRenderer
- a - Variable in class org.jmol.util.SimpleUnitCell
- a_ - Variable in class org.jmol.util.SimpleUnitCell
- A4 - Class in javajs.util
-
A 4 element axis angle represented by single precision floating point x,y,z,angle components.
- A4() - Constructor for class javajs.util.A4
-
Constructs and initializes a AxisAngle4f to (0,0,1,0).
- aaTest1 - Variable in class org.jmol.viewer.TransformManager
- aatoken - Variable in class org.jmol.script.ScriptEval
- AB - Enum constant in enum class jspecview.common.PanelData.LinkMode
- ABC - Enum constant in enum class jspecview.common.PanelData.LinkMode
- ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
- ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
- AbinitReader - Class in org.jmol.adapter.readers.xtal
- AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
- aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
- AboutDialog - Class in jspecview.application
-
The
About Dialog
class is the help | about window for JSpecView. - AboutDialog - Class in org.openscience.jmol.app.jmolpanel
- AboutDialog(Frame) - Constructor for class jspecview.application.AboutDialog
-
Constructor that initalises the Dialog a parent frame, no title and modality to true
- AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
- abs - Static variable in class org.jmol.script.T
- absolute - Static variable in class org.jmol.script.T
- ABSOLUTE - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
- AbstractButton - Class in org.jmol.awtjs.swing
- AbstractButton(String) - Constructor for class org.jmol.awtjs.swing.AbstractButton
- AbstractTableModel - Interface in org.jmol.awtjs.swing
- ac - Variable in class org.jmol.adapter.readers.cif.CifReader
- ac - Variable in class org.jmol.adapter.readers.simple.InputReader
- ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- ac - Variable in class org.jmol.atomdata.AtomData
- ac - Variable in class org.jmol.jvxl.readers.JvxlReader
- ac - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- ac - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- ac - Variable in class org.jmol.modelset.AtomCollection
- ac - Variable in class org.jmol.util.JmolMolecule
- accept(File) - Method in class jspecview.java.AwtDialogFileFilter
-
Implementation of method from interface
FileFilter
. - accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
- accept(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- ACCEPTOR - Enum constant in enum class org.jmol.c.HB
- acm - Variable in class org.jmol.viewer.Viewer
- acos - Static variable in class org.jmol.script.T
- act - Variable in class org.jmol.modelset.Model
-
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- action(String) - Method in interface org.jmol.api.JmolAudioPlayer
- action(String) - Method in class org.jmol.util.JmolAudio
-
Execute an action from load audio "xxxxx.wav" filter "id=a1 action=xxx"
- ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
- ACTION_center - Static variable in class org.jmol.viewer.ActionManager
- ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
- ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
- ACTION_count - Static variable in class org.jmol.viewer.ActionManager
- ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
- ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
- ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
- ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
- ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
- ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_select - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
- ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
- ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
- ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
- ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
- ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
- ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
- ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
- ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
- ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
- actionCommand - Variable in class org.jmol.awtjs.swing.JComponent
- actionListener - Variable in class org.jmol.awtjs.swing.JComponent
- actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- ActionManager - Class in org.jmol.viewer
- ActionManager() - Constructor for class org.jmol.viewer.ActionManager
- ActionManagerMT - Class in org.jmol.multitouch
- ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
- actionPerformed(ActionEvent) - Method in class jspecview.application.PreferencesDialog
-
Sets the color of the selected element on the current color button
- actionPerformed(ActionEvent) - Method in class jspecview.java.AwtDialogManager
-
ActionListener callback
- actionPerformed(ActionEvent) - Method in class org.jmol.awt.AwtPopupHelper
- actionPerformed(ActionEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ImageDialog
- actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
- actionPerformed(String) - Method in class jspecview.js2d.JsDialogManager
-
Jmol.Swing.click() callback (via SwingController)
- actionRotateBond(int, int, int, int, boolean) - Method in class org.jmol.modelkit.ModelKit
-
Actually rotate the bond.
- activate() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- activate() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- activateQuery() - Method in class jme.JME
- add - Static variable in class org.jmol.script.T
- add(float) - Method in class javajs.util.Quat
- add(int, V) - Method in class javajs.util.Lst
- add(String) - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- add(Map<String, Object>, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
- add(M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to sum of itself and matrix m1.
- add(Matrix) - Method in class javajs.util.Matrix
-
add two matrices
- add(T3) - Method in class javajs.util.M4
-
add to translation
- add(T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the vector sum of itself and tuple t1.
- add(T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the vector sum of itself and tuple t1.
- add(T3i) - Method in class javajs.util.T3i
-
Sets the value of this tuple to the sum of itself and t1.
- add(SC) - Method in interface org.jmol.api.SC
- add(SC) - Method in class org.jmol.awt.AwtSwingComponent
- add(SC) - Method in class org.jmol.awtjs.swing.AbstractButton
- add(SC) - Method in class org.jmol.awtjs.swing.ButtonGroup
- add(Component) - Method in class org.jmol.awtjs.swing.Container
- add(JComponent, Object) - Method in class org.jmol.awtjs.swing.JPanel
- add(JComponent, GridBagConstraints) - Method in class org.jmol.awtjs.swing.Grid
- add(V) - Method in class javajs.util.Lst
-
Deprecated.
- ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
- add2(T3d, T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the vector sum of tuples t1 and t2.
- add2(T3, T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the vector sum of tuples t1 and t2.
- add3(float, float, float) - Method in class javajs.util.T3
-
Add {a b c}
- add33(M34) - Method in class javajs.util.M34
- addActionListener(Object) - Method in interface org.jmol.api.SC
- addActionListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addActionListener(Object) - Method in class org.jmol.awtjs.swing.JComponent
-
Note that it will be the job of the JavaScript on the page to do with actionListener what is desired.
- addActions(List<Action>) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- addAnnotation(Lst<String>) - Method in class jspecview.common.PanelData
- addApplyBtn - Variable in class jspecview.dialog.JSVDialog
- addAssembly(String[]) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addAtom(double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
-
add a proton to the atom list
- addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst<Object>, boolean, byte, BS, float) - Method in class org.jmol.modelset.ModelSet
- addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtoms(int) - Method in class org.jmol.modelset.Group
- addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
- addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
turns this into a SPHERICAL iterator for "within Distance" measures
- addAtoms(BS) - Method in class org.jmol.symmetry.UnitCellIterator
- addAtomSet(String) - Method in class org.jmol.modelkit.ModelKit
- addAtomstoMatrix() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Generate noeMatrix and map fields for DistanceJMolecule.
- addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addAttribute(SB, String, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- addAttributes(SB, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
- addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
- addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
- addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
- addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
- addBondNoCheck(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addBonds - Variable in class org.jmol.adapter.writers.CMLWriter
- addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
- addButton(String, String) - Method in interface jspecview.api.PlatformDialog
- addButton(String, String) - Method in class jspecview.java.AwtDialog
- addButton(String, String) - Method in class jspecview.js2d.JsDialog
- addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
- addBytes(byte[], int, int) - Method in class javajs.util.ZipData
- addCheckBox(String, String, int, boolean) - Method in interface jspecview.api.PlatformDialog
- addCheckBox(String, String, int, boolean) - Method in class jspecview.java.AwtDialog
- addCheckBox(String, String, int, boolean) - Method in class jspecview.js2d.JsDialog
- addCifAtom(Atom, String, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- addCoef(Map<String, Object>, float[], String, float, float, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- addCommand(int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addCommand(String) - Method in class org.jmol.util.CommandHistory
-
Adds any number of lines to the command history
- addCommand(String) - Method in class org.jmol.viewer.Viewer
-
Adds one or more commands to the command history
- addComponent(Component) - Method in class org.jmol.awtjs.swing.Container
- addConnectedHAtoms(Atom, BS) - Method in class org.jmol.modelset.BondCollection
- addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
- addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
- addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
- addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
- addContourPoints(Lst<Object>, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- addCouple(int, int, int, int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- addData(MOCalculation, boolean) - Method in interface org.jmol.quantum.mo.DataAdder
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder11H
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder13I
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder7F
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder9G
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderF
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderG
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderH
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderI
- addDialog(int, Annotation.AType, AnnotationData) - Method in class jspecview.common.PanelData
- addDisplayedBackbone(Atom, boolean) - Method in class org.jmol.shapebio.Backbone
- addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addEquiv(double[], double[], double[]) - Method in class org.jmol.quantum.NMRNoeMatrix
- addExplicitLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addExtension(String) - Method in class jspecview.java.AwtDialogFileFilter
-
Adds an extension to the JSpecViewFileFilter
- addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
- addFunction(ScriptFunction) - Method in class org.jmol.script.ScriptEval
- addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
- addHeader() - Method in class org.jmol.adapter.readers.cif.CifReader
- addHeader() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- addHeader(Lst<String[]>, String, String) - Static method in class jspecview.source.JDXReader
- addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addHetero(String, String, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addHighlight(double, double, int, int, int, int) - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a
JSVPanel
- addHighlight(double, double, int, int, int, int) - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a
JSVPanel
- addHighlight(double, double, int, int, int, int) - Method in class jspecview.appletjs.JSVApplet
- addHighlight(double, double, int, int, int, int) - Method in class jspecview.application.MainFrame
- addHighlight(GraphSet, double, double, Spectrum, int, int, int, int) - Method in class jspecview.common.PanelData
-
Add information about a region of the displayed spectrum to be highlighted applet only right now
- addHistoryWindowDimInfo(String, Component, Dimension) - Method in interface org.jmol.api.JmolAppAPI
- addHistoryWindowDimInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.JmolApp
- addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
- addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
- addHydrogenBond(Lst<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
- addhydrogens - Static variable in class org.jmol.script.T
- addHydrogens(BS, int) - Method in class org.jmol.viewer.Viewer
- addHydrogens(Lst<Atom>, P3[]) - Method in class org.jmol.modelset.ModelSet
-
these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in interface org.jmol.api.JmolScriptManager
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.script.ScriptManager
-
Add hydrogens to a model
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- addImageResource(Object, int, int, int[], boolean) - Method in class javajs.export.PDFCreator
- addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.BioResolver
-
Get bonding info for double bonds and add implicit hydrogen atoms, if needed.
- addInfo(Map<String, String>) - Method in class javajs.export.PDFCreator
- addIntegralRegion(double, double) - Method in class jspecview.common.IntegralData
- addItemListener(Object) - Method in interface org.jmol.api.SC
- addItemListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addItemListener(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
- addItems(String[][]) - Method in class org.jmol.popup.PopupResource
- addJDXSpectrum(String, Spectrum, boolean) - Method in class jspecview.source.JDXSource
-
Adds a Spectrum to the list
- addJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- addJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Add using Jmol atom index
- addJmolProperties(Properties) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addJmolWindowInfo(String, Component, Point) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Deprecated.
- addJmolWindowInnerInfo(String, Component, Dimension) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addLast(V) - Method in class javajs.util.Lst
- addLatticeVector(Lst<float[]>, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addLatticeVector(Lst<float[]>, String) - Method in interface org.jmol.adapter.smarter.MSInterface
- addLatticeVectors(Lst<float[]>) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.SpaceGroup
- addListener(PanelListener) - Method in class jspecview.common.PanelData
- addListSelectionListener(Object) - Method in class org.jmol.awtjs.swing.JTable
-
It will be the function of the JavaScript on the page to do with selectionListener what is desired.
- addListSelectionListener(Object) - Method in interface org.jmol.awtjs.swing.ListSelectionModel
- addLockedAtoms(SymmetryInterface, BS) - Method in class org.jmol.modelkit.ModelKit
-
Only for the current model
- addMacrosMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addMarks(String) - Method in class jspecview.common.IntegralData
-
INTEGRATION MARK list where list is a comma-separated list of ppm1-ppm2 with :x.x added to normalize one of them and starting with 0-0 clears the integration
- addMatrix(String, M4, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtJmolPopup
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtModelKitPopup
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.popup.GenericPopup
- addMenuItem(JMenu, String, char, ActionListener) - Static method in class jspecview.application.ApplicationMenu
- addMenuItem(SC, String) - Method in class org.jmol.popup.GenericPopup
- addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericPopup
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
- addMethyl(double, double, double, double, double, double, double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
-
Add a methyl group to the atom list
- addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- addMOData(int, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
- addModulation(Map<String, double[]>, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
- addModulation(Map<String, double[]>, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
- addMol() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- addMol() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
- addMolFile(String, int, SB, BS, BS, boolean, boolean, boolean, Quat, boolean) - Method in class org.jmol.adapter.writers.MOLWriter
- addMouseListener(Object) - Method in interface org.jmol.api.SC
- addMouseListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addMouseListener(Object) - Method in class org.jmol.awtjs.swing.Component
- addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNOE(int, int, String, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
-
addOp The primary driver of the Reverse Polish Notation evaluation engine.
- addPeakData(String) - Method in class jspecview.source.JDXReader
- addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
- addPeakHighlight(PeakInfo) - Method in class jspecview.common.PanelData
- addPluginMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
- addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
- addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
- addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
- addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
- addPopulation(double[]) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
- addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
- addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the given properties to the history.
- addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the given property to the history.
- addPropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
- addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
- addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
- addRenderer(int) - Method in class org.jmol.export.Export3D
- addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
-
allows core JavaScript loading to not involve these classes
- addRenderer(int) - Method in class org.jmol.util.GData
- addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
- addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
- addRotatedTensor(Atom, Tensor, int, boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
- addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
- addSelectOption(String, String, String[], int, boolean) - Method in interface jspecview.api.PlatformDialog
- addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.java.AwtDialog
- addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.js2d.JsDialog
- addSGTransform(SymmetryInterface, String, M4, M4) - Static method in class org.jmol.modelkit.ModelKit
- addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AmsReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.DgridReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
See MopacSlaterReader
- addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
- addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
- addSpecShift(double) - Method in class jspecview.common.Measurement
- addSpecShift(double) - Method in class jspecview.common.Spectrum
- addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addStructure(STR, String, String, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructureProtected(STR, String, String, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructureSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
We must add groups to the proper bsStructure element
- addSubSpectrum(Spectrum, boolean) - Method in class jspecview.common.Spectrum
-
adds an nD subspectrum and titles it "Subspectrum
" These spectra can be iterated over using the UP and DOWN keys. - addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
- addSubSystemOp(String, Matrix, Matrix, Matrix) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
- addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
- addTextField(String, String, String, String, String, boolean) - Method in interface jspecview.api.PlatformDialog
- addTextField(String, String, String, String, String, boolean) - Method in class jspecview.java.AwtDialog
- addTextField(String, String, String, String, String, boolean) - Method in class jspecview.js2d.JsDialog
- addTo(GenericZipTools, SB) - Method in class javajs.util.ZipData
- addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
- addTo(T3, float) - Method in class org.jmol.util.ModulationSet
- addToken(String, T) - Static method in class org.jmol.script.T
- addToList(int, Lst<Spectrum>) - Method in class jspecview.common.PanelData
- addTracePt(int, Point3fi) - Method in class org.jmol.util.Vibration
- addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
- addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
- addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
- addTuple(int, P3) - Method in class org.jmol.bspt.Bspf
- addTuple(T3) - Method in class org.jmol.bspt.Bspt
-
Iterate through all of your data points, calling addTuple
- addUniqueControls() - Method in class jspecview.dialog.IntegrationDialog
- addUniqueControls() - Method in class jspecview.dialog.JSVDialog
- addUniqueControls() - Method in class jspecview.dialog.MeasurementsDialog
- addUniqueControls() - Method in class jspecview.dialog.OverlayLegendDialog
- addUniqueControls() - Method in class jspecview.dialog.PeakListDialog
- addUniqueControls() - Method in class jspecview.dialog.ViewsDialog
- addUniqueControls(DialogManager) - Method in class jspecview.dialog.JSVDialog
- addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
- addUTens(String, float) - Method in class org.jmol.util.ModulationSet
- addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
- addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
- addVectors(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addVertexCopy(T3, float, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
- addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window informations to the history.
- addWindowInfo(String, Component, Point, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowInnerInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowListener() - Method in class org.jmol.console.JmolConsole
- addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
- addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
- addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
- addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
- addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
- addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
- addXList(Lst<?>) - Method in class org.jmol.script.ScriptMathProcessor
- addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
- addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
- addXMap(Map<String, ?>) - Method in class org.jmol.script.ScriptMathProcessor
- addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
- addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
- addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
- addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
- addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
- addZipEntry(Object, String) - Method in interface javajs.api.GenericZipTools
- addZipEntry(Object, String) - Method in class javajs.util.ZipTools
- AdfReader - Class in org.jmol.adapter.readers.quantum
-
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
- AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
- AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
- adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
- adjustForWindow - Variable in class org.jmol.modelset.Text
- Adler32 - Class in com.jcraft.jzlib
- Adler32() - Constructor for class com.jcraft.jzlib.Adler32
- adpmax - Static variable in class org.jmol.script.T
- ADPMAX - Enum constant in enum class org.jmol.c.VDW
- adpmin - Static variable in class org.jmol.script.T
- ADPMIN - Enum constant in enum class org.jmol.c.VDW
- adpMode - Variable in class org.jmol.atomdata.AtomData
- advanceSubSpectrum(int) - Method in class jspecview.common.PanelData
- advanceSubSpectrum(int) - Method in class jspecview.common.Spectrum
- AFLOWReader - Class in org.jmol.adapter.readers.more
-
A reader for various AFLOW file types.
- AFLOWReader() - Constructor for class org.jmol.adapter.readers.more.AFLOWReader
- afterClear - Variable in class jme.JME
- AimsReader - Class in org.jmol.adapter.readers.xtal
-
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
- AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
- AjaxURLConnection - Class in javajs.util
-
A method to allow a JavaScript Ajax
- AjaxURLConnection(URL) - Constructor for class javajs.util.AjaxURLConnection
- AjaxURLStreamHandler - Class in javajs.util
-
A method to allow a JavaScript AJAX adapter to deliver web content to JSmol.
- AjaxURLStreamHandler(String) - Constructor for class javajs.util.AjaxURLStreamHandler
- AjaxURLStreamHandlerFactory - Class in javajs.util
-
For handling URL file IO via AJAX in JavaScript version
- AjaxURLStreamHandlerFactory() - Constructor for class javajs.util.AjaxURLStreamHandlerFactory
- AlchemyReader - Class in org.jmol.adapter.readers.simple
-
TRIPOS simple Alchemy reader.
- AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
- alert(String) - Method in class org.jmol.viewer.Viewer
- align - Variable in class org.jmol.modelset.Text
- align - Static variable in class org.jmol.script.T
- ALIGN_CENTER - Static variable in class jme.JMEUtil
- ALIGN_LEFT - Static variable in class jme.JMEUtil
- ALIGN_RIGHT - Static variable in class jme.JMEUtil
- alignment - Variable in class jme.AtomDisplayLabel
- all - Static variable in class org.jmol.script.T
- ALL - Enum constant in enum class jspecview.common.PanelData.LinkMode
- ALL - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
- ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- allconnected - Static variable in class org.jmol.script.T
- allEmptyString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- ALLENE - Static variable in class org.jmol.smiles.SmilesStereo
- allfloat - Static variable in class org.jmol.script.T
- allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- allHs - Variable in class jme.JME
- allNaN() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allNull() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allocateColix(int, boolean) - Static method in class org.jmol.util.C
- allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
- allocateExpCouples(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- allocateExpNoes(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.java.AwtPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.js2d.JsPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in interface org.jmol.api.GenericPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
-
Create an "image" that is either a canvas with width/height/buf32 (from g3d.Platform32) or just an associative array with those (image writing
- allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
-
a simpler option
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
-
legacy only
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
-
This is the older main access point for creating an application or applet vwr.
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
-
old way...
- allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
- allocMesh(String, Mesh) - Method in class org.jmol.shapecgo.CGO
- allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
- allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
- allocTempEnum(int) - Method in class org.jmol.util.TempArray
- allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
- allocTempPoints(int) - Method in class org.jmol.util.TempArray
- allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
- allocTempScreens(int) - Method in class org.jmol.util.TempArray
- allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
- allow_a_len_1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- allowAromaticBond(Bond) - Method in class org.jmol.modelset.BondCollection
- allowArrayDotNotation - Variable in class org.jmol.viewer.Viewer
- allowaudio - Static variable in class org.jmol.script.T
- allowCapture() - Method in class org.jmol.viewer.Viewer
- allowDashed - Variable in class org.jmol.render.MeshRenderer
- allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
- allowembeddedscripts - Static variable in class org.jmol.script.T
- allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
- allowgestures - Static variable in class org.jmol.script.T
- allowJavaConsole - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- allowkeystrokes - Static variable in class org.jmol.script.T
- allowMenu - Variable in class jspecview.common.JSViewer
- allowmodelkit - Static variable in class org.jmol.script.T
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
- allowmoveatoms - Static variable in class org.jmol.script.T
- allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- allowmultitouch - Static variable in class org.jmol.script.T
- allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
- allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allowrotateselected - Static variable in class org.jmol.script.T
- allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
- allowSignedFeatures - Variable in class org.jmol.popup.GenericPopup
- allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
- allowSubSpec(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
- allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
- allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
- allSame() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allTrajectories - Variable in class org.jmol.adapter.writers.CMLWriter
- allZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- alpha - Variable in class org.jmol.util.SimpleUnitCell
- ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
- ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
- ALPHA_SHIFT - Static variable in class org.jmol.util.C
- ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
- alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- AlphaMonomer - Class in org.jmol.modelsetbio
- AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
- AlphaPolymer - Class in org.jmol.modelsetbio
- ALT - Static variable in class org.jmol.util.ColorEncoder
- ALT - Static variable in class org.jmol.viewer.binding.Binding
- ALT_MASK - Static variable in class org.jmol.awtjs.Event
- altArgbsCpk - Static variable in class org.jmol.viewer.JC
- altElementCounts - Variable in class org.jmol.util.JmolMolecule
- altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
- altElementMax - Static variable in class org.jmol.util.Elements
-
length of the altElementSymbols, altElementNames, altElementNumbers arrays
- altElementMax - Variable in class org.jmol.util.JmolMolecule
- altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
- altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
- altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
- altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
- altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
- altloc - Variable in class org.jmol.modelset.Atom
- altloc - Static variable in class org.jmol.script.T
- altLoc - Variable in class org.jmol.adapter.smarter.Atom
- ALTLOC - Enum constant in enum class org.jmol.c.PAL
- altLocCount - Variable in class org.jmol.modelset.Model
- altType - Variable in class org.jmol.util.Tensor
- altVertices - Variable in class org.jmol.util.MeshSurface
- am - Variable in class org.jmol.modelset.ModelSet
- am - Variable in class org.jmol.viewer.Viewer
- ambientocclusion - Static variable in class org.jmol.script.T
- ambientOcclusion - Variable in class org.jmol.util.GData
- ambientpercent - Static variable in class org.jmol.script.T
- amino - Static variable in class org.jmol.script.T
- AMINO - Enum constant in enum class org.jmol.c.PAL
- AMINO - Static variable in class org.jmol.util.ColorEncoder
- AminoMonomer - Class in org.jmol.modelsetbio
- AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
- AminoPolymer - Class in org.jmol.modelsetbio
- AML - Enum constant in enum class jspecview.common.ExportType
- AMLExporter - Class in jspecview.export
-
class
AnIMLExporter
contains static methods to export a Graph as as AnIML. - AMLExporter() - Constructor for class jspecview.export.AMLExporter
- AmpacReader - Class in org.jmol.adapter.readers.simple
-
A reader for AMPAC output.
- AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
- AmsReader - Class in org.jmol.adapter.readers.quantum
-
A reader for AMS output subclassing the older AdfReader.
- AmsReader() - Constructor for class org.jmol.adapter.readers.quantum.AmsReader
- anchor - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- and(BS) - Method in class javajs.util.BS
-
Performs a logical AND of this target bit set with the argument bit set.
- andequals - Static variable in class org.jmol.script.T
- andNot(BS) - Method in class javajs.util.BS
-
Clears all of the bits in this
BitSet
whose corresponding bit is set in the specifiedBitSet
. - andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
- angle - Variable in class javajs.util.A4
-
The angle.
- angle - Static variable in class org.jmol.script.T
- angle(V3) - Method in class javajs.util.V3
-
Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
- angle(V3d) - Method in class javajs.util.V3d
- angstroms - Static variable in class org.jmol.script.T
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
- animation - Static variable in class org.jmol.script.T
- animationfps - Static variable in class org.jmol.script.T
- animationFps - Variable in class org.jmol.viewer.AnimationManager
- AnimationManager - Class in org.jmol.viewer
- animationmode - Static variable in class org.jmol.script.T
- animationOn - Variable in class org.jmol.viewer.AnimationManager
- animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
- animationThread - Variable in class org.jmol.viewer.AnimationManager
- AnimationThread - Class in org.jmol.thread
- AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
- AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- ANIMFRAME - Enum constant in enum class org.jmol.c.CBK
- AnIMLReader - Class in jspecview.source
-
Representation of a XML Source.
- AnIMLReader() - Constructor for class jspecview.source.AnIMLReader
- anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
- anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
- anisotropy - Static variable in class org.jmol.script.T
- anisotropy() - Method in class org.jmol.util.Tensor
-
anisotropy = directed distance from (center of two closest) to (the furthest)
- Annotation - Class in jspecview.common
-
The
Annotation
class stores the spectral x and pixel y values of an annotation text along with its text - Annotation - Class in org.jmol.modelsetbio
- Annotation() - Constructor for class jspecview.common.Annotation
- Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
- ANNOTATION - Enum constant in enum class org.jmol.c.STR
- Annotation.AType - Enum Class in jspecview.common
- AnnotationData - Interface in jspecview.api
- AnnotationParser - Class in org.jmol.dssx
-
A parser for output from 3DNA web service.
- AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
- antialias - Variable in class org.jmol.render.MeshRenderer
- antialias - Variable in class org.jmol.viewer.TransformManager
- antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- antialiasdisplay - Static variable in class org.jmol.script.T
- antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
- antialiased - Variable in class org.jmol.viewer.Viewer
- antialiasEnabled - Variable in class org.jmol.util.GData
- antialiasimages - Static variable in class org.jmol.script.T
- antialiasThisFrame - Variable in class org.jmol.util.GData
- antialiastranslucent - Static variable in class org.jmol.script.T
- aperatureAngle - Variable in class org.jmol.viewer.TransformManager
- apertureAngle - Variable in class org.jmol.export.___Exporter
- apiPlatform - Variable in class jspecview.common.JSViewer
- apiPlatform - Variable in class org.jmol.api.JmolViewer
- apiPlatform - Variable in class org.jmol.util.GData
- apivot - Static variable in class org.jmol.script.T
- apointx - Variable in class jme.JME
- apointy - Variable in class jme.JME
- apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
- app - Variable in class jspecview.appletjs.JSVApplet
- appCheckItem(String, SC) - Method in class jspecview.popup.JSVGenericPopup
- appCheckItem(String, SC) - Method in class org.jmol.popup.GenericPopup
-
Opportunity to do something special with an item.
- appCheckItem(String, SC) - Method in class org.jmol.popup.JmolPopup
- appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericPopup
-
Opportunity to do something special with a given submenu is created
- appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolPopup
- AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
- appConsole - Variable in class org.jmol.viewer.Viewer
- AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
- AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
- AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
-
general entry point
- append - Static variable in class org.jmol.script.T
- append(String) - Method in class javajs.util.OC
-
will go to string buffer if bw == null and os == null
- append(String) - Method in class javajs.util.SB
- append(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
- append(String) - Method in interface org.jmol.console.GenericTextArea
- append(String) - Method in class org.jmol.util.JSONWriter
- appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Appends an AtomSetCollection
- appendAttrib(SB, Object, Object) - Static method in class javajs.util.XmlUtil
- appendB(boolean) - Method in class javajs.util.SB
- appendC(char) - Method in class javajs.util.SB
- appendCB(char[], int, int) - Method in class javajs.util.SB
- appendCdata(SB, String, Object[], String) - Static method in class javajs.util.XmlUtil
-
" will convert ]]> to ]] > - appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
- appendContourTriangleIntersection(int, float, float, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
- appendD(double) - Method in class javajs.util.SB
- appendEmptyTag(SB, String, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
- appendF(float) - Method in class javajs.util.SB
-
note that JavaScript could drop off the ".0" in "1.0"
- appendFontCmd(SB) - Method in class org.jmol.modelset.Text
- appendI(int) - Method in class javajs.util.SB
- appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appendnew - Static variable in class org.jmol.script.T
- appendNew - Variable in class org.jmol.viewer.GlobalSettings
- appendO(Object) - Method in class javajs.util.SB
- appendSB(SB) - Method in class javajs.util.SB
- appendTag(SB, String, Object) - Static method in class javajs.util.XmlUtil
-
standard
data " standard" - appendTagAll(SB, String, Object[], Object, boolean, boolean) - Static method in class javajs.util.XmlUtil
- appendTagObj(SB, String, Object[], Object) - Static method in class javajs.util.XmlUtil
-
standard
data " - appendUunitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appFixLabel(String) - Method in class jspecview.popup.JSVGenericPopup
- appFixLabel(String) - Method in class org.jmol.popup.GenericPopup
- appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
- appGetBooleanProperty(String) - Method in class jspecview.popup.JSVGenericPopup
- appGetBooleanProperty(String) - Method in class org.jmol.modelkit.ModelKitPopup
- appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericPopup
- appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
- appGetMenuAsString(String) - Method in class jspecview.popup.JSVGenericPopup
- appGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
- appGetMenuAsString(String) - Method in class org.jmol.popup.JmolPopup
- appletCodeBase - Static variable in class org.jmol.viewer.Viewer
- AppletConsole - Class in org.jmol.console
- AppletConsole - Class in org.jmol.consolejs
-
An interface to Jmol.Console.
- AppletConsole() - Constructor for class org.jmol.console.AppletConsole
- AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
- appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- appletDocumentBase - Static variable in class jspecview.common.JSVFileManager
- appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
- appletFrame - Variable in class jspecview.app.JSVApp
- AppletFrame - Interface in jspecview.api
- APPLETID - Enum constant in enum class jspecview.common.ScriptToken
- appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
- appletName - Variable in class jspecview.common.JSViewer
- appletName - Variable in class org.jmol.viewer.Viewer
- appletObject - Variable in class org.jmol.util.GenericApplet
- appletproxy - Static variable in class org.jmol.script.T
- APPLETREADY - Enum constant in enum class org.jmol.c.CBK
- appletReadyCallbackFunctionName - Variable in class jspecview.app.JSVApp
- APPLETREADYCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
- application - Variable in class jme.JME
- ApplicationMenu - Class in jspecview.application
-
The Main Class or Entry point of the JSpecView Application.
- ApplicationMenu(MainFrame) - Constructor for class jspecview.application.ApplicationMenu
- apply(Object[]) - Method in class jspecview.dialog.JSVDialog
- applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
- applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
- applyFromFields() - Method in class jspecview.dialog.IntegrationDialog
- applyFromFields() - Method in class jspecview.dialog.JSVDialog
- applyFromFields() - Method in class jspecview.dialog.ViewsDialog
- applyFunc(Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
- applyLeftMouse(int) - Static method in class jspecview.app.GenericMouse
- applyScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
-
Apply the scale factor to the coordinates
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- applySymmetryBio(Map<String, Object>, boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- applysymmetrytobonds - Static variable in class org.jmol.script.T
- applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appRestorePopupMenu() - Method in class jspecview.popup.JSVGenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.GenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.JmolPopup
- approx(float, float) - Static method in class javajs.util.PT
- approx0(float) - Static method in class org.jmol.util.SimpleUnitCell
- appRunScript(String) - Method in class jspecview.popup.JSVGenericPopup
- appRunScript(String) - Method in class org.jmol.popup.GenericPopup
- appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
- AppToolBar - Class in jspecview.application
- AppToolBar(MainFrame) - Constructor for class jspecview.application.AppToolBar
- appUpdateForShow() - Method in class jspecview.popup.JSVGenericPopup
- appUpdateForShow() - Method in class org.jmol.modelkit.ModelKitPopup
- appUpdateForShow() - Method in class org.jmol.popup.GenericPopup
- appUpdateForShow() - Method in class org.jmol.popup.JmolPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
-
Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
-
(1) setOption --> set setOption true or set setOption false
- arc - Static variable in class org.jmol.script.T
- ARC - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- area - Static variable in class org.jmol.script.T
- areAxesTainted() - Method in class org.jmol.viewer.Viewer
- areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
- areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
- areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
- areEqual(SV, SV) - Static method in class org.jmol.script.SV
-
For legacy reasons, "x" == "X" but see isLike()
- areEqualTest(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
-
for JUnit test, mainly
- areLinkableX(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
- areLinkableY(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
- areXScalesCompatible(Spectrum, Spectrum, boolean, boolean) - Static method in class jspecview.common.Spectrum
- areYScalesSame(int, int) - Method in class jspecview.common.ViewData
- argb - Variable in class org.jmol.awtjs.swing.Color
- argbCurrent - Variable in class org.jmol.util.GData
- argbNoisyDn - Variable in class org.jmol.util.GData
- argbNoisyUp - Variable in class org.jmol.util.GData
- argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
- argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
- argbsCpk - Static variable in enum class org.jmol.c.PAL
-
Default table of CPK atom colors.
- argbsCpkRasmol - Static variable in enum class org.jmol.c.PAL
- argbsFormalCharge - Static variable in class org.jmol.viewer.JC
- argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
- argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
- argbsRoygbScale - Static variable in class org.jmol.viewer.JC
- argbsRwbScale - Static variable in class org.jmol.viewer.JC
- aromatic - Static variable in class org.jmol.script.T
- array - Static variable in class org.jmol.script.T
- arrayAdd(Object) - Method in class org.jmol.util.JSONWriter
- arrayClose(boolean) - Method in class org.jmol.util.JSONWriter
- arrayCopyBool(boolean[], int) - Static method in class javajs.util.AU
- arrayCopyByte(byte[], int) - Static method in class javajs.util.AU
- arrayCopyF(float[], int) - Static method in class javajs.util.AU
- arrayCopyI(int[], int) - Static method in class javajs.util.AU
- arrayCopyII(int[][], int) - Static method in class javajs.util.AU
- arrayCopyObject(Object, int) - Static method in class javajs.util.AU
-
note -- cannot copy if array is null! does not copy if length is unchanged
- arrayCopyPt(T3[], int) - Static method in class javajs.util.AU
- arrayCopyRangeI(int[], int, int) - Static method in class javajs.util.AU
-
a specialized method that allows copying from a starting point either to the end or to the middle (color schemes, especially)
- arrayCopyRangeRevI(int[], int, int) - Static method in class javajs.util.AU
- arrayCopyS(String[], int) - Static method in class javajs.util.AU
- arrayCopyShort(short[], int) - Static method in class javajs.util.AU
- ArrayDataReader - Class in javajs.util
-
ArrayDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with String[] arrays without any further adaptation.
- ArrayDataReader() - Constructor for class javajs.util.ArrayDataReader
- arrayDiv(Quat[], Quat[], int, boolean) - Static method in class javajs.util.Quat
- arrayOpen(boolean) - Method in class org.jmol.util.JSONWriter
- arrayToList(SV) - Method in class org.jmol.script.SV
- arrow - Static variable in class org.jmol.script.T
- ARROW - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- as - Static variable in class org.jmol.script.T
- asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
- asBoolean() - Method in class org.jmol.script.SV
- asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ASCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- ascent - Variable in class org.jmol.render.LabelsRenderer
- asFloat() - Method in class org.jmol.script.SV
- asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
- ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- asInt() - Method in class org.jmol.script.SV
- asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
- asObject - Variable in class javajs.util.CifDataParser
-
A flag to create and return Java objects, not strings.
- asPDF - Variable in class jspecview.common.PrintLayout
- assign - Static variable in class org.jmol.script.T
- assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
-
algorithm discussed above.
- assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
- assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
- ASSOCIATION - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- asString() - Method in class javajs.util.T3i
- asString() - Method in class org.jmol.script.SV
- asString() - Method in class org.jmol.symmetry.SpaceGroup
- astrType - Static variable in class org.jmol.script.T
- asymMatrix - Variable in class org.jmol.util.Tensor
- asymmetry() - Method in class org.jmol.util.Tensor
-
asymmetry = deviation from a symmetric tensor
- async - Static variable in class org.jmol.script.T
- async - Variable in class org.jmol.viewer.Viewer
- at - Variable in class org.jmol.modelset.AtomCollection
- atNos - Variable in class org.jmol.util.JmolMolecule
- atokenInfix - Variable in class org.jmol.script.ScriptCompiler
- atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
- atom - Variable in class org.jmol.minimize.MinAtom
- Atom - Class in org.jmol.adapter.smarter
- Atom - Class in org.jmol.modelset
- Atom() - Constructor for class org.jmol.adapter.smarter.Atom
- Atom() - Constructor for class org.jmol.modelset.Atom
- ATOM_INFRAME - Static variable in class org.jmol.modelset.Atom
- ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
- ATOM_NOFLAGS - Static variable in class org.jmol.modelset.Atom
- ATOM_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
- ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.modelset.Atom
- ATOM_VISIBLE - Static variable in class org.jmol.modelset.Atom
- ATOM_VISSET - Static variable in class org.jmol.modelset.Atom
- atom1 - Variable in class org.jmol.modelset.Bond
- atom2 - Variable in class org.jmol.modelset.Bond
- atomCenterOrCoordinateParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
- AtomCollection - Class in org.jmol.modelset
- AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
- AtomCollection.AtomSorter - Class in org.jmol.modelset
- AtomData - Class in org.jmol.atomdata
- AtomData() - Constructor for class org.jmol.atomdata.AtomData
- atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- AtomDataServer - Interface in org.jmol.atomdata
- AtomDisplayLabel - Class in jme
- AtomDisplayLabel(double, double, String, int, int, int, int, int, int, int, int, FontMetrics, double, boolean) - Constructor for class jme.AtomDisplayLabel
- atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
- atomExpression(T[], int, int, boolean, boolean, Object[], boolean) - Method in class org.jmol.script.ScriptEval
- atomExpressionAt(int) - Method in class org.jmol.script.ScriptEval
- atomExpressionAt(int) - Method in class org.jmol.scriptext.ScriptExt
- atomExpressionCommand - Static variable in class org.jmol.script.T
- atomFormats - Variable in class org.jmol.shape.Hover
- atomHighlighted - Variable in class org.jmol.viewer.Viewer
- atomicMass - Static variable in class org.jmol.util.Elements
- atomicNumber - Variable in class org.jmol.atomdata.AtomData
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
- atomicorbital - Static variable in class org.jmol.script.T
- atomid - Static variable in class org.jmol.script.T
- atomID - Variable in class org.jmol.modelset.Atom
- ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
- ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
- ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C2 - Static variable in class org.jmol.viewer.JC
- ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C4 - Static variable in class org.jmol.viewer.JC
- ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C5 - Static variable in class org.jmol.viewer.JC
- ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C5M - Static variable in class org.jmol.viewer.JC
- ATOMID_C6 - Static variable in class org.jmol.viewer.JC
- ATOMID_C7 - Static variable in class org.jmol.viewer.JC
- ATOMID_C8 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
- ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
- ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_MAX - Static variable in class org.jmol.modelsetbio.BioResolver
- ATOMID_N1 - Static variable in class org.jmol.viewer.JC
- ATOMID_N2 - Static variable in class org.jmol.viewer.JC
- ATOMID_N3 - Static variable in class org.jmol.viewer.JC
- ATOMID_N4 - Static variable in class org.jmol.viewer.JC
- ATOMID_N6 - Static variable in class org.jmol.viewer.JC
- ATOMID_N7 - Static variable in class org.jmol.viewer.JC
- ATOMID_N9 - Static variable in class org.jmol.viewer.JC
- ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
- ATOMID_O1 - Static variable in class org.jmol.viewer.JC
- ATOMID_O1P - Static variable in class org.jmol.viewer.JC
- ATOMID_O2 - Static variable in class org.jmol.viewer.JC
- ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O2P - Static variable in class org.jmol.viewer.JC
- ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O4 - Static variable in class org.jmol.viewer.JC
- ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_O6 - Static variable in class org.jmol.viewer.JC
- ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
- ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
- ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_S4 - Static variable in class org.jmol.viewer.JC
- ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
- atomindex - Static variable in class org.jmol.script.T
- atomIndex - Variable in class org.jmol.atomdata.AtomData
- atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
- atomIndex - Variable in class org.jmol.shape.Hover
- atomIndex - Variable in class org.jmol.shape.Mesh
- atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
- atomIndex1 - Variable in class org.jmol.util.Tensor
- atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
- atomIndex2 - Variable in class org.jmol.util.Tensor
- AtomIndexIterator - Interface in org.jmol.api
-
note: YOU MUST RELEASE THE ITERATOR
- AtomIteratorWithinModel - Class in org.jmol.modelset
- AtomIteratorWithinModelSet - Class in org.jmol.modelset
- AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
- atomLabelBoundingBox - Variable in class jme.AtomDisplayLabel
- atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- atomList - Variable in class org.jmol.util.JmolMolecule
- atomMapAnyCase - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomMapX - Variable in class jme.AtomDisplayLabel
- atomMapY - Variable in class jme.AtomDisplayLabel
- atomMolecule - Variable in class org.jmol.atomdata.AtomData
- ATOMMOVED - Enum constant in enum class org.jmol.c.CBK
- atomname - Static variable in class org.jmol.script.T
- atomName - Variable in class org.jmol.adapter.smarter.Atom
- atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- atomno - Static variable in class org.jmol.script.T
- atomNo - Variable in class org.jmol.quantum.SlaterData
- atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
- atomPicked(int) - Method in class org.jmol.jsv.JSpecView
- atompicking - Static variable in class org.jmol.script.T
- atomproperty - Static variable in class org.jmol.script.T
- atomPropertyFloat(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
-
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
- atomPropertyInt(int) - Method in class org.jmol.modelset.Atom
-
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
- atomPropertyString(Viewer, int) - Method in class org.jmol.modelset.Atom
- atomPropertyTuple(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
- atomPt - Variable in class org.jmol.render.LabelsRenderer
- atomRadius - Variable in class org.jmol.atomdata.AtomData
- atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
- atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atoms - Variable in class org.jmol.atomdata.AtomData
- atoms - Variable in class org.jmol.minimize.Minimizer
- atoms - Static variable in class org.jmol.script.T
- atoms - Variable in class org.jmol.shapespecial.Dipole
- atoms - Variable in class org.jmol.shapesurface.Contact
- atomSerial - Variable in class org.jmol.adapter.smarter.Atom
- atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
-
A JFrame that allows for choosing an Atomset to view.
- AtomSetChooser(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
- AtomSetCollection - Class in org.jmol.adapter.smarter
- AtomSetCollection(String, AtomSetCollectionReader, AtomSetCollection[], Lst<?>) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
- AtomSetCollectionReader - Class in org.jmol.adapter.smarter
- AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
- atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
- atomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetObject
- atomSetInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- AtomSetObject - Class in org.jmol.adapter.smarter
- AtomSetObject() - Constructor for class org.jmol.adapter.smarter.AtomSetObject
- AtomShape - Class in org.jmol.shape
- AtomShape() - Constructor for class org.jmol.shape.AtomShape
- atomSite - Variable in class org.jmol.adapter.smarter.Atom
- atomsMax - Variable in class org.jmol.adapter.writers.CMLWriter
- AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
- atomStartEnd - Variable in class org.jmol.adapter.smarter.Structure
- atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSymmetry - Variable in class org.jmol.modelset.Atom
- atomTensorList - Variable in class org.jmol.modelset.AtomCollection
- atomTensors - Variable in class org.jmol.modelset.AtomCollection
- atomtype - Static variable in class org.jmol.script.T
- AtomType - Class in org.jmol.minimize.forcefield
- atomtypes - Static variable in class org.jmol.script.T
- atomx - Static variable in class org.jmol.script.T
- atomX - Variable in class org.jmol.modelset.Text
- atomy - Static variable in class org.jmol.script.T
- atomY - Variable in class org.jmol.modelset.Text
- atomz - Static variable in class org.jmol.script.T
- atomZ - Variable in class org.jmol.modelset.Text
- attEcho - Variable in class org.jmol.console.ScriptEditor
- attError - Variable in class org.jmol.console.ScriptEditor
- attHighlight - Variable in class org.jmol.console.ScriptEditor
- attrList - Variable in class jspecview.source.AnIMLReader
- atts - Variable in class org.jmol.adapter.readers.xml.XmlReader
- AU - Class in javajs.util
- AU() - Constructor for class javajs.util.AU
- audio - Static variable in class org.jmol.script.T
- AUDIO - Enum constant in enum class org.jmol.c.CBK
- auto - Static variable in class org.jmol.script.T
- AUTO - Enum constant in enum class jspecview.common.IntegralData.IntMode
- AUTO - Enum constant in enum class org.jmol.c.VDW
- AUTO_BABEL - Enum constant in enum class org.jmol.c.VDW
- AUTO_JMOL - Enum constant in enum class org.jmol.c.VDW
- AUTO_RASMOL - Enum constant in enum class org.jmol.c.VDW
- autoAddImplicitH - Variable in class org.jmol.smiles.SmilesSearch
- autoAnimationDelay - Variable in class org.openscience.jmol.app.JmolApp
- autobond - Static variable in class org.jmol.script.T
- autoBondBs4(BS, BS, BS, BS, short, boolean, SB) - Method in class org.jmol.modelset.ModelSet
- autoCalculate(int, String) - Method in class org.jmol.viewer.Viewer
- autoExit - Variable in class org.jmol.viewer.Viewer
- autoez - Variable in class jme.JME
- autofps - Static variable in class org.jmol.script.T
- autoHbond(BS, BS, boolean) - Method in class org.jmol.modelset.ModelSet
-
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
- autoHbond(BS, BS, boolean) - Method in class org.jmol.viewer.Viewer
- autoIntegrate - Variable in class jspecview.common.JSViewer
- autoIntegrate() - Method in class jspecview.common.IntegralData
- AUTOINTEGRATE - Enum constant in enum class jspecview.common.ScriptToken
- autonumber - Variable in class jme.JME
- autoplaymovie - Static variable in class org.jmol.script.T
- autoScrolls - Variable in class org.jmol.awtjs.swing.JComponent
- autoSelectOnLoad() - Method in class jspecview.common.PeakInfo
-
a spectrum which, when loaded, should fire a message to load first peak -- GC for now
- autoShowLegend - Variable in class jspecview.common.JSViewer
- auxiliaryInfo - Variable in class org.jmol.modelset.Model
- avail_in - Variable in class com.jcraft.jzlib.ZStream
- available() - Method in class com.jcraft.jzlib.InflaterInputStream
- ave(T3, T3) - Method in class javajs.util.T3
-
average of two tuples
- average - Static variable in class org.jmol.script.T
- AviCreator - Class in org.jmol.image
- AviCreator() - Constructor for class org.jmol.image.AviCreator
- awaken(boolean) - Method in class jspecview.application.MainFrame
- AwtClipboard - Class in jspecview.java
-
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
- AwtClipboard - Class in org.jmol.awt
-
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
- AwtColor - Class in jspecview.java
- AwtColor - Class in org.jmol.awt
- AwtColor(int) - Constructor for class jspecview.java.AwtColor
- AwtColor(int) - Constructor for class org.jmol.awt.AwtColor
- AwtColor(int, int, int) - Constructor for class jspecview.java.AwtColor
- AwtColor(int, int, int) - Constructor for class org.jmol.awt.AwtColor
- AwtColor(int, int, int, int) - Constructor for class jspecview.java.AwtColor
- AwtColor(int, int, int, int) - Constructor for class org.jmol.awt.AwtColor
- AwtDialog - Class in jspecview.java
-
AwtDialog extends JDialog, interpreting DialogManager's requests in terms of Swing and AWT.
- AwtDialog(DialogManager, JSVDialog, String) - Constructor for class jspecview.java.AwtDialog
- AwtDialogFileFilter - Class in jspecview.java
-
A implementation of the
FileFilter
that filters out all files except those with extensions that are added. - AwtDialogFileFilter() - Constructor for class jspecview.java.AwtDialogFileFilter
-
Intialises a
JSpecViewFileFilter
- AwtDialogFileFilter(String[]) - Constructor for class jspecview.java.AwtDialogFileFilter
-
Initialises the
JSpecViewFileFilter
with an list of extensions to filter - AwtDialogFileFilter(String[], String) - Constructor for class jspecview.java.AwtDialogFileFilter
-
Initialises the
JSpecViewFileFilter
with an list of extensions to filter and a description of the filter - AwtDialogManager - Class in jspecview.java
-
just a class I made to separate the construction of the AnnotationDialogs from their use
- AwtDialogManager() - Constructor for class jspecview.java.AwtDialogManager
- AwtFileDropper - Class in jspecview.java
- AwtFileDropper() - Constructor for class jspecview.java.AwtFileDropper
- AwtFileHelper - Class in jspecview.java
- AwtFileHelper() - Constructor for class jspecview.java.AwtFileHelper
- AwtG2D - Class in jspecview.java
-
generic 2D drawing methods -- AWT version
- AwtG2D - Class in org.jmol.awt
-
generic 2D drawing methods -- AWT version
- AwtG2D() - Constructor for class jspecview.java.AwtG2D
- AwtG2D() - Constructor for class org.jmol.awt.AwtG2D
- AwtJmolPopup - Class in org.jmol.awt
- AwtJmolPopup() - Constructor for class org.jmol.awt.AwtJmolPopup
- AwtMainPanel - Class in jspecview.java
- AwtMainPanel(BorderLayout) - Constructor for class jspecview.java.AwtMainPanel
- AwtModelKitPopup - Class in org.jmol.awt
- AwtModelKitPopup() - Constructor for class org.jmol.awt.AwtModelKitPopup
- AwtPanel - Class in jspecview.java
-
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
- AwtPanel.RequestThread - Class in jspecview.java
- AwtParameters - Class in jspecview.java
- AwtParameters() - Constructor for class jspecview.java.AwtParameters
- AwtPlatform - Class in jspecview.java
- AwtPlatform() - Constructor for class jspecview.java.AwtPlatform
- AwtPopup - Class in jspecview.java
- AwtPopup() - Constructor for class jspecview.java.AwtPopup
- AwtPopupHelper - Class in org.jmol.awt
-
all popup-related awt/swing class references are in this file.
- AwtPopupHelper(GenericPopup) - Constructor for class org.jmol.awt.AwtPopupHelper
- AwtPrintDialog - Class in jspecview.java
-
Dialog to set print preferences for JSpecview.
- AwtPrintDialog() - Constructor for class jspecview.java.AwtPrintDialog
- AwtSwingComponent - Class in org.jmol.awt
-
A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.
- AwtSwingComponent() - Constructor for class org.jmol.awt.AwtSwingComponent
- AwtTree - Class in jspecview.application
- AwtTree(JSViewer) - Constructor for class jspecview.application.AwtTree
- AwtTreeNode - Class in jspecview.application
- AwtTreeNode(String, PanelNode) - Constructor for class jspecview.application.AwtTreeNode
- AwtTreePath - Class in jspecview.application
- AwtTreePath(Object[]) - Constructor for class jspecview.application.AwtTreePath
- axes - Static variable in class org.jmol.script.T
- Axes - Class in org.jmol.shape
- Axes() - Constructor for class org.jmol.shape.Axes
- AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- axes2 - Variable in class org.jmol.shape.Axes
- axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- axescolor - Static variable in class org.jmol.script.T
- axesmode - Static variable in class org.jmol.script.T
- axesMode - Variable in class org.jmol.viewer.GlobalSettings
- axesmolecular - Static variable in class org.jmol.script.T
- axesoffset - Static variable in class org.jmol.script.T
- axesorientationrasmol - Static variable in class org.jmol.script.T
- AxesRenderer - Class in org.jmol.render
- AxesRenderer() - Constructor for class org.jmol.render.AxesRenderer
- axesscale - Static variable in class org.jmol.script.T
- axesTypes - Static variable in class org.jmol.viewer.JC
- axesunitcell - Static variable in class org.jmol.script.T
- axeswindow - Static variable in class org.jmol.script.T
- axis - Static variable in class org.jmol.script.T
- AXIS_A - Static variable in class org.jmol.viewer.JC
- axis1color - Static variable in class org.jmol.script.T
- axis2color - Static variable in class org.jmol.script.T
- axis3color - Static variable in class org.jmol.script.T
- axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
- axisangle - Static variable in class org.jmol.script.T
- axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
- axisLabels - Static variable in class org.jmol.viewer.JC
- axisNX - Static variable in class org.jmol.viewer.JC
- axisNY - Static variable in class org.jmol.viewer.JC
- axisNZ - Static variable in class org.jmol.viewer.JC
- axisPoints - Variable in class org.jmol.shape.Axes
-
[x, y, z, -x, -y, -z] or [a, b, c, -a, -b, -c]
- axisType - Variable in class org.jmol.shape.Axes
- axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
- axisX - Static variable in class org.jmol.viewer.JC
- axisXY - Variable in class org.jmol.shape.Axes
- axisY - Static variable in class javajs.util.Measure
- axisY - Static variable in class org.jmol.viewer.JC
- axisZ - Static variable in class org.jmol.viewer.JC
B
- b - Variable in class org.jmol.g3d.PrecisionRenderer
- b - Variable in class org.jmol.util.Rgb16
- b - Variable in class org.jmol.util.SimpleUnitCell
- b - Variable in class org.jmol.viewer.ActionManager
- b_ - Variable in class org.jmol.util.SimpleUnitCell
- babel - Static variable in class org.jmol.script.T
- BABEL - Enum constant in enum class org.jmol.c.VDW
- babel21 - Static variable in class org.jmol.script.T
- BABEL21 - Enum constant in enum class org.jmol.c.VDW
- back - Static variable in class org.jmol.script.T
- backbone - Static variable in class org.jmol.script.T
- Backbone - Class in org.jmol.shapebio
- Backbone() - Constructor for class org.jmol.shapebio.Backbone
- backboneBlockVis - Variable in class org.jmol.modelsetbio.Monomer
- BackboneRenderer - Class in org.jmol.renderbio
- BackboneRenderer() - Constructor for class org.jmol.renderbio.BackboneRenderer
- background - Static variable in class org.jmol.script.T
- backgroundColix - Variable in class org.jmol.export.___Exporter
- backgroundColix - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- backgroundcolor - Static variable in class org.jmol.script.T
- BACKGROUNDCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- backgroundImage - Variable in class org.jmol.util.GData
- backgroundmodel - Static variable in class org.jmol.script.T
- backlit - Static variable in class org.jmol.script.T
- backshell - Static variable in class org.jmol.script.T
- bad() - Method in class org.jmol.script.ScriptError
- balls - Static variable in class org.jmol.script.T
- Balls - Class in org.jmol.shape
- Balls() - Constructor for class org.jmol.shape.Balls
- BallsRenderer - Class in org.jmol.render
- BallsRenderer() - Constructor for class org.jmol.render.BallsRenderer
- bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- BannerFrame - Class in org.openscience.jmol.app.jsonkiosk
-
A simple class that throws up a white rectangle that has a single centered label.
- BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jsonkiosk.BannerFrame
- barb - Static variable in class org.jmol.script.T
- barDistance - Variable in class org.jmol.modelset.Text
- barPixels - Variable in class org.jmol.modelset.Text
- barPixelsXYZ - Variable in class org.jmol.modelset.Text
- barray - Static variable in class org.jmol.script.T
- BArray - Class in javajs.util
- BArray(byte[]) - Constructor for class javajs.util.BArray
- Base64 - Class in javajs.util
- Base64() - Constructor for class javajs.util.Base64
- baseAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
first atom index for this collection, current modelset.ac
- baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
- baseBlockSize - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- baseBondIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- baseColor - Variable in class org.jmol.jvxl.data.JvxlData
- baseFont3d - Variable in class org.jmol.shape.Frank
- baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
- basemodel - Static variable in class org.jmol.script.T
- baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
- basepair - Static variable in class org.jmol.script.T
- BasePair - Class in org.jmol.modelsetbio
- baseStrandOffset - Variable in class org.jmol.renderbio.StrandsRenderer
- baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
- BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
- BasisFunctionReader.MOEnergySorter - Class in org.jmol.adapter.readers.quantum
- Bbcage - Class in org.jmol.shape
- Bbcage() - Constructor for class org.jmol.shape.Bbcage
- BbcageRenderer - Class in org.jmol.render
- BbcageRenderer() - Constructor for class org.jmol.render.BbcageRenderer
- bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
- bbCorner0 - Variable in class org.jmol.util.BoxInfo
- bbCorner1 - Variable in class org.jmol.util.BoxInfo
- bboxModels - Variable in class org.jmol.modelset.ModelSet
- BC - Class in javajs.util
-
byte converter
- BC() - Constructor for class javajs.util.BC
- BCIFReader - Class in org.jmol.adapter.readers.cif
-
A very simple Binary CIF file reader extention of MMCifReader extends CifReader.
- BCIFReader() - Constructor for class org.jmol.adapter.readers.cif.BCIFReader
- BEGIN - Static variable in class org.jmol.shapecgo.CGOMesh
- beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
- beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.util.GData
- best - Static variable in class org.jmol.script.T
- beta - Static variable in class org.jmol.script.T
- beta - Variable in class org.jmol.util.SimpleUnitCell
- bfactor - Variable in class org.jmol.adapter.smarter.Atom
- bgcolix - Variable in class org.jmol.modelset.Text
- bgcolix - Variable in class org.jmol.render.LabelsRenderer
- bgcolixes - Variable in class org.jmol.shape.Labels
- bgcolor - Variable in class jspecview.common.PanelData
- bgcolor - Variable in class org.jmol.util.GData
- BGYOR - Static variable in class org.jmol.util.ColorEncoder
- bigEndian - Variable in class javajs.util.OC
- BilbaoReader - Class in org.jmol.adapter.readers.xtal
-
Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.
- BilbaoReader() - Constructor for class org.jmol.adapter.readers.xtal.BilbaoReader
- bin - Static variable in class org.jmol.script.T
- binary - Static variable in class org.jmol.script.T
- BinaryDcdReader - Class in org.jmol.adapter.readers.more
-
DCD binary trajectory file reader.
- BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
- binarydoc - Variable in class org.jmol.jvxl.readers.JvxlReader
- binarydoc - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- binarydoc - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- binaryDoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- BinaryDocument - Class in javajs.util
- BinaryDocument() - Constructor for class javajs.util.BinaryDocument
- binaryOp(T, SV, SV) - Method in class org.jmol.script.ScriptMathProcessor
- bind - Static variable in class org.jmol.script.T
- bindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
- bindAction(String, String) - Method in class org.jmol.viewer.Viewer
- Binding - Class in org.jmol.viewer.binding
- Binding() - Constructor for class org.jmol.viewer.binding.Binding
- bindName(int, String) - Method in class org.jmol.viewer.binding.Binding
- BioExt - Class in org.jmol.modelsetbio
- BioExt() - Constructor for class org.jmol.modelsetbio.BioExt
- BioMeshRenderer - Class in org.jmol.renderbio
- BioMeshRenderer() - Constructor for class org.jmol.renderbio.BioMeshRenderer
- BioModel - Class in org.jmol.modelsetbio
- BioModel() - Constructor for class org.jmol.modelsetbio.BioModel
- bioModelset - Variable in class org.jmol.modelset.AtomCollection
-
If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning
- BioModelSet - Class in org.jmol.modelsetbio
- BioModelSet() - Constructor for class org.jmol.modelsetbio.BioModelSet
- biomtChainAtomCounts - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
- bioPolymer - Variable in class org.jmol.shapebio.BioShape
- BioPolymer - Class in org.jmol.modelsetbio
-
A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers", which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone), Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
- BioPolymer(Monomer[], boolean) - Constructor for class org.jmol.modelsetbio.BioPolymer
- bioPolymerIndexInModel - Variable in class org.jmol.modelsetbio.BioPolymer
- bioPolymers - Variable in class org.jmol.modelsetbio.BioModel
- BioResolver - Class in org.jmol.modelsetbio
-
a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
- BioResolver() - Constructor for class org.jmol.modelsetbio.BioResolver
- BioShape - Class in org.jmol.shapebio
- BioShapeCollection - Class in org.jmol.shapebio
-
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set.
- BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
- bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
- biosymmetry - Variable in class org.jmol.modelset.Model
- BIRTH - Static variable in class com.sparshui.common.TouchState
- BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
- bis - Variable in class javajs.util.BinaryDocument
- bitset - Static variable in class org.jmol.script.T
- BLACK - Static variable in class jspecview.common.ColorParameters
- BLACK - Variable in class jspecview.common.PanelData
- BLACK - Static variable in class org.jmol.util.C
- blockdata - Static variable in class org.jmol.script.T
- blockID - Variable in class jspecview.source.JDXDataObject
- BLUE - Static variable in class jspecview.common.ColorParameters
- BLUE - Static variable in class org.jmol.util.C
- BMPDecoder - Class in javajs.img
-
src: http://www.javaworld.com/article/2077542/learn-java/java-tip-43--how-to- read-8--and-24-bit-microsoft-windows-bitmaps-in-java-applications.html see also: http://en.wikipedia.org/wiki/BMP_file_format Modified by Bob Hanson hansonr@stolaf.edu
- BMPDecoder() - Constructor for class javajs.img.BMPDecoder
- bo - Variable in class org.jmol.modelset.BondCollection
- bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
- bond - Variable in class org.jmol.adapter.readers.xml.XmlReader
- bond - Variable in class org.jmol.shapespecial.Dipole
- Bond - Class in org.jmol.adapter.smarter
- Bond - Class in org.jmol.modelset
- Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
- Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
- BOND_AROMATIC - Static variable in class org.jmol.util.Edge
- BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
- BOND_AROMATIC_MASK - Static variable in class org.jmol.util.Edge
- BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_MASK - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_QUINTUPLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_sextuple - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.Edge
- BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
- BOND_H_CALC - Static variable in class org.jmol.util.Edge
- BOND_H_CALC_MASK - Static variable in class org.jmol.util.Edge
- BOND_H_MINUS_3 - Static variable in class org.jmol.util.Edge
- BOND_H_MINUS_4 - Static variable in class org.jmol.util.Edge
- BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_2 - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_3 - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_4 - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_5 - Static variable in class org.jmol.util.Edge
- BOND_H_REGULAR - Static variable in class org.jmol.util.Edge
- BOND_HBOND_SHIFT - Static variable in class org.jmol.util.Edge
- BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.Edge
- BOND_NEW - Static variable in class org.jmol.util.Edge
- BOND_ORDER_ANY - Static variable in class org.jmol.util.Edge
- BOND_ORDER_NULL - Static variable in class org.jmol.util.Edge
- BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL_MASK - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL01 - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL12 - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL23 - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL32 - Static variable in class org.jmol.util.Edge
- BOND_PYMOL_MULT - Static variable in class org.jmol.util.Edge
- BOND_PYMOL_NOMULT - Static variable in class org.jmol.util.Edge
- BOND_RENDER_MASK - Static variable in class org.jmol.util.Edge
-
Extended Bond Definition Types Originally these were short 16-bit values
- BOND_RENDER_SINGLE - Static variable in class org.jmol.util.Edge
- BOND_STEREO_EITHER - Static variable in class org.jmol.util.Edge
- BOND_STEREO_FAR - Static variable in class org.jmol.util.Edge
- BOND_STEREO_MASK - Static variable in class org.jmol.util.Edge
- BOND_STEREO_NEAR - Static variable in class org.jmol.util.Edge
- BOND_STRUT - Static variable in class org.jmol.util.Edge
- BOND_SULFUR_MASK - Static variable in class org.jmol.util.Edge
- bondAtoms(Atom, Atom, int, short, BS, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
- BondCollection - Class in org.jmol.modelset
- BondCollection() - Constructor for class org.jmol.modelset.BondCollection
- bondcount - Static variable in class org.jmol.script.T
- bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bondCount - Variable in class org.jmol.modelset.BondCollection
- bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
- bonded - Static variable in class org.jmol.script.T
- BONDING - Enum constant in enum class org.jmol.c.VDW
- bondingradius - Static variable in class org.jmol.script.T
- bondingRadius - Variable in class org.jmol.adapter.smarter.Atom
- bondingversion - Static variable in class org.jmol.script.T
- bondingVersion - Static variable in class org.jmol.util.Elements
- bondingVersion - Variable in class org.jmol.viewer.GlobalSettings
- BondIterator - Interface in org.jmol.modelset
- bondmode - Static variable in class org.jmol.script.T
- bondmodeor - Static variable in class org.jmol.script.T
- bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
- bondorder - Static variable in class org.jmol.script.T
- bondpicking - Static variable in class org.jmol.script.T
- bondradiusmilliangstroms - Static variable in class org.jmol.script.T
- bondRotationCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
- bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bonds - Variable in class org.jmol.minimize.Minimizer
- bonds - Variable in class org.jmol.modelset.Atom
-
MAY BE NULL
- bonds - Static variable in class org.jmol.script.T
- bondset - Static variable in class org.jmol.script.T
- BondSet - Class in org.jmol.modelset
- BondSet() - Constructor for class org.jmol.modelset.BondSet
- bondtolerance - Static variable in class org.jmol.script.T
- booleanparam - Static variable in class org.jmol.script.T
- BorderLayout - Class in org.jmol.awtjs.swing
- BorderLayout() - Constructor for class org.jmol.awtjs.swing.BorderLayout
- bottom - Static variable in class org.jmol.script.T
- bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- bottomMargin - Static variable in class jspecview.common.PanelData
- boundbox - Static variable in class org.jmol.script.T
- boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- boundboxcolor - Static variable in class org.jmol.script.T
- boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
- boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
- boundingBox - Variable in class org.jmol.jvxl.readers.JvxlReader
- boundingBox - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- boundingBox - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- boxHeight - Variable in class org.jmol.modelset.Text
- BoxInfo - Class in org.jmol.util
-
The BoxInfo class holds critical information about boundboxes.
- BoxInfo() - Constructor for class org.jmol.util.BoxInfo
- boxWidth - Variable in class org.jmol.modelset.Text
- boxX - Variable in class org.jmol.modelset.Text
- boxXY - Variable in class org.jmol.modelset.Text
- boxY - Variable in class org.jmol.modelset.Text
- boxYoff2 - Variable in class org.jmol.modelset.Text
- bp - Variable in class jspecview.export.AMLExporter
- bp - Variable in class jspecview.export.CMLExporter
- bpointx - Variable in class jme.JME
- bpointy - Variable in class jme.JME
- br - Variable in class org.jmol.jvxl.readers.JvxlReader
- br - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- br - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- branch - Static variable in class org.jmol.script.T
- breakcmd - Static variable in class org.jmol.script.T
- brillouin - Static variable in class org.jmol.script.T
- BrukerReader - Class in jspecview.source
-
A class to read Bruker ZIP files and directories.
- BrukerReader() - Constructor for class jspecview.source.BrukerReader
- BS - Class in javajs.util
-
a fast 32-bit BitSet optimized for Java2Script -- about 25 times faster than java.util.BitSet
- BS() - Constructor for class javajs.util.BS
-
Creates a new bit set.
- bs14 - Variable in class org.jmol.minimize.MinAtom
- bsA() - Method in class org.jmol.viewer.Viewer
- bsAll - Variable in class org.jmol.adapter.smarter.Structure
- bsAll - Variable in class org.jmol.modelset.ModelSet
- bsAromatic - Variable in class org.jmol.modelset.BondCollection
- bsAsymmetricUnit - Variable in class org.jmol.modelset.Model
-
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.
- bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bsAtoms - Variable in class org.jmol.minimize.Minimizer
- bsAtoms - Variable in class org.jmol.modelset.Model
-
Note that this bitset may or may not include bsAtomsDeleted
- bsAtomsDeleted - Variable in class org.jmol.modelset.Model
- bsBgColixSet - Variable in class org.jmol.shape.Labels
- bsClickable - Variable in class org.jmol.modelset.AtomCollection
- bsColixSet - Variable in class org.jmol.shape.Shape
- bsDeleted - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- bsDeleted - Variable in class org.jmol.viewer.SelectionManager
- bsDisplay - Variable in class org.jmol.shape.MeshCollection
- bsDisplay - Variable in class org.jmol.util.MeshSurface
- bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
- bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
- bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- bsFontSet - Variable in class org.jmol.shape.Labels
- bsFrameOffsets - Variable in class org.jmol.viewer.TransformManager
- bsHighlight - Variable in class org.jmol.shape.Halos
- bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
- bsIgnored - Variable in class org.jmol.atomdata.AtomData
- bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
- bsMinFixed - Variable in class org.jmol.minimize.Minimizer
- bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- bsModulated - Variable in class org.jmol.modelset.AtomCollection
- bsMolecule - Variable in class org.jmol.shapespecial.Dipole
- bsMolecules - Variable in class org.jmol.atomdata.AtomData
- bsOrderSet - Variable in class org.jmol.shape.Sticks
- bsPartialCharges - Variable in class org.jmol.modelset.AtomCollection
- bspf - Variable in class org.jmol.modelset.AtomCollection
-
Binary Space Partitioning Forest
- bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- Bspf - Class in org.jmol.bspt
-
A Binary Space Partitioning Forest
- Bspf(int) - Constructor for class org.jmol.bspt.Bspf
- bsPolygons - Variable in class org.jmol.render.MeshRenderer
- bsPolygons - Variable in class org.jmol.util.MeshSurface
- bsPolygonsToExport - Variable in class org.jmol.render.MeshRenderer
- Bspt - Class in org.jmol.bspt
-
a Binary Space Partitioning Tree
- Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
-
Create a bspt with the specified number of dimensions.
- bspts - Variable in class org.jmol.bspt.Bspf
- bsRenderableAtoms - Variable in class org.jmol.viewer.ShapeManager
- bsSelected - Variable in class org.jmol.atomdata.AtomData
- bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
- bsSelected - Variable in class org.jmol.modelset.MeasurementData
- bsSizeDefault - Variable in class org.jmol.shape.AtomShape
- bsSizeSet - Variable in class org.jmol.shape.Shape
- bsSlabbedInternal - Variable in class org.jmol.viewer.ShapeManager
- bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
- bsSlabGhost - Variable in class org.jmol.util.MeshSurface
- bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
- bsStructuredModels - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bsSubset - Variable in class org.jmol.viewer.SelectionManager
- bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
- bsSymmetry - Variable in class org.jmol.modelset.ModelSet
- bsTemp - Variable in class org.jmol.shape.Mesh
- bsToArray(BS) - Method in class org.jmol.scriptext.ScriptExt
- BSUtil - Class in org.jmol.util
- BSUtil() - Constructor for class org.jmol.util.BSUtil
- bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- bsVdw - Variable in class org.jmol.minimize.MinAtom
- bsVisible - Variable in class org.jmol.modelset.AtomCollection
- bsVisible - Variable in class org.jmol.renderbio.BackboneRenderer
- bsVisible - Variable in class org.jmol.renderbio.CartoonRenderer
- bsVisible - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- bsVisible - Variable in class org.jmol.renderbio.RibbonsRenderer
- bsVisible - Variable in class org.jmol.renderbio.RocketsRenderer
- bsVisible - Variable in class org.jmol.renderbio.StrandsRenderer
- bsVisible - Variable in class org.jmol.renderbio.TraceRenderer
- bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
- btnType - Variable in class org.jmol.awtjs.swing.JMenuItem
- buf - Variable in class com.jcraft.jzlib.InflaterInputStream
- buffer - Variable in class com.jcraft.jzlib.DeflaterOutputStream
- bufferSize - Variable in class org.jmol.util.GData
- buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- buildStructure(String) - Method in class jspecview.popup.JSVPopupResourceBundle
- buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
- buildStructure(String) - Method in class org.jmol.popup.PopupResource
- BUTTON_MASK - Static variable in class org.jmol.awtjs.Event
- BUTTON_MASK - Static variable in class org.jmol.viewer.binding.Binding
- BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
- buttonGroup - Variable in class org.jmol.popup.GenericPopup
- ButtonGroup - Class in org.jmol.awtjs.swing
- ButtonGroup() - Constructor for class org.jmol.awtjs.swing.ButtonGroup
- bValue(T) - Static method in class org.jmol.script.SV
- BW - Static variable in class org.jmol.util.ColorEncoder
- bwMode - Variable in class jme.JME
- BWR - Static variable in class org.jmol.util.ColorEncoder
- BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
- BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
- byteArrayToFloat(byte[], int) - Static method in class com.sparshui.common.utils.Converter
- byteArrayToInt(byte[]) - Static method in class com.sparshui.common.utils.Converter
-
Converts a byte array to an integer.
- byteArrayToInt(byte[], int) - Static method in class com.sparshui.common.utils.Converter
- byteArrayToJSON(byte[]) - Static method in class javajs.util.PT
- byteArrayToLong(byte[], int) - Static method in class com.sparshui.common.utils.Converter
- byteArrayToString(byte[]) - Static method in class com.sparshui.common.utils.Converter
- bytePos - Variable in class javajs.img.PngEncoder
- BytePoster - Interface in javajs.api
- bytesToDoubleToFloat(byte[], int, boolean) - Static method in class javajs.util.BC
-
see http://en.wikipedia.org/wiki/Binary64 not concerning ourselves with very small or very large numbers and getting this exactly right.
- bytesToFloat(byte[], int, boolean) - Static method in class javajs.util.BC
- bytesToInt(byte[], int, boolean) - Static method in class javajs.util.BC
- bytesToShort(byte[], int, boolean) - Static method in class javajs.util.BC
- bz - Variable in class org.jmol.util.BZone
-
overall object
- BZip2Constants - Interface in org.apache.tools.bzip2
-
Base class for both the compress and decompress classes.
- BZone - Class in org.jmol.util
-
A class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells.
- BZone() - Constructor for class org.jmol.util.BZone
C
- c - Variable in class org.jmol.util.SimpleUnitCell
- C - Class in org.jmol.util
-
Note: Color table is now in javajs/util/CU.java
- C() - Constructor for class org.jmol.util.C
- c_ - Variable in class org.jmol.util.SimpleUnitCell
- cA_ - Variable in class org.jmol.util.SimpleUnitCell
- cache - Static variable in class org.jmol.script.T
- cacheClear() - Method in class org.jmol.viewer.Viewer
- cacheFileByName(String, boolean) - Method in interface javajs.api.JSInterface
- cacheFileByName(String, boolean) - Method in class jspecview.appletjs.JSVApplet
- cacheFileByName(String, boolean) - Method in class org.jmol.util.GenericApplet
- cacheFileByName(String, boolean) - Method in class org.jmol.viewer.Viewer
- cacheFileByNameAdd(String, boolean) - Method in class org.jmol.viewer.FileManager
- cacheGet(String) - Static method in class jspecview.common.JSVFileManager
- cacheGet(String, boolean) - Method in class org.jmol.viewer.FileManager
- cacheList() - Method in class org.jmol.viewer.FileManager
- cachePut(String, Object) - Method in interface javajs.api.JSInterface
- cachePut(String, Object) - Method in class jspecview.appletjs.JSVApplet
- cachePut(String, Object) - Method in class org.jmol.util.GenericApplet
- cachePut(String, Object) - Method in class org.jmol.viewer.Viewer
-
JSInterface -- allows saving files in memory for later retrieval
- cachePut(String, String) - Static method in class jspecview.common.JSVFileManager
- cacheZipContents(BufferedInputStream, String, Map<String, Object>, boolean) - Method in interface javajs.api.GenericZipTools
- cacheZipContents(BufferedInputStream, String, Map<String, Object>, boolean) - Method in class javajs.util.ZipTools
- CACTUS_FILE_TYPES - Static variable in class org.jmol.viewer.JC
- calc(double[][]) - Method in class javajs.util.Eigen
-
Check for symmetry, then construct the eigenvalue decomposition
- CALC_H_ALLOW_H - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_DOALL - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_HAVEH - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_IGNORE_H - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_JUSTC - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_QUICK - Static variable in class org.jmol.modelset.AtomCollection
- calc2or3JorNOE(Viewer, Atom[], String, int) - Static method in class org.jmol.quantum.NMRCalculation
-
Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;
- calc3JCH(String, double, boolean) - Static method in class org.jmol.quantum.NMRCalculation
- calcAllRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
-
only for base models, not trajectories
- calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.api.JmolViewer
- calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.modelset.ModelSet
- calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.viewer.Viewer
- calcAveragePoint(P3, P3, P3) - Static method in class javajs.util.Measure
- calcAveragePointN(P3[], int, P3) - Static method in class javajs.util.Measure
- calcAxis() - Method in class org.jmol.modelsetbio.Helix
- calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
- calcAxis() - Method in class org.jmol.modelsetbio.Sheet
- calcBestAxisThroughPoints(P3[], int, P3, V3, V3, int) - Static method in class javajs.util.Measure
- calcBestPlaneThroughPoints(P3[], int, P4) - Static method in class javajs.util.Measure
-
Calculate the best ax + by + cz + d = 0 plane through a number of points using a three-step check for the best plane based on normal distance.
- calcBoundBoxDimensions(BS, float) - Method in class org.jmol.modelset.ModelSet
- calcBoundBoxDimensions(BS, float) - Method in class org.jmol.viewer.Viewer
- calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
-
sets all camera and scale factors needed by the specific perspective model instantiated
- calcCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- calcEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
- calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
- calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
- calcJKarplus(double) - Static method in class org.jmol.quantum.NMRCalculation
- calcJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- calcNavigationPoint() - Method in interface org.jmol.api.JmolNavigatorInterface
- calcNavigationPoint() - Method in class org.jmol.navigate.Navigator
- calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
-
All the magic happens here.
- calcNOE(Viewer, Atom, Atom) - Static method in class org.jmol.quantum.NMRCalculation
- calcNOEs() - Method in class org.jmol.quantum.NMRNoeMatrix
-
calculate the NOESY spectrum at a particular mixing time.
- calcNOEs() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- calcNormalizedNormal(T3, T3, T3, T3, T3) - Static method in class javajs.util.Measure
-
note that if vAB or vAC is dispensible, vNormNorm can be one of them
- calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
- calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
- calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
- calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
-
For reduced density only; coloring is done point by point.
- calcPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Fill this plane with data based on the current set of raw data planes.
- calcPlaneForMode(P3[], int, P4, char) - Static method in class javajs.util.Measure
-
Compact calculation of the best pane using a simple method discussed at https://stackoverflow.com/questions/12299540/plane-fitting-to-4-or-more-xyz-points (A^T A)^-1 A^T B run three times to ensure that at least one is not perpendicular.
- calcRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
-
These are not actual hydrogen bonds.
- calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
- calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
- calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
- calcRopeMidPoints() - Method in class org.jmol.renderbio.RocketsRenderer
- calcRotationRadius(int, P3, boolean) - Method in class org.jmol.modelset.ModelSet
- calcRotationRadiusBs(BS) - Method in class org.jmol.modelset.ModelSet
- calcScreenControlPoints() - Method in class org.jmol.renderbio.BackboneRenderer
- calcScreenControlPoints() - Method in class org.jmol.renderbio.CartoonRenderer
- calcScreenControlPoints() - Method in class org.jmol.renderbio.MeshRibbonRenderer
- calcScreenControlPoints() - Method in class org.jmol.renderbio.RibbonsRenderer
- calcScreenControlPoints() - Method in class org.jmol.renderbio.RocketsRenderer
- calcScreenControlPoints() - Method in class org.jmol.renderbio.StrandsRenderer
- calcScreenControlPoints() - Method in class org.jmol.renderbio.TraceRenderer
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.BackboneRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.CartoonRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.MeshRibbonRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.RibbonsRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.RocketsRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.StrandsRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.TraceRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcSelectedGroupsCount() - Method in class org.jmol.modelset.ModelSet
- calcSelectedMoleculesCount() - Method in class org.jmol.modelset.ModelSet
- calcSelectedMonomersCount() - Method in class org.jmol.modelset.ModelSet
- calcSelectedMonomersCount() - Method in class org.jmol.modelsetbio.BioModelSet
- calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioPolymer
- calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
-
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
- calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
- calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager4D
- calculate - Static variable in class org.jmol.script.T
- calculate(T3, boolean) - Method in class org.jmol.util.ModulationSet
-
Calculate r_I internal d-space coordinate of an atom.
- calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolEnvCalc
- calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
- calculate(VolumeData, BS, P3[], Atom[], float[], int) - Method in class org.jmol.quantum.MepCalculation
- calculateAllPolymers(Group[], int, int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateAllStructuresExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateAllStuctures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateChirality(BS) - Method in class org.jmol.viewer.Viewer
- calculateChiralityForAtoms(BS, boolean) - Method in class org.jmol.modelset.ModelSet
- calculateChiralityForSmiles(String) - Method in class org.jmol.viewer.Viewer
- calculateCIPChiralityForAtoms(Viewer, BS) - Method in interface org.jmol.api.SymmetryInterface
- calculateCIPChiralityForAtoms(Viewer, BS) - Method in class org.jmol.symmetry.Symmetry
- calculateCIPChiralityForSmiles(Viewer, String) - Method in interface org.jmol.api.SymmetryInterface
- calculateCIPChiralityForSmiles(Viewer, String) - Method in class org.jmol.symmetry.Symmetry
- calculateDssp(Object[], int, Object, boolean, boolean, boolean, int) - Method in class org.jmol.dssx.DSSP
- calculateDssrProperty(String) - Method in class org.jmol.modelset.ModelSet
- calculateDSSRStructure(Viewer, BS) - Method in interface org.jmol.api.JmolAnnotationParser
- calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.AnnotationParser
- calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.DSSR1
- calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
- calculateFormalCharges(BS) - Method in class org.jmol.viewer.Viewer
- calculateFractionalPoint(float, P3, P3, float, float, P3) - Method in class org.jmol.jvxl.data.VolumeData
- calculateGeodesicSurface(BS, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
- calculateGeodesicSurface(BS, float) - Method in class org.jmol.shapesurface.Isosurface
- calculateHydrogens(BS, int[], Lst<Atom>, int) - Method in class org.jmol.modelset.AtomCollection
-
get a list of potential H atom positions based on elemental valence and formal charge
- calculateIntegral() - Method in class jspecview.common.IntegralData
- calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
- calculateMolecularDipole(int, BS) - Method in class org.jmol.modelset.ModelSet
- calculateMolecularDipole(BS) - Method in class org.jmol.viewer.Viewer
- calculatePartialCharges(BS) - Method in class org.jmol.viewer.Viewer
- calculatePartialCharges(Bond[], int[], Atom[], int[], BS, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
assign partial charges ala MMFF94
- calculatePartialCharges(ModelSet, BS, BS) - Method in class org.jmol.minimize.Minimizer
- calculatePointGroup(BS) - Method in class org.jmol.modelset.ModelSet
- calculatePolymers(Group[], int, int, BS) - Method in class org.jmol.modelset.ModelSet
- calculateQuaternionRotation(P3[][], float[]) - Static method in class javajs.util.Measure
-
Closed-form solution of absolute orientation requiring 1:1 mapping of positions.
- calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
- calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
- calculateStraightness() - Method in class org.jmol.viewer.Viewer
- calculateStraightnessAll() - Method in class org.jmol.modelset.ModelSet
- calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioModelSet
- calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
Uses Levitt invalid input: '&' Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
- calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
- calculateStructures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
- calculateStructures(BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
- calculateStructuresAllExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
-
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
- calculateStruts(BS, BS) - Method in class org.jmol.modelset.ModelSet
-
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
- calculateStruts(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateStruts(BS, BS) - Method in class org.jmol.viewer.Viewer
- calculateSurface(BS, float) - Method in class org.jmol.modelset.AtomCollection
- calculateSurface(BS, float) - Method in class org.jmol.viewer.Viewer
- calculateVolume(BS, VDW) - Method in class org.jmol.modelset.AtomCollection
- calculateVolumeOrArea(MeshData, BS, boolean, boolean) - Static method in class org.jmol.jvxl.data.MeshData
- calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
The number of the calculation being interpreted.
- calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- calcVertexPoint(int, int, int, int, P3) - Method in class org.jmol.jvxl.calc.MarchingCubes
- calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
- callback(String, String) - Method in class jspecview.dialog.IntegrationDialog
- callback(String, String) - Method in class jspecview.dialog.JSVDialog
- callback(String, String) - Method in class jspecview.dialog.MeasurementsDialog
- callback(String, String) - Method in class jspecview.dialog.OverlayLegendDialog
- callback(String, String) - Method in class jspecview.dialog.PeakListDialog
- callback(String, String) - Method in class jspecview.dialog.ViewsDialog
- callbackAD(String, String) - Method in class jspecview.dialog.JSVDialog
- callbacks - Variable in class org.jmol.util.GenericApplet
- callToJavaScript(String, Object[]) - Method in interface jspecview.api.AppletFrame
- callToJavaScript(String, Object[]) - Method in class jspecview.appletjs.JSVApplet
-
Calls a javascript function given by the function name passing to it the string parameters as arguments
- camera - Variable in class org.jmol.viewer.TransformManager
- cameradepth - Static variable in class org.jmol.script.T
- cameraDepth - Variable in class org.jmol.viewer.TransformManager
- cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
- cameraDistance - Variable in class org.jmol.export.___Exporter
- cameraDistance - Variable in class org.jmol.viewer.TransformManager
- cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
- cameraPosition - Variable in class org.jmol.export.___Exporter
- cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
- cameraSetting - Variable in class org.jmol.viewer.TransformManager
- canBeNormalized(V3d) - Static method in class org.jmol.minimize.Util
- canBeSquared(double) - Static method in class org.jmol.minimize.Util
- canCapCylinders - Variable in class org.jmol.export.__CartesianExporter
- cancel - Static variable in class org.jmol.script.T
- cancel() - Method in class javajs.util.OC
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- canConvertTransAbs() - Method in class jspecview.source.JDXDataObject
- canDo(int) - Method in class org.jmol.viewer.StateManager
- canDoLineTo() - Method in class javajs.export.PDFCreator
- canDoLineTo() - Method in class jspecview.common.PDFWriter
- canDoLineTo() - Method in class jspecview.java.AwtG2D
- canDoLineTo() - Method in class jspecview.js2d.JsG2D
- canDoLineTo() - Method in interface org.jmol.api.GenericGraphics
- canDoLineTo() - Method in class org.jmol.awt.AwtG2D
- canDoLineTo() - Method in class org.jmol.awtjs2d.JsG2D
- canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
- canDownsample - Variable in class org.jmol.jvxl.readers.JvxlReader
- canDownsample - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- canDownsample - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- canIntegrate() - Method in class jspecview.source.JDXDataObject
- CANONICAL_DC_LIST - Static variable in class org.jmol.quantum.QS
- CANONICAL_DS_LIST - Static variable in class org.jmol.quantum.QS
- CANONICAL_FC_LIST - Static variable in class org.jmol.quantum.QS
- CANONICAL_FS_LIST - Static variable in class org.jmol.quantum.QS
- canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- canonize - Variable in class jme.JME
- canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
- canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
- canSaveAsJDX() - Method in class jspecview.source.JDXDataObject
- canShowSolutionColor() - Method in class jspecview.source.JDXDataObject
- canSkipLoad - Variable in class org.jmol.modelset.AtomCollection
- canvas - Variable in class org.jmol.console.ImageDialog
- cap - Static variable in class org.jmol.script.T
- capData(P4, float) - Method in class org.jmol.jvxl.data.VolumeData
- cappingObject - Variable in class org.jmol.shape.Mesh
- capture - Static variable in class org.jmol.script.T
- captureParams - Variable in class org.jmol.viewer.Viewer
- carbohydrate - Static variable in class org.jmol.script.T
- CARBOHYDRATE - Enum constant in enum class org.jmol.c.STR
- CarbohydrateMonomer - Class in org.jmol.modelsetbio
- CarbohydratePolymer - Class in org.jmol.modelsetbio
- cardinality() - Method in class javajs.util.BS
-
Returns the number of bits set to
true
in thisBitSet
. - cardinalityN(int) - Method in class javajs.util.BS
- cardinalityOf(BS) - Static method in class org.jmol.util.BSUtil
-
cardinality = "total number of set bits"
- CARTESIAN_PRECISION - Static variable in class javajs.util.PT
- cartoon - Static variable in class org.jmol.script.T
- Cartoon - Class in org.jmol.shapebio
- Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
- cartoonbaseedges - Static variable in class org.jmol.script.T
- cartoonblockheight - Static variable in class org.jmol.script.T
- cartoonblocks - Static variable in class org.jmol.script.T
- cartoonladders - Static variable in class org.jmol.script.T
- CartoonRenderer - Class in org.jmol.renderbio
- CartoonRenderer() - Constructor for class org.jmol.renderbio.CartoonRenderer
- cartoonribose - Static variable in class org.jmol.script.T
- cartoonrockets - Static variable in class org.jmol.script.T
- cartoonsfancy - Static variable in class org.jmol.script.T
- cartoonsFancy - Variable in class org.jmol.renderbio.BackboneRenderer
- cartoonsFancy - Variable in class org.jmol.renderbio.CartoonRenderer
- cartoonsFancy - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- cartoonsFancy - Variable in class org.jmol.renderbio.RibbonsRenderer
- cartoonsFancy - Variable in class org.jmol.renderbio.RocketsRenderer
- cartoonsFancy - Variable in class org.jmol.renderbio.StrandsRenderer
- cartoonsFancy - Variable in class org.jmol.renderbio.TraceRenderer
- cartoonsteps - Static variable in class org.jmol.script.T
- casecmd - Static variable in class org.jmol.script.T
- casName - Variable in class jspecview.export.AMLExporter
- casName - Variable in class jspecview.export.CMLExporter
- casName - Variable in class jspecview.source.AnIMLReader
- casRN - Variable in class jspecview.export.AMLExporter
- casRN - Variable in class jspecview.export.CMLExporter
- casRN - Variable in class jspecview.source.AnIMLReader
- CastepReader - Class in org.jmol.adapter.readers.xtal
-
CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.
- CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
- CAT_ASSEM - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_ATOM_SITE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CAT_ATOM_SITES - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CAT_ATOM_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CAT_CELL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CAT_CHEMCOMP - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_COMPBOND - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_NCS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_OPER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_SEQUENCEDIF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_SHEET - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_STRUCSITE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_STRUCTCONF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CAT_STRUCTCONN - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
- catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
- catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
- catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
-
Returns a Lst
- catchcmd - Static variable in class org.jmol.script.T
- cavity - Static variable in class org.jmol.script.T
- cB_ - Variable in class org.jmol.util.SimpleUnitCell
- CBK - Enum Class in org.jmol.c
- cbl - Variable in class org.jmol.viewer.StatusManager
- CBZip2InputStream - Class in org.apache.tools.bzip2
-
An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
- CBZip2InputStream(InputStream) - Constructor for class org.apache.tools.bzip2.CBZip2InputStream
-
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
- CBZip2InputStream(InputStream, boolean) - Constructor for class org.apache.tools.bzip2.CBZip2InputStream
-
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
- CBZip2InputStreamFactory - Class in org.apache.tools.bzip2
- CBZip2InputStreamFactory() - Constructor for class org.apache.tools.bzip2.CBZip2InputStreamFactory
- cch - Variable in class javajs.util.CifDataParser
-
length of str
- cd - Static variable in class org.jmol.script.T
- cd(String) - Method in class org.jmol.viewer.Viewer
- CDXMLWriter - Class in org.jmol.adapter.writers
-
Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the basic necessities for XmlCDXReader.
- CDXMLWriter() - Constructor for class org.jmol.adapter.writers.CDXMLWriter
- CDXReader - Class in org.jmol.adapter.readers.more
-
A reader for ChemDraw binary CDX files.
- CDXReader() - Constructor for class org.jmol.adapter.readers.more.CDXReader
- ce - Variable in class org.jmol.viewer.ColorManager
- cell - Static variable in class org.jmol.script.T
- Cell - Class in org.jmol.awtjs.swing
- Cell(JComponent, GridBagConstraints) - Constructor for class org.jmol.awtjs.swing.Cell
- CELL_TYPE_CONVENTIONAL - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- CELL_TYPE_MAGNETIC_PARENT - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CELL_TYPE_MAGNETIC_STANDARD - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CELL_TYPE_PRIMITIVE - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- CELL_TYPE_SUPER - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- cellParamNames - Static variable in class org.jmol.api.JmolAdapter
- cellSlop - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- celshading - Static variable in class org.jmol.script.T
- celshadingpower - Static variable in class org.jmol.script.T
- CENATT - Static variable in class javajs.api.GenericZipInputStream
- CENATX - Static variable in class javajs.api.GenericZipInputStream
- CENCOM - Static variable in class javajs.api.GenericZipInputStream
- CENCRC - Static variable in class javajs.api.GenericZipInputStream
- CENDSK - Static variable in class javajs.api.GenericZipInputStream
- CENEXT - Static variable in class javajs.api.GenericZipInputStream
- CENFLG - Static variable in class javajs.api.GenericZipInputStream
- CENHDR - Static variable in class javajs.api.GenericZipInputStream
- CENHOW - Static variable in class javajs.api.GenericZipInputStream
- CENLEN - Static variable in class javajs.api.GenericZipInputStream
- CENNAM - Static variable in class javajs.api.GenericZipInputStream
- CENOFF - Static variable in class javajs.api.GenericZipInputStream
- CENSIG - Static variable in class javajs.api.GenericZipInputStream
- CENSIZ - Static variable in class javajs.api.GenericZipInputStream
- center - Variable in class org.jmol.export.___Exporter
- center - Variable in class org.jmol.jvxl.readers.SurfaceReader
- center - Static variable in class org.jmol.script.T
- center - Variable in class org.jmol.shapespecial.Dipole
- center - Variable in class org.jmol.shapespecial.Ellipsoid
- center - Variable in class org.jmol.shapespecial.Polyhedron
- center - Variable in class org.jmol.util.BZone
- center - Static variable in class org.jmol.viewer.JC
- center() - Method in class jme.JMEmol
- CENTER - Static variable in class org.jmol.awtjs.swing.BorderLayout
- CENTER - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- CENTER - Static variable in class org.jmol.awtjs.swing.SwingConstants
- centerat - Static variable in class org.jmol.script.T
- centerAt(int, int, P3) - Method in class org.jmol.viewer.TransformManager
- centerDialog() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- centerDialog() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Centers the dialog on the screen.
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- centerings - Variable in class org.jmol.symmetry.WyckoffFinder
- centeringStr - Variable in class org.jmol.symmetry.WyckoffFinder
- centerParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- centerParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
- centerParameterForModel(int, int, Object[]) - Method in class org.jmol.script.ScriptParam
- CENTIM - Static variable in class javajs.api.GenericZipInputStream
- centralAtom - Variable in class org.jmol.shapespecial.Polyhedron
- centralize() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- centroid - Static variable in class org.jmol.script.T
- centroidPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- CENVEM - Static variable in class javajs.api.GenericZipInputStream
- CENVER - Static variable in class javajs.api.GenericZipInputStream
- CgdReader - Class in org.jmol.adapter.readers.xtal
-
A reader for TOPOS systre file Crystal Graph Data format.
- CgdReader() - Constructor for class org.jmol.adapter.readers.xtal.CgdReader
- cgo - Static variable in class org.jmol.script.T
- CGO - Class in org.jmol.shapecgo
- CGO() - Constructor for class org.jmol.shapecgo.CGO
- CGOMesh - Class in org.jmol.shapecgo
- CGORenderer - Class in org.jmol.rendercgo
-
Something like a PyMOL Compiled Graphical Object, but more interesting!
- CGORenderer() - Constructor for class org.jmol.rendercgo.CGORenderer
- chain - Variable in class org.jmol.modelset.Group
-
required
- chain - Static variable in class org.jmol.script.T
- Chain - Class in org.jmol.modelset
-
A Model is a collection of Chains of Groups of Atoms.
- CHAIN - Enum constant in enum class org.jmol.c.PAL
- chaincasesensitive - Static variable in class org.jmol.script.T
- chainCount - Variable in class org.jmol.modelset.Model
- chainID - Variable in class org.jmol.adapter.smarter.Atom
- chainID - Variable in class org.jmol.modelset.Chain
-
chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
- chainMap - Variable in class org.jmol.viewer.Viewer
- chainno - Static variable in class org.jmol.script.T
- chainNo - Variable in class org.jmol.modelset.Chain
-
chainNo is for information purposes only; retrieved by {atoms}.chainNo
- chains - Variable in class org.jmol.modelset.Model
- chainToUpper(int) - Method in class org.jmol.modelset.AtomCollection
- CHANGEABLE_MASK - Static variable in class org.jmol.util.C
- changeableColixMap - Variable in class org.jmol.util.GData
- changeColixArgb(int, int) - Method in class org.jmol.util.GData
- CHAR - Static variable in class org.jmol.shapecgo.CGOMesh
- characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- CHARACTERS - Static variable in class jspecview.source.XMLParser
- charAt(int) - Method in class javajs.util.SB
- charCodeAt(int) - Method in class javajs.util.SB
- chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
- check - Static variable in class org.jmol.script.T
- check(boolean, boolean) - Method in class org.jmol.renderbio.BioMeshRenderer
- check(int, int, int, int, long, long) - Method in class org.jmol.viewer.MouseState
- check(String) - Method in class jspecview.dialog.ViewsDialog
- CHECK_DIMS - Static variable in interface org.jmol.api.JmolScriptManager
- CHECK1 - Static variable in class org.jmol.thread.JmolThread
- CHECK2 - Static variable in class org.jmol.thread.JmolThread
- CHECK3 - Static variable in class org.jmol.thread.JmolThread
- checkAllFieldsPresent(String[], int, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
- checkAndRemoveFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkAromaticDefined() - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
- checkAtomicSymbol(String) - Static method in class jme.JMEUtil
-
Return the JME atoming number associated to the given symbol
- checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.JvxlReader
-
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
- checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
-
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
- checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
-
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
- checkAutoIntegrate() - Method in class jspecview.common.JSViewer
- checkBoundsMinMax(P3, P3) - Method in class org.jmol.shape.Shape
- CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- checkByteCount - Variable in class org.jmol.shape.Mesh
- checkcir - Static variable in class org.jmol.script.T
- checkColixLength(short, int) - Method in class org.jmol.shape.AtomShape
- checkCommandLineForTip(char, String, boolean) - Method in class jspecview.common.JSViewer
- checkConsoleScript(String) - Method in class org.jmol.viewer.Viewer
- checkCoordinatesChanged(BS) - Method in class org.jmol.viewer.Viewer
- checkCurrentLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
- checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.UnitCell
- checkEnables() - Method in class jspecview.dialog.JSVDialog
- checkEnables() - Method in class jspecview.dialog.ViewsDialog
- checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
- checkExtension(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- checkFileExists(String, boolean, String, int, boolean) - Method in class org.jmol.script.ScriptEval
- checkFileIndex(String, String, String) - Method in class jspecview.common.PeakInfo
- checkFileTypeModel(String, String, String) - Method in class jspecview.common.PeakInfo
-
type checks true for MS in GC/MS; reverse of checkType
- checkFilterAssembly(String, Map<String, Object>) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- checkFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkFront(short, short, short) - Method in class org.jmol.render.MeshRenderer
- checkHalt(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
- checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
- checkHalt(String, boolean) - Method in class org.jmol.script.ScriptManager
- checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
- checkHKL(T3) - Method in class org.jmol.script.ScriptParam
-
Note - this check does not allow a 0 for h, k, or l.
- checkHover() - Method in class org.jmol.viewer.ActionManager
- checkInheritedShapes() - Method in class org.jmol.viewer.ShapeManager
-
starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms.
- checkInMotion(int) - Method in class org.jmol.viewer.Viewer
- checkIntegral(Parameters, String) - Method in class jspecview.common.PanelData
- checkInterrupted(JmolThread) - Method in class org.jmol.thread.JmolThread
- checkJDXRequiredTokens() - Method in class jspecview.source.JDXDataObject
-
for JDXReader only
- checkKeyControl(int, boolean) - Method in class jspecview.common.PanelData
- checkLast(int) - Method in class org.jmol.script.ScriptParam
- checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
sets continuing and doProcessLines
- checkLength(int) - Method in class org.jmol.script.ScriptParam
- checkLength(int) - Method in class org.jmol.scriptext.ScriptExt
- checkLength23() - Method in class org.jmol.script.ScriptParam
- checkLength34() - Method in class org.jmol.script.ScriptParam
- checkLengthErrorPt(int, int) - Method in class org.jmol.script.ScriptParam
- checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
- checkLine() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
- checkLine() - Method in class org.jmol.adapter.readers.more.JcampdxReader
- checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
- checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
- checkLine() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Reads a Collection of AtomSets from a BufferedReader.
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.FAHReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.InputReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- checkLine() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.
- checkLine() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkMemory() - Static method in class org.jmol.util.Logger
- checkMenuFocus(String, String, boolean) - Method in class jspecview.java.AwtPopup
- checkMenuUpdate() - Method in class org.jmol.viewer.Viewer
- checkMod(int, int) - Method in class jspecview.common.PanelData
- checkMotionRendering(int) - Method in class org.jmol.viewer.Viewer
-
check motion for rendering during mouse movement, spin, vibration, and animation
- checkMovedAtoms(BS, BS, P3[]) - Method in class org.jmol.modelkit.ModelKit
-
Something has changed atom positions.
- checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
- checkNearAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkNewModel() - Method in class org.jmol.modelkit.ModelKit
- checkNoEmptyModel() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- checkObjectClicked(boolean, int, int, BS) - Method in class org.jmol.modelset.Text
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Labels
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Shape
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Sticks
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.TextShape
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Draw
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Ellipsoids
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapesurface.Isosurface
- checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Labels
- checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Shape
- checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shapespecial.Draw
- checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Frank
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Shape
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Sticks
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.TextShape
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Draw
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shapesurface.Isosurface
- checkOption(char, String) - Method in class org.jmol.modelkit.ModelKit
-
MODELKIT SET options for syntax checking.
- checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
- checkOvelayInterface(String) - Method in class jspecview.common.JSViewer
- checkOverlay() - Method in class jspecview.common.JSViewer
- checkPaused(Viewer) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
- checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- checkPeriodic(P3) - Method in interface org.jmol.api.SymmetryInterface
- checkPeriodic(P3) - Method in class org.jmol.symmetry.Symmetry
- checkPointCount() - Method in class jspecview.source.AnIMLReader
- checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
-
Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
- checkPropertyParameter(String) - Method in interface org.jmol.api.JmolPropertyManager
- checkPropertyParameter(String) - Method in class org.jmol.viewer.PropertyManager
- checkPropertyParameter(String) - Method in class org.jmol.viewer.Viewer
- checkRange(int, double) - Method in class jspecview.common.PeakInfo
- checkRemark() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
- checkRemark() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkScript(int) - Method in class org.jmol.console.ScriptEditor
- checkScript(String) - Method in interface jspecview.api.JSVAppletInterface
- checkScript(String) - Method in class jspecview.app.JSVApp
- checkScript(String) - Method in class jspecview.appletjs.JSVApplet
- checkScript(String) - Method in class jspecview.application.MainFrame
- checkScript(String) - Method in class jspecview.common.JSViewer
- checkScriptSilent(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- checkScriptSilent(String) - Method in class org.jmol.script.ScriptEval
-
a method for just checking a script
- checkSelect(Map<String, SV>, T[]) - Method in interface org.jmol.api.JmolScriptEvaluator
- checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
-
Check a map for a WHERE phrase
- checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.viewer.Viewer
- checkStart() - Method in class jspecview.source.AnIMLReader
- checkStereoForAtom(SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesStereo
- checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
- checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- Checksum - Interface in com.jcraft.jzlib
- checkSupercell(Viewer, Symmetry, BS, int, P3) - Method in class org.jmol.symmetry.SpaceGroupFinder
-
Look for a supercell and adjust lattice down if necessary.
- checkTickTemps() - Method in class org.jmol.render.FontLineShapeRenderer
- checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
- checkToken(int) - Method in class org.jmol.script.ScriptParam
- checkTrailingText(String, int, int) - Static method in class javajs.util.PT
- checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
- checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
- checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
- checkTypeMatch(PeakInfo) - Method in class jspecview.common.PeakInfo
- checkTypeModel(String, String) - Method in class jspecview.common.PeakInfo
- checkUndoEnabled() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- checkVisible() - Method in class org.jmol.modelset.Atom
- checkWithin(T3, Lst<P3>, float, boolean) - Static method in class org.jmol.shape.Mesh
- chemFileProperty - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- chemical - Static variable in class org.jmol.script.T
- chemicalshift - Static variable in class org.jmol.script.T
- CHequation - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- children() - Method in interface jspecview.api.JSVTreeNode
- children() - Method in class jspecview.tree.SimpleTreeNode
- ChimeMessenger - Class in org.jmol.viewer
-
A legacy Chime-compatible messenger.
- ChimeMessenger() - Constructor for class org.jmol.viewer.ChimeMessenger
- chirality - Static variable in class org.jmol.script.T
- chk - Variable in class org.jmol.script.ScriptError
- chk - Variable in class org.jmol.scriptext.ScriptExt
- chord - Variable in class org.jmol.util.ContactPair
- Cif2DataParser - Class in org.jmol.adapter.readers.cif
-
Fully implemented 2016.12.1 see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html Will deliver JSON versions of the data while file reading and Java List/Map structures when called by x = getProperty("cifInfo", filename) Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org) found at https://github.com/COMCIFS/cif_api
- Cif2DataParser() - Constructor for class org.jmol.adapter.readers.cif.Cif2DataParser
- Cif2Reader - Class in org.jmol.adapter.readers.cif
-
Preliminary Cif2 reader.
- Cif2Reader() - Constructor for class org.jmol.adapter.readers.cif.Cif2Reader
- CifDataParser - Class in javajs.util
-
A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
- CifDataParser() - Constructor for class javajs.util.CifDataParser
- CifReader - Class in org.jmol.adapter.readers.cif
-
A true line-free CIF file reader for CIF files.
- CifReader() - Constructor for class org.jmol.adapter.readers.cif.CifReader
- CIFWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
- CIFWriter() - Constructor for class org.jmol.adapter.writers.CIFWriter
- CIP_CHIRALITY_AXIAL_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_CANTDETERMINE - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_EZ_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_m_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_M_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_NAME_MASK - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_NAME_OFFSET - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_NONE - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_p_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_P_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_PSEUDO_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_r_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_R_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_s_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_S_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqcis_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqCis_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqtrans_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqTrans_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_UNKNOWN - Static variable in class org.jmol.viewer.JC
- CIPChirality - Class in org.jmol.symmetry
-
A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
- CIPChirality() - Constructor for class org.jmol.symmetry.CIPChirality
- CIPData - Class in org.jmol.symmetry
-
A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.
- CIPData() - Constructor for class org.jmol.symmetry.CIPData
- CIPDataSmiles - Class in org.jmol.symmetry
-
A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
- CIPDataSmiles() - Constructor for class org.jmol.symmetry.CIPDataSmiles
- CIPDataTracker - Class in org.jmol.symmetry
-
An optional class to track digraph paths to decisions.
- CIPDataTracker() - Constructor for class org.jmol.symmetry.CIPDataTracker
- ciprule - Static variable in class org.jmol.script.T
- ciprule6full - Static variable in class org.jmol.script.T
- circle - Static variable in class org.jmol.script.T
- CIRCLE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- CircleRenderer - Class in org.jmol.g3d
-
Implements flat circle drawing/filling routines.
- CircleRenderer() - Constructor for class org.jmol.g3d.CircleRenderer
- CIRCULARPLANE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
- clash - Static variable in class org.jmol.script.T
- clean() - Method in class org.jmol.shape.MeshCollection
- clean() - Method in class org.jmol.shapecgo.CGO
- clean() - Method in class org.jmol.shapespecial.Draw
- clean(float) - Method in class org.jmol.adapter.writers.XtlWriter
- clean(String) - Static method in class javajs.util.PT
- cleanLabel(String) - Static method in class jspecview.source.JDXSourceStreamTokenizer
-
Extracts spaces, underscores etc.
- cleanSmiles(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- cleanSmiles(String) - Method in class org.jmol.smiles.SmilesMatcher
- cleanT(float) - Method in class org.jmol.adapter.writers.XtlWriter
-
right-zero-trimmed
- cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
- clear - Static variable in class org.jmol.script.T
- clear() - Method in class jme.JME
- clear() - Method in class jspecview.app.GenericMouse
- clear() - Method in class jspecview.common.IntegralData
- clear() - Method in interface org.jmol.api.GenericMouseInterface
- clear() - Method in interface org.jmol.api.JmolDataManager
- clear() - Method in class org.jmol.awtjs2d.Mouse
- clear() - Method in class org.jmol.g3d.Graphics3D
- clear() - Method in class org.jmol.jvxl.data.JvxlData
- clear() - Method in class org.jmol.minimize.forcefield.ForceField
- clear() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- clear() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- clear() - Method in class org.jmol.multitouch.ActionManagerMT
- clear() - Method in class org.jmol.shape.Measures
- clear() - Static method in exception class org.jmol.smiles.InvalidSmilesException
- clear() - Method in class org.jmol.util.CommandHistory
-
clears the history.
- clear() - Method in class org.jmol.util.GData
- clear() - Method in class org.jmol.util.TempArray
- clear() - Method in class org.jmol.viewer.ActionManager
- clear() - Method in class org.jmol.viewer.DataManager
- clear() - Method in class org.openscience.jmol.app.HistoryFile
- clear(boolean) - Method in interface org.jmol.api.JmolScriptManager
- clear(boolean) - Method in class org.jmol.script.ScriptManager
- clear(double, double) - Method in class jspecview.common.MeasurementData
- clear(int) - Method in class javajs.util.BS
-
Sets the bit specified by the index to
false
. - clear(int) - Method in interface org.jmol.api.JmolRepaintManager
- clear(int) - Method in class org.jmol.render.RepaintManager
- clear(String) - Method in class org.jmol.shape.Mesh
- clear(String) - Method in class org.jmol.shapecgo.CGOMesh
- clear(String) - Method in class org.jmol.shapespecial.DrawMesh
- clear(Map<String, Object>) - Static method in class org.jmol.thread.TimeoutThread
- CLEAR - Enum constant in enum class jspecview.common.IntegralData.IntMode
- clear33() - Method in class javajs.util.M34
- clearAll() - Method in class javajs.util.BS
-
Sets all of the bits in this BitSet to
false
. - clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
- clearAllView() - Method in class jspecview.common.PanelData
-
Clears all views in the zoom list
- clearAtomConstraints() - Method in class org.jmol.modelkit.ModelKit
- clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
- clearBindings() - Method in class org.jmol.viewer.ActionManager
- clearBits(int, int) - Method in class javajs.util.BS
-
Sets the bits from the specified
fromIndex
(inclusive) to the specifiedtoIndex
(exclusive) tofalse
. - clearCache() - Method in class org.jmol.modelset.ModelSet
- clearCache() - Method in class org.jmol.util.ColorEncoder
- clearCommandWatcherThread() - Method in class org.jmol.script.ScriptManager
- clearConsole() - Method in class org.jmol.viewer.StatusManager
- clearConsole(JSAppletObject) - Method in interface javajs.api.js.J2SObjectInterface
- clearContent(String) - Method in class org.jmol.console.GenericConsole
- clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelSet
- clearDB(int) - Method in class org.jmol.modelset.ModelSet
- clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEval
- clearFontCache() - Method in class org.jmol.g3d.Graphics3D
- clearFontCache() - Method in class org.jmol.util.GData
- clearFunctions() - Method in class org.jmol.viewer.Viewer
- clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- clearInButton - Variable in class org.jmol.console.GenericConsole
- clearLastModelSet() - Method in class org.jmol.modelkit.ModelKitPopup
- clearLinkViews(GraphSet) - Method in class jspecview.common.PanelData
- clearMeasurements() - Method in class org.jmol.api.JmolViewer
- clearMeasurements() - Method in class org.jmol.viewer.Viewer
- clearMesh(String) - Method in class org.jmol.shape.Mesh
- clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
- clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
- clearOrbitals() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- clearOutButton - Variable in class org.jmol.console.GenericConsole
- clearQueue() - Method in interface org.jmol.api.JmolScriptManager
- clearQueue() - Method in class org.jmol.script.ScriptManager
- clearScriptQueue() - Method in class org.jmol.viewer.Viewer
- clearSelection() - Method in class org.jmol.api.JmolViewer
- clearSelection() - Method in class org.jmol.awtjs.swing.JTable
- clearSelection() - Method in class org.jmol.viewer.Viewer
- clearSg() - Method in class org.jmol.shapesurface.Isosurface
- clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
- clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
- clearSourceMenu(JDXSource) - Method in class jspecview.application.ApplicationMenu
- clearStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
- clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
- clearThreads() - Method in class org.jmol.viewer.Viewer
- clearTimeout(String) - Method in class org.jmol.viewer.Viewer
- clearTimeouts() - Method in class org.jmol.viewer.Viewer
- clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- clearUnitCell(int) - Method in class org.jmol.modelset.ModelSet
- clearVisibleSets() - Method in class org.jmol.modelset.AtomCollection
- click(HTMLElement, HTMLWindowEvent) - Method in interface org.jmol.awtjs.swing.SwingController
-
Fired from clicking an element such as a button or check box or table entry, or from entering text in a text box.
- CLICK - Enum constant in enum class org.jmol.c.CBK
- CLICK - Static variable in class com.sparshui.common.TouchState
- CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
- CLICK - Static variable in class org.jmol.viewer.binding.Binding
- CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- clickabilityFlags - Variable in class org.jmol.modelset.Atom
- clickable - Static variable in class org.jmol.script.T
- clickAssignAtom(int, String, P3) - Method in class org.jmol.modelkit.ModelKit
-
From Mouse or handleAtomOrBondBicked
- clicked(long, int, int, int, int) - Method in class jspecview.app.GenericMouse
- CLICKED - Static variable in class org.jmol.awtjs.Event
- clickedCount - Variable in class org.jmol.viewer.ActionManager
- clickProcessXtal(String, String) - Method in class org.jmol.modelkit.ModelKit
- client - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- CLIENT - Static variable in class com.sparshui.common.ConnectionType
- CLIENT_PORT - Static variable in class com.sparshui.common.NetworkConfiguration
- ClientProtocol - Class in com.sparshui.common
-
The abstract class for the client protocol that defines members common to both the server-side and client-side protocols.
- ClientProtocol(Socket) - Constructor for class com.sparshui.common.ClientProtocol
-
Create a new ClientProtocol object.
- ClientProtocol.MessageType - Class in com.sparshui.common
- ClientServerConnection - Class in com.sparshui.client
-
Represents the connection to the GestureServer.
- ClientServerConnection(String, SparshClient) - Constructor for class com.sparshui.client.ClientServerConnection
-
Instantiate a Server Connection object.
- clientService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ClientToServerProtocol - Class in com.sparshui.client
-
ClientToServerProtocol implements the Client side protocol.
- ClientToServerProtocol(Socket) - Constructor for class com.sparshui.client.ClientToServerProtocol
-
Constructor calls ClientProtocol's constructor and sets up data input and output streams for the specified socket.
- clipboard - Static variable in class org.jmol.script.T
- clipCode(int) - Method in class org.jmol.util.GData
- clipCode(int, int, int) - Method in class org.jmol.export.Export3D
- clipCode3(int, int, int) - Method in class org.jmol.util.GData
- clipImageOrPasteText(String) - Method in class org.jmol.api.JmolViewer
- clipImageOrPasteText(String) - Method in class org.jmol.viewer.Viewer
- cList - Variable in class org.jmol.shapecgo.CGOMesh
- clone() - Method in class com.jcraft.jzlib.GZIPHeader
- clone() - Method in class com.sparshui.server.TouchPoint
- clone() - Method in class javajs.util.BS
-
Cloning this
BitSet
produces a newBitSet
that is equal to it. - clone() - Method in class javajs.util.Matrix
-
Clone the Matrix object.
- clone() - Method in class org.jmol.adapter.smarter.Structure
- clone() - Method in class org.jmol.util.Vibration
- cloneAtomSetWithBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneLastAtomSet(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- cloneLastAtomSetFromPoints(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- close() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- close() - Method in class com.jcraft.jzlib.InflaterInputStream
- close() - Method in class com.sparshui.client.ClientServerConnection
- close() - Method in interface javajs.api.GenericBinaryDocument
- close() - Method in class javajs.img.GifEncoder
- close() - Method in class javajs.img.ImageEncoder
- close() - Method in class javajs.util.BinaryDocument
- close() - Method in class javajs.util.OC
-
Deprecated.
- close() - Method in class jspecview.common.JSVZipFileSequentialReader
- close() - Method in class org.apache.tools.bzip2.CBZip2InputStream
- close() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- close() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- close() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- close() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- close(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- close(String) - Method in class jspecview.common.JSViewer
- CLOSE - Enum constant in enum class jspecview.common.ScriptToken
- closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
- closeAllDialogsExcept(Annotation.AType) - Method in class jspecview.common.PanelData
- closeChannel() - Method in interface javajs.api.GenericOutputChannel
- closeChannel() - Method in class javajs.util.OC
- closeDocument() - Method in class javajs.export.PDFCreator
- closeMe() - Method in interface org.jmol.api.GenericImageDialog
- closeMe() - Method in class org.jmol.console.ImageDialog
- closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
- closeReader() - Method in class org.jmol.jvxl.readers.JvxlReader
- closeReader() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- closeReader() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- closeReaderSFR() - Method in class org.jmol.jvxl.readers.JvxlReader
- closeReaderSFR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- closeReaderSFR() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- closeSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
- closeSelected() - Method in class jspecview.dialog.ViewsDialog
- closeSource(JDXSource) - Method in class jspecview.common.JSViewer
- closeSpectrum() - Method in class jspecview.common.PanelData
- closest - Variable in class org.jmol.modelset.ModelSet
- closeStream() - Method in class org.jmol.util.JSONWriter
- closeTag(SB, String) - Static method in class javajs.util.XmlUtil
- closeTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- closeZipEntry(Object) - Method in interface javajs.api.GenericZipTools
- closeZipEntry(Object) - Method in class javajs.util.ZipTools
- cm - Variable in class org.jmol.viewer.Viewer
- cmdAssignAddAtoms(String, P3[], BS, String, String) - Method in class org.jmol.modelkit.ModelKit
-
MODELKIT ADD @3 ...
- cmdAssignAtom(BS, P3, String, String) - Method in class org.jmol.modelkit.ModelKit
-
A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom via MODELKIT ASSIGN ATOM
- cmdAssignBond(int, char, String) - Method in class org.jmol.modelkit.ModelKit
- cmdAssignConnect(int, int, char, String) - Method in class org.jmol.modelkit.ModelKit
- cmdAssignDeleteAtoms(BS) - Method in class org.jmol.modelkit.ModelKit
-
Delete all atoms that are equivalent to this atom.
- cmdAssignMoveAtoms(BS, int, P3, P3[], boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
- cmdAssignSpaceGroup(BS, String, Object, boolean, String) - Method in class org.jmol.modelkit.ModelKit
-
MODELKIT SPACEGROUP Assign a given space group, currently only "P1" Do all the necessary changes in unit cells and atom site assignments.
- cmdAssignSpaceGroupPacked(BS, String, String) - Method in class org.jmol.modelkit.ModelKit
-
MODELKIT SPACEGROUP ....
- CmdExt - Class in org.jmol.scriptext
- CmdExt() - Constructor for class org.jmol.scriptext.CmdExt
- CmdfReader - Class in org.jmol.adapter.readers.xtal
-
A reader for CrystalMaker CMDF binary/text files.
- CmdfReader() - Constructor for class org.jmol.adapter.readers.xtal.CmdfReader
- cmdLoad() - Method in class org.jmol.script.ScriptEval
- cmdMinimize(JmolScriptEvaluator, BS, int, float, float, int) - Method in class org.jmol.modelkit.ModelKit
-
Minimize a unit cell with full symmetry constraints.
- cmdRotate(boolean, boolean) - Method in class org.jmol.script.ScriptEval
- cmdRotateAtoms(BS, P3[], float) - Method in class org.jmol.modelkit.ModelKit
- cmds - Variable in class org.jmol.shapecgo.CGOMesh
- cmdScript(int, String, String, Lst<SV>) - Method in class org.jmol.script.ScriptEval
- cmdUndoRedo(int) - Method in class org.jmol.script.ScriptEval
- cmi - Variable in class org.jmol.viewer.AnimationManager
-
current model index
- CML - Enum constant in enum class jspecview.common.ExportType
- CML - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CMLExporter - Class in jspecview.export
-
class
CMLExporter
contains static methods to export a Graph as as CIML. - CMLExporter() - Constructor for class jspecview.export.CMLExporter
- CMLWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
- CMLWriter() - Constructor for class org.jmol.adapter.writers.CMLWriter
- code - Variable in class org.jmol.i18n.Language
- codeBase - Variable in class org.jmol.util.GenericApplet
- codePath - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- coef - Variable in class org.jmol.quantum.SlaterData
- coeffs - Variable in class org.jmol.quantum.MOCalculation
- col - Static variable in class org.jmol.script.T
- colix - Variable in class org.jmol.adapter.smarter.Bond
- colix - Variable in class org.jmol.modelset.Bond
- colix - Variable in class org.jmol.modelset.Measurement
- colix - Variable in class org.jmol.modelset.MeasurementData
- colix - Variable in class org.jmol.modelset.Text
- colix - Variable in class org.jmol.render.ShapeRenderer
- colix - Variable in class org.jmol.shape.Measures
- colix - Variable in class org.jmol.shape.MeshCollection
- colix - Variable in class org.jmol.shapespecial.Dipole
- colix - Variable in class org.jmol.shapespecial.Ellipsoid
- colix - Variable in class org.jmol.shapespecial.Polyhedron
- colix - Variable in class org.jmol.util.MeshSurface
- COLIX_CONTRAST - Static variable in class org.jmol.util.C
- colixA - Variable in class org.jmol.render.FontLineShapeRenderer
- colixAtom - Variable in class org.jmol.modelset.Atom
- colixB - Variable in class org.jmol.render.FontLineShapeRenderer
- colixBack - Variable in class org.jmol.util.MeshSurface
- colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
- colixCurrent - Variable in class org.jmol.util.GData
- colixEdge - Variable in class org.jmol.shapespecial.Polyhedron
- colixes - Variable in class org.jmol.renderbio.BackboneRenderer
- colixes - Variable in class org.jmol.renderbio.CartoonRenderer
- colixes - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- colixes - Variable in class org.jmol.renderbio.RibbonsRenderer
- colixes - Variable in class org.jmol.renderbio.RocketsRenderer
- colixes - Variable in class org.jmol.renderbio.StrandsRenderer
- colixes - Variable in class org.jmol.renderbio.TraceRenderer
- colixes - Variable in class org.jmol.shape.AtomShape
- colixesBack - Variable in class org.jmol.renderbio.BackboneRenderer
- colixesBack - Variable in class org.jmol.renderbio.CartoonRenderer
- colixesBack - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- colixesBack - Variable in class org.jmol.renderbio.RibbonsRenderer
- colixesBack - Variable in class org.jmol.renderbio.RocketsRenderer
- colixesBack - Variable in class org.jmol.renderbio.StrandsRenderer
- colixesBack - Variable in class org.jmol.renderbio.TraceRenderer
- colixesBack - Variable in class org.jmol.shapebio.BioShape
- colixHighlight - Variable in class org.jmol.shape.Halos
- colixRubberband - Variable in class org.jmol.viewer.ColorManager
- colixSelection - Variable in class org.jmol.shape.Halos
- collapsed - Static variable in class org.jmol.script.T
- collapsed - Variable in class org.jmol.shapespecial.Polyhedron
- colon - Static variable in class org.jmol.script.T
- color - Variable in class org.jmol.jvxl.data.JvxlData
- color - Static variable in class org.jmol.script.T
- color - Variable in class org.jmol.shape.Mesh
- color - Variable in class org.jmol.shape.MeshCollection
- color - Variable in class org.jmol.util.BZone
- Color - Class in org.jmol.awtjs.swing
- Color() - Constructor for class org.jmol.awtjs.swing.Color
- COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
- COLOR_CONTRAST - Static variable in class org.jmol.viewer.JC
- colorCommand - Variable in class org.jmol.shape.Mesh
- colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
- colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
- colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
- colorDensity - Variable in class org.jmol.shape.Mesh
- ColoredAnnotation - Class in jspecview.common
-
ColoredAnnotation is a label on the spectrum; not an integralRegion
- ColoredAnnotation() - Constructor for class jspecview.common.ColoredAnnotation
- colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
- colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- ColorEncoder - Class in org.jmol.util
- ColorEncoder(ColorEncoder, Viewer) - Constructor for class org.jmol.util.ColorEncoder
- colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
- colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
- colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
- colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
- ColorManager - Class in org.jmol.viewer
- colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
- ColorParameters - Class in jspecview.common
-
This a representation of the Display Scheme for the spectral display.
- ColorParameters() - Constructor for class jspecview.common.ColorParameters
- colorPhased - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- colorPos - Variable in class org.jmol.jvxl.readers.Parameters
- colorPtFromInt(int, P3) - Static method in class javajs.util.CU
- colorPtFromString(String) - Static method in class javajs.util.CU
- colorPtToFFRGB(T3) - Static method in class javajs.util.CU
- colorrasmol - Static variable in class org.jmol.script.T
- colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
- colorscheme - Static variable in class org.jmol.script.T
- colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
- colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
- colorsExplicit - Variable in class org.jmol.util.MeshSurface
- colorTriadToFFRGB(float, float, float) - Static method in class javajs.util.CU
- colorType - Variable in class org.jmol.shape.Mesh
- columnCount - Variable in class javajs.util.CifDataParser
- columnNames - Variable in class javajs.util.CifDataParser
- ColumnSelectionModel - Interface in org.jmol.awtjs.swing
- com.jcraft.jzlib - package com.jcraft.jzlib
- com.sparshui - package com.sparshui
- com.sparshui.client - package com.sparshui.client
- com.sparshui.common - package com.sparshui.common
- com.sparshui.common.messages.events - package com.sparshui.common.messages.events
- com.sparshui.common.utils - package com.sparshui.common.utils
- com.sparshui.gestures - package com.sparshui.gestures
- com.sparshui.inputdevice - package com.sparshui.inputdevice
- com.sparshui.server - package com.sparshui.server
- combineSelected() - Method in class jspecview.dialog.ViewsDialog
- combineSpectra(String) - Method in class jspecview.common.JSViewer
- combo1 - Variable in class jspecview.dialog.JSVDialog
- comma - Static variable in class org.jmol.script.T
- command - Static variable in class org.jmol.script.T
- commandExpected() - Method in class org.jmol.script.ScriptCompiler
- CommandHistory - Class in jspecview.application
-
CommandHistory keeps a command history and responds to key events
- CommandHistory - Class in org.jmol.util
-
Implements a queue for a bash-like command history.
- CommandHistory() - Constructor for class org.jmol.util.CommandHistory
-
Creates a new instance using the default size (100)
- CommandHistory(JSViewer, JTextField) - Constructor for class jspecview.application.CommandHistory
- commandHistoryLevelMax - Static variable in class org.jmol.script.ScriptEval
- commandLineOptions - Variable in class org.jmol.export.___Exporter
- commands - Static variable in class org.jmol.script.T
- commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CommandWatcherThread - Class in org.jmol.script
- CommandWatcherThread() - Constructor for class org.jmol.script.CommandWatcherThread
- commensurateSection1 - Variable in class org.jmol.adapter.readers.cif.MSRdr
- COMMENT - Static variable in class jspecview.source.XMLParser
- commentChar - Variable in class org.jmol.export.___Exporter
- COMPARABLE_COMAPRATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- comparator - Static variable in class org.jmol.script.T
- compare - Static variable in class org.jmol.script.T
- compare(JmolTouchSimulator.TouchData, JmolTouchSimulator.TouchData) - Method in class com.sparshui.inputdevice.JmolTouchSimulator.TouchDataComparator
- compare(Object[], Object[]) - Method in class org.jmol.shapespecial.Polyhedra
- compare(Object, Object) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
- compare(String[], String[]) - Method in class org.jmol.modelsetbio.BioResolver
- compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
- compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
- compare(SV, SV) - Method in class org.jmol.script.SV.Sort
- compare(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.MeshCapperSorter
- compareAngles(double, double, double, double) - Static method in class jme.JMEUtil
- compareAtoms(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- compareAtoms(int, int) - Method in interface org.jmol.api.PymolAtomReader
- compareFloat(int, float, float) - Method in class org.jmol.script.ScriptEval
- compareFloatData(int, float[], int, float) - Method in class org.jmol.script.ScriptEval
- compareTo(Measure) - Method in class org.openscience.jmol.app.janocchio.Measure
- Comparision to Daylight SMARTS - Search tag in package org.jmol.smiles
- Section
- Comparision to Daylight SMILES - Search tag in package org.jmol.smiles
- Section
- compile(String, boolean) - Method in class org.jmol.util.PatternMatcher
- compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
-
Compiles a set of tokens for each primitive element of a label.
- compileExpr(String) - Method in class org.jmol.viewer.Viewer
- compileExpression() - Method in class org.jmol.script.ScriptCompiler
- compileExpressions() - Method in class org.jmol.script.ScriptCompiler
- compiler - Variable in class org.jmol.script.ScriptEval
- compiler - Variable in class org.jmol.viewer.Viewer
- compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEval
- compileScriptFile(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEval
- compileScriptString(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEval
- compileSearchTarget(Node[], int, BS) - Method in interface org.jmol.api.SmilesMatcherInterface
- compileSearchTarget(Node[], int, BS) - Method in class org.jmol.smiles.SmilesMatcher
- compileSmartsPattern(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- compileSmartsPattern(String) - Method in class org.jmol.smiles.SmilesMatcher
- completeCommand(String) - Method in class org.jmol.console.GenericConsole
- completeCommand(Map<String, ?>, boolean, boolean, String, int) - Static method in class org.jmol.script.T
- completeMolecule() - Method in class jme.JMEmol
- Component - Class in org.jmol.awtjs.swing
- Component(String) - Constructor for class org.jmol.awtjs.swing.Component
- componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- CompoundDocument - Class in javajs.util
- CompoundDocument() - Constructor for class javajs.util.CompoundDocument
- COMPOUNDMENUON - Enum constant in enum class jspecview.common.ScriptToken
- computeAngle(T3, T3, T3, V3, V3, boolean) - Static method in class javajs.util.Measure
- computeAngleABC(T3, T3, T3, boolean) - Static method in class javajs.util.Measure
- computeHelicalAxis(P3, P3, Quat) - Static method in class javajs.util.Measure
-
This method calculates measures relating to two points in space with related quaternion frame difference.
- computeTorsion(T3, T3, T3, T3, boolean) - Static method in class javajs.util.Measure
- concatList(SV, SV, boolean) - Static method in class org.jmol.script.SV
- CONE - Static variable in class org.jmol.shapecgo.CGOMesh
- configuration - Static variable in class org.jmol.script.T
- confirm(String, String) - Method in class jspecview.java.AwtPlatform
- confirm(String, String) - Method in class jspecview.js2d.JsPlatform
- confirm(String, String) - Method in interface org.jmol.api.GenericPlatform
- confirm(String, String) - Method in class org.jmol.awt.Platform
- confirm(String, String) - Method in class org.jmol.awtjs2d.Platform
- confirm(String, String) - Method in class org.jmol.viewer.Viewer
- connect - Static variable in class org.jmol.script.T
- connect() - Method in class javajs.util.AjaxURLConnection
- connect(float[][]) - Method in class org.jmol.modelset.ModelSet
- connected - Static variable in class org.jmol.script.T
- connectedAtoms - Variable in class org.jmol.shape.Mesh
- connections - Variable in class org.jmol.shape.MeshCollection
- ConnectionType - Class in com.sparshui.common
- ConnectionType() - Constructor for class com.sparshui.common.ConnectionType
- connectNBO(int, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- connectNBO(String) - Method in class org.jmol.viewer.Viewer
- console - Static variable in class org.jmol.script.T
- console - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
- consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- consoleGetImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel.console
- ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
- ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
- constraint - Static variable in class org.jmol.script.T
- constraints - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
- constraints - Variable in class org.jmol.minimize.Minimizer
- contact - Static variable in class org.jmol.script.T
- Contact - Class in org.jmol.shapesurface
- Contact() - Constructor for class org.jmol.shapesurface.Contact
- contactPair - Variable in class org.jmol.jvxl.readers.Parameters
- ContactPair - Class in org.jmol.util
- ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
- ContactRenderer - Class in org.jmol.rendersurface
- ContactRenderer() - Constructor for class org.jmol.rendersurface.ContactRenderer
- contactType - Variable in class org.jmol.util.ContactPair
- Container - Class in org.jmol.awtjs.swing
- Container(String) - Constructor for class org.jmol.awtjs.swing.Container
- contains(int[], int) - Static method in class jme.JMEUtil
- contains(int, int) - Method in class org.jmol.util.Rectangle
- contentDisabled - Variable in class org.molecularplayground.MPJmolApp
- context - Static variable in class org.jmol.script.T
- CONTEXT_DELAY - Static variable in class org.jmol.script.ScriptEval
- CONTEXT_HOLD_QUEUE - Static variable in class org.jmol.script.ScriptEval
- contextdepthmax - Static variable in class org.jmol.script.T
- contextFunctions - Variable in class org.jmol.script.ScriptParam
- contextPath - Variable in class org.jmol.script.ScriptContext
- contextVariables - Variable in class org.jmol.script.ScriptParam
- continuecmd - Static variable in class org.jmol.script.T
- continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- continuous - Variable in class jspecview.export.AMLExporter
- continuous - Variable in class jspecview.export.CMLExporter
- continuous - Variable in class jspecview.source.AnIMLReader
- contour - Static variable in class org.jmol.script.T
- CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
- contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
- contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
- contourColors - Variable in class org.jmol.jvxl.data.JvxlData
- contourlines - Static variable in class org.jmol.script.T
- contours - Static variable in class org.jmol.script.T
- contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
- contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
- contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourType - Variable in class org.jmol.jvxl.readers.Parameters
- contourValues - Variable in class org.jmol.jvxl.data.JvxlData
- contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
- contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
- contrastColix - Variable in class org.jmol.util.GData
-
WHITE or BLACK
- controlPoints - Variable in class org.jmol.modelsetbio.BioPolymer
- controlPoints - Variable in class org.jmol.renderbio.BackboneRenderer
- controlPoints - Variable in class org.jmol.renderbio.CartoonRenderer
- controlPoints - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- controlPoints - Variable in class org.jmol.renderbio.RibbonsRenderer
- controlPoints - Variable in class org.jmol.renderbio.RocketsRenderer
- controlPoints - Variable in class org.jmol.renderbio.StrandsRenderer
- controlPoints - Variable in class org.jmol.renderbio.TraceRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.BackboneRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.CartoonRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.RocketsRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.StrandsRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.TraceRenderer
- Converter - Class in com.sparshui.common.utils
-
Contains conversion methods that are needed by several elements of the Gesture Server.
- Converter() - Constructor for class com.sparshui.common.utils.Converter
- convertPointFromScreen(Object, P3) - Method in class jspecview.java.AwtPlatform
- convertPointFromScreen(Object, P3) - Method in class jspecview.js2d.JsPlatform
- convertPointFromScreen(Object, P3) - Method in interface org.jmol.api.GenericPlatform
- convertPointFromScreen(Object, P3) - Method in class org.jmol.awt.Platform
- convertPointFromScreen(Object, P3) - Method in class org.jmol.awtjs2d.Platform
- convertToMegabytes(long) - Static method in class org.jmol.popup.GenericPopup
- convertTransform(String, M4) - Method in interface org.jmol.api.SymmetryInterface
- convertTransform(String, M4) - Method in class org.jmol.symmetry.Symmetry
-
Convert to/from string/matrix representation
- convertValue(Map<String, Object>, String) - Static method in class org.qcschema.QCSchemaUnits
-
Read a {value:xxxx, units:["name",toAU]} map, converting it to the desired units.
- coord - Variable in class org.jmol.minimize.MinAtom
- coord - Static variable in class org.jmol.script.T
- COORDCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
- coordClicked - Variable in class jspecview.common.PanelData
- Coordinate - Class in jspecview.common
-
The
Coordinate
class stores the x and y values of a coordinate. - Coordinate() - Constructor for class jspecview.common.Coordinate
-
Constructor
- coordinateInRange(int, int, T3, int, P3i) - Method in class org.jmol.shape.Shape
- coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- coordinatesAreFractional - Variable in class org.jmol.script.ScriptParam
-
set in getPointOrPlane
- coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the boolean whether coordinates are fractional.
- coordinatesColor - Variable in class jspecview.common.PanelData
- COORDINATESCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- COORDINATESON - Enum constant in enum class jspecview.common.ScriptToken
- coordsClicked - Variable in class jspecview.common.PanelData
- coordStr - Variable in class jspecview.common.PanelData
- copy() - Method in class javajs.util.Matrix
-
Make a deep copy of a matrix
- copy() - Method in class jspecview.common.ColorParameters
-
Returns a copy of this
DisplayScheme
- copy() - Method in class jspecview.common.Coordinate
-
Returns a new coordinate that has the same x and y values of this coordinate
- copy() - Method in class jspecview.common.Spectrum
-
specifically for Abs/Trans conversion.
- copy() - Method in class org.jmol.util.Point3fi
- copy(String) - Method in class jspecview.common.ColorParameters
-
Returns a copy of this
DisplayScheme
with a new name - copy(String) - Method in class jspecview.java.AwtParameters
- copy(String) - Method in class jspecview.js2d.JsParameters
- copy(BS) - Static method in class javajs.util.BS
-
fast copy
- copy(BS) - Static method in class org.jmol.util.BSUtil
- copy2(BS, BS) - Static method in class org.jmol.util.BSUtil
- copyArray(double[]) - Static method in class jme.JMEUtil
- copyArray(int[]) - Static method in class jme.JMEUtil
- copyArray(int[], int) - Static method in class jme.JMEUtil
- copyArray(String[]) - Static method in class jme.JMEUtil
- copyColixTranslucency(short, short) - Static method in class org.jmol.util.C
- copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
- copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- copyInvert(BS, int) - Static method in class org.jmol.util.BSUtil
- copyM() - Method in class jspecview.common.Measurement
- copyOf(T[], int) - Static method in class jme.JMEUtil
-
Copies the specified array, truncating or padding with nulls (if necessary) so the copy has the specified length.
- copyOf(U[], int, Class<? extends T[]>) - Static method in class jme.JMEUtil
-
Copies the specified array, truncating or padding with nulls (if necessary) so the copy has the specified length.
- copyright - Static variable in class org.jmol.viewer.JC
- copySafely(SV) - Static method in class org.jmol.script.SV
-
Make a copy if this is a variable -- if it has myName != null.
- copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
- copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- copyTensor() - Method in class org.jmol.util.Tensor
- copyTo(P3, AtomSetCollection) - Method in class org.jmol.adapter.smarter.Atom
- copyTo(JDXDataObject) - Method in class jspecview.source.JDXDataObject
- cordMidPoints - Variable in class org.jmol.renderbio.RocketsRenderer
- corners - Static variable in class org.jmol.script.T
- cos - Static variable in class org.jmol.script.T
- cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
- cosBeta - Variable in class org.jmol.util.SimpleUnitCell
- cosGamma - Variable in class org.jmol.util.SimpleUnitCell
- count - Variable in class org.jmol.modelset.Measurement
- count - Static variable in class org.jmol.script.T
- COUNT_MASK - Static variable in class org.jmol.viewer.binding.Binding
- countChar(String, char) - Static method in class javajs.util.PT
- counter - Variable in class org.jmol.script.ScriptParallelProcessor
- countPlusIndices - Variable in class org.jmol.modelset.Measurement
- countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
- countTokens(String, int) - Static method in class javajs.util.PT
- coupleColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- CoupleColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
- CoupleColourSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- CoupleParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
- CoupleParameterSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
-
Creates new form noeParameterSelectionPanel
- couples - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- couplesWhole - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- coupleTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- CoupleTable - Class in org.openscience.jmol.app.janocchio
- CoupleTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.CoupleTable
-
Constructor
- covalentradius - Static variable in class org.jmol.script.T
- covalentVersion - Static variable in class org.jmol.util.Elements
- CPK - Enum constant in enum class org.jmol.c.PAL
- cr - Variable in class org.jmol.adapter.readers.cif.MSRdr
- CRC32 - Class in com.jcraft.jzlib
- CRC32() - Constructor for class com.jcraft.jzlib.CRC32
- create - Static variable in class org.jmol.script.T
- create(BZone) - Method in class org.jmol.util.BZone
- createAndShowGUI(Viewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
- createArray(int) - Static method in class jme.JMEUtil
- createArray(int, int) - Static method in class jme.JMEUtil
- createArrayOfArrayList(int) - Static method in class javajs.util.AU
-
Helper method for creating a List
[] without warnings. - createArrayOfHashtable(int) - Static method in class javajs.util.AU
-
Helper method for creating a Mapinvalid input: '<'K, V>[] without warnings.
- createAtomDataSet(Viewer, ModelSet, int, Object, BS) - Static method in class org.jmol.modelset.ModelLoader
- createBArray(int) - Static method in class jme.JMEUtil
- createBZ(Viewer, int, Object[], boolean, String, float, float, P3) - Method in class org.jmol.util.BZone
-
Create a Brillouin zone.
- createColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
- createCompatibleUnitCell(SpaceGroup, float[], float[], boolean) - Static method in class org.jmol.symmetry.UnitCell
-
Create a unit cell compatible with
- createCube() - Method in class org.jmol.quantum.MepCalculation
- createCube() - Method in class org.jmol.quantum.MOCalculation
- createCube() - Method in class org.jmol.quantum.NciCalculation
- createCube() - Method in class org.jmol.quantum.QuantumCalculation
- CREATED - Enum constant in enum class org.jmol.c.FIL
- createDArray(int) - Static method in class jme.JMEUtil
- createDFMap(int[], String, String, int) - Static method in class org.jmol.quantum.QS
- createDialog(Component) - Method in class org.jmol.dialog.FileChooser
- createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createEllipsoidShades() - Method in class org.jmol.util.Shader
- createFileData(String) - Method in interface org.jmol.api.JmolDataManager
- createFileData(String) - Method in class org.jmol.viewer.DataManager
- createFont3D(int, int, float, float, FontManager, Object) - Static method in class org.jmol.util.Font
- createGeodesic(int) - Static method in class org.jmol.util.Geodesic
- createGuiMap() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createGuiMap() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createImage(Object) - Method in class jspecview.java.AwtPlatform
-
could be byte[] (from ZIP file) or String (local file name) or URL
- createImage(Object) - Method in class jspecview.js2d.JsPlatform
-
could be byte[] (from ZIP file) or String (local file name) or URL
- createImage(Object) - Method in interface org.jmol.api.GenericPlatform
-
can be ignored (return null) if platform cannot save images
- createImage(Object) - Method in class org.jmol.awt.Platform
-
could be byte[] (from ZIP file) or String (local file name) or URL
- createImage(Object) - Method in class org.jmol.awtjs2d.Platform
- createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
-
Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
- createImage(String, String, Object, int) - Method in class org.jmol.util.GenericApplet
- createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- createImage(String, OC, Map<String, Object>) - Method in interface javajs.api.GenericImageEncoder
- createImage(String, OC, Map<String, Object>) - Method in class javajs.img.ImageEncoder
- createItemKeys(JmolPanel) - Method in class org.jmol.console.KeyJMenu
- createJDXSource(GenericFileInterface, Object, String, boolean, boolean, int, int, float) - Static method in class jspecview.source.JDXReader
-
general entrance method
- createJDXSourceFromStream(InputStream, boolean, boolean, float) - Static method in class jspecview.source.JDXReader
-
used only for preferences display and Android
- createLArray(int) - Static method in class jme.JMEUtil
- createMainPanel(JSViewer) - Method in interface jspecview.api.AppletFrame
- createMainPanel(JSViewer) - Method in class jspecview.appletjs.JSVApplet
- createMatrix(Viewer, BS, String[], NMRNoeMatrix.NOEParams) - Static method in class org.jmol.quantum.NMRNoeMatrix
- createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create a menu for the app.
- createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create the menubar for the app.
- createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
This is the hook through which all menu items are created.
- createModels(int) - Method in class org.jmol.modelset.ModelSet
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
-
create a movie from a set of image files
- createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.image.AviCreator
- createPdfDocument(OC, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
- createPdfDocument(JSVPanel, PrintLayout, OutputStream) - Method in interface jspecview.api.JSVPdfWriter
- createPdfDocument(JSVPanel, PrintLayout, OutputStream) - Method in class jspecview.common.PDFWriter
- createSArray(int) - Static method in class jme.JMEUtil
- createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerAwt
- createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerJS
- createSpaceGroup(int, String, Object, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- createSpaceGroup(int, String, Object, int) - Static method in class org.jmol.symmetry.SpaceGroup
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createStatusBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createStatusBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createTable(Object[][], String[], int[]) - Method in interface jspecview.api.PlatformDialog
- createTable(Object[][], String[], int[]) - Method in class jspecview.dialog.JSVDialog
- createTable(Object[][], String[], int[]) - Method in class jspecview.java.AwtDialog
- createTable(Object[][], String[], int[]) - Method in class jspecview.js2d.JsDialog
- createToolBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createToolBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create the toolbar.
- createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create a button to go inside of the toolbar.
- createTree(int, JDXSource, JSVPanel[]) - Method in interface jspecview.api.JSVTree
- createTree(int, JDXSource, JSVPanel[]) - Method in class jspecview.application.AwtTree
- createTree(int, JDXSource, JSVPanel[]) - Method in class jspecview.tree.SimpleTree
- createURLStreamHandler(String) - Method in class javajs.util.AjaxURLStreamHandlerFactory
- createView(Lst<Spectrum>) - Static method in class jspecview.source.JDXSource
- createZip(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- CREATING_MODELSET - Enum constant in enum class org.jmol.c.FIL
- creatingImage - Variable in class org.jmol.viewer.Viewer
- CREDITS - Static variable in class jspecview.app.JSVApp
- creditsAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CreditsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
- CreditsDialog - Class in org.openscience.jmol.app.jmolpanel
- CreditsDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.CreditsDialog
- criterion - Static variable in class org.jmol.script.T
- cross - Static variable in class org.jmol.script.T
- cross(T3, T3) - Method in class javajs.util.T3
-
Sets this tuple to be the vector cross product of vectors v1 and v2.
- cross(V3d, V3d) - Method in class javajs.util.V3d
-
Sets this vector to be the vector cross product of vectors v1 and v2.
- crossed - Static variable in class org.jmol.script.T
- CRYSTAL - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CRYSTAL_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CRYSTAL_SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CRYSTAL_SYMMETRY_TRANSFORM3 - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CrystalReader - Class in org.jmol.adapter.readers.xtal
-
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
- CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
- crystalReaderLatticeOpsOnly - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- CsfReader - Class in org.jmol.adapter.readers.quantum
-
CSF file reader based on CIF idea -- fluid property fields.
- CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
- cterm - Variable in class javajs.util.CifDataParser
-
optional token terminator; in CIF 2.0 could be } or ]
- CTRL - Static variable in class org.jmol.viewer.binding.Binding
- CTRL_ALT - Static variable in class org.jmol.awtjs.Event
- CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
- CTRL_MASK - Static variable in class org.jmol.awtjs.Event
- CTRL_SHIFT - Static variable in class org.jmol.awtjs.Event
- CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
- ctrlPressed - Variable in class jspecview.common.PanelData
- CU - Class in javajs.util
-
ColorUtility
- CU() - Constructor for class javajs.util.CU
- cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- CubeIterator - Class in org.jmol.bspt
-
Iterator used for finding all points within a box or a hemi-box
- CubeReader - Class in org.jmol.adapter.readers.simple
-
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
- CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
- cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
- cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- current - Variable in class org.jmol.viewer.ActionManager
- currentCursor - Variable in class org.jmol.viewer.Viewer
- currentDir - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- currentFont - Variable in class org.jmol.util.GData
- currentFrameIs(int) - Method in class org.jmol.viewer.AnimationManager
- currentIsLast() - Method in class org.jmol.viewer.AnimationManager
- currentlocalpath - Static variable in class org.jmol.script.T
- currentlyRendering - Variable in class org.jmol.util.GData
- currentMenuItemId - Variable in class org.jmol.popup.GenericPopup
- currentMesh - Variable in class org.jmol.shape.MeshCollection
- currentPalette - Variable in class org.jmol.util.ColorEncoder
- currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
- currentSource - Variable in class jspecview.common.JSViewer
- currentSplitPoint - Variable in class jspecview.common.PanelData
- currentTime - Variable in class org.jmol.thread.JmolThread
- CURSOR_CROSSHAIR - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_DEFAULT - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_HAND - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_MOVE - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_WAIT - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_ZOOM - Static variable in interface org.jmol.api.GenericPlatform
- curve - Static variable in class org.jmol.script.T
- CURVE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- CUSTOM - Enum constant in enum class org.jmol.c.STER
- CUSTOM - Static variable in class org.jmol.util.ColorEncoder
- CUSTOM_CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
- cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cutoff - Variable in class org.jmol.jvxl.data.JvxlData
- cutoff - Variable in class org.jmol.jvxl.readers.Parameters
- cutoff - Static variable in class org.jmol.script.T
- cutoffRange - Variable in class org.jmol.jvxl.data.JvxlData
- cutoffRange - Variable in class org.jmol.jvxl.readers.Parameters
- CYAN - Static variable in class org.jmol.util.C
- cyclicFlag - Variable in class org.jmol.modelsetbio.BioPolymer
- cylinder - Static variable in class org.jmol.script.T
- CYLINDER - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
D
- d - Variable in class org.jmol.util.ContactPair
- DARK_GRAY - Static variable in class jspecview.common.ColorParameters
- dashDots - Variable in class org.jmol.render.FontLineShapeRenderer
- dashes - Static variable in class org.jmol.render.FontLineShapeRenderer
- data - Variable in class javajs.util.BArray
- data - Variable in class org.jmol.minimize.MinObject
- data - Static variable in class org.jmol.script.T
- DATA_ATOM_PROP_ENTRY - Static variable in interface org.jmol.api.JmolDataManager
- DATA_LABEL - Static variable in interface org.jmol.api.JmolDataManager
- DATA_SAVE_IN_STATE - Static variable in interface org.jmol.api.JmolDataManager
- DATA_SELECTION - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_AF - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_AFF - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_AFFF - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_LAST - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_STRING - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_UNKNOWN - Static variable in interface org.jmol.api.JmolDataManager
- DATA_VALUE - Static variable in interface org.jmol.api.JmolDataManager
- DataAdder - Interface in org.jmol.quantum.mo
- DataAdder11H - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributions
- DataAdder11H() - Constructor for class org.jmol.quantum.mo.DataAdder11H
- DataAdder13I - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributions
- DataAdder13I() - Constructor for class org.jmol.quantum.mo.DataAdder13I
- DataAdder7F - Class in org.jmol.quantum.mo
-
adds 7 spherical F orbital contributions
- DataAdder7F() - Constructor for class org.jmol.quantum.mo.DataAdder7F
- DataAdder9G - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributions
- DataAdder9G() - Constructor for class org.jmol.quantum.mo.DataAdder9G
- DataAdderF - Class in org.jmol.quantum.mo
-
adds 10 cartesian F orbital contributions
- DataAdderF() - Constructor for class org.jmol.quantum.mo.DataAdderF
- DataAdderG - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributions
- DataAdderG() - Constructor for class org.jmol.quantum.mo.DataAdderG
- DataAdderH - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributions
- DataAdderH() - Constructor for class org.jmol.quantum.mo.DataAdderH
- DataAdderI - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributions
- DataAdderI() - Constructor for class org.jmol.quantum.mo.DataAdderI
- dataClass - Variable in class jspecview.source.JDXHeader
- dataLen - Variable in class javajs.img.PngEncoder
- DataManager - Class in org.jmol.viewer
- DataManager() - Constructor for class org.jmol.viewer.DataManager
- dataMax - Variable in class org.jmol.jvxl.data.JvxlData
- dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
- dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
- dataMin - Variable in class org.jmol.jvxl.data.JvxlData
- dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
- dataOnly - Variable in class org.jmol.util.MeshSurface
- DataReader - Class in javajs.util
-
Just a simple abstract class to join a String reader and a String[] reader under the same BufferedReader umbrella.
- DataReader() - Constructor for class javajs.util.DataReader
- DataReader(Reader) - Constructor for class javajs.util.DataReader
- dataseparator - Static variable in class org.jmol.script.T
- datatype - Variable in class jspecview.export.AMLExporter
- datatype - Variable in class jspecview.export.CMLExporter
- dataType - Variable in class jspecview.source.JDXHeader
- dataType - Variable in class org.jmol.jvxl.readers.Parameters
- dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- date - Variable in class javajs.img.ImageEncoder
- date - Static variable in class jspecview.common.JSVersion
- date - Variable in class jspecview.common.PrintLayout
- date - Variable in class jspecview.export.AMLExporter
- date - Variable in class jspecview.export.CMLExporter
- date - Variable in class jspecview.source.JDXHeader
- date - Static variable in class org.jmol.viewer.JC
- dBb(BS, boolean) - Method in class org.jmol.modelset.BondCollection
- DBLCLK_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- DBLCLK_EVENT - Static variable in class com.sparshui.GestureType
- DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- DBLCLK_GESTURE - Static variable in class com.sparshui.GestureType
- DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- DC - Static variable in class org.jmol.quantum.QS
- dclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- ddata - Variable in class org.jmol.minimize.MinObject
- DEATH - Static variable in class com.sparshui.common.TouchState
- DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
- debug - Static variable in class org.jmol.script.T
- debug(String) - Method in class org.jmol.util.DefaultLogger
- debug(String) - Static method in class org.jmol.util.Logger
-
Writes a log at DEBUG level.
- debug(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at DEBUG level.
- DEBUG - Enum constant in enum class jspecview.common.ScriptToken
- debugging - Variable in class javajs.util.CifDataParser
-
debugging flag passed from reader; unused
- debugging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- debugging - Static variable in class org.jmol.util.Logger
- debuggingHigh - Static variable in class org.jmol.util.Logger
- debughigh - Static variable in class org.jmol.script.T
- debugHigh - Variable in class org.jmol.script.ScriptEval
- DebugJS - Class in javajs.util
-
A class to insert a JavaScript debug statement for Firefox or Chrome debugger
- DebugJS() - Constructor for class javajs.util.DebugJS
- debugPrint(String) - Method in class org.jmol.export._ObjExporter
-
Debug print utility.
- debugscript - Static variable in class org.jmol.script.T
- decimal - Static variable in class org.jmol.script.T
- decimalScale - Static variable in class javajs.util.PT
- decode(byte[]) - Static method in class javajs.util.MessagePackReader
-
This single method takes care of all MMTF needs.
- decodeBase64(String) - Static method in class javajs.util.Base64
- decodeInchiStereo(SimpleNode[]) - Method in class org.jmol.inchi.InChIJNI
- decodeKey(Integer) - Static method in class org.jmol.minimize.MinObject
- decodeWindowsBMP(byte[]) - Method in class javajs.img.BMPDecoder
-
original comment: loadbitmap() method converted from Windows C code.
- decompressData(SB) - Method in class jspecview.source.JDXDecompressor
-
Determines the type of compression, decompresses the data and stores coordinates in an array to be returned
- deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
- deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
- deepCopy(Object, boolean, boolean) - Static method in class org.jmol.script.SV
-
Copies a hash or array deeply; invoked by Jmol script x = @a where a.type == "hash" or a.type == "varray"
- DEF_WBITS - Static variable in class com.jcraft.jzlib.JZlib
- DEFAULT - Static variable in class org.jmol.smiles.SmilesStereo
- DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JC
- DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JC
- DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_BUFSIZE - Static variable in class com.jcraft.jzlib.InflaterInputStream
- DEFAULT_DRAG_DROP_SCRIPT - Static variable in class org.jmol.viewer.JC
- DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JC
- DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JC
- DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
- DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JC
- DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_MINY - Static variable in class jspecview.common.IntegralData
- DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
- DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
- DEFAULT_OFFSET - Static variable in class jspecview.common.IntegralData
- DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JC
- DEFAULT_RANGE - Static variable in class jspecview.common.IntegralData
- DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JC
- DEFAULT_VISUAL_RANGE - Static variable in class org.jmol.viewer.TransformManager
- defaultAlignment - Variable in class org.jmol.shape.Labels
- defaultanglelabel - Static variable in class org.jmol.script.T
- defaultBgcolix - Variable in class org.jmol.shape.Labels
- defaultBondingMars - Static variable in class org.jmol.util.Elements
-
Default table of bonding radii stored as a short mar ...
- defaultcmd - Static variable in class org.jmol.script.T
- defaultColix - Variable in class org.jmol.shape.Labels
- defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultcolorscheme - Static variable in class org.jmol.script.T
- defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
- defaultdirectory - Static variable in class org.jmol.script.T
- defaultDisplaySchemeName - Variable in class jspecview.application.JSpecView
- defaultdistancelabel - Static variable in class org.jmol.script.T
- defaultdrawarrowscale - Static variable in class org.jmol.script.T
- defaultdropscript - Static variable in class org.jmol.script.T
- defaultDropScript - Variable in class org.jmol.viewer.GlobalSettings
- defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultFontId - Variable in class org.jmol.shape.Labels
- defaultFontId - Variable in class org.jmol.shapespecial.Draw
- defaultFontId0 - Variable in class org.jmol.shapespecial.Draw
- defaultHeight - Variable in class org.jmol.awtjs.swing.JDialog
- defaultlabelpdb - Static variable in class org.jmol.script.T
- defaultLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- defaultlabelxyz - Static variable in class org.jmol.script.T
- defaultlattice - Static variable in class org.jmol.script.T
- defaultloadfilter - Static variable in class org.jmol.script.T
- defaultLoadFilter - Variable in class org.jmol.viewer.GlobalSettings
- defaultloadscript - Static variable in class org.jmol.script.T
- defaultLoadScript - Variable in class org.jmol.viewer.GlobalSettings
- DEFAULTLOADSCRIPT - Enum constant in enum class jspecview.common.ScriptToken
- DefaultLogger - Class in org.jmol.util
-
Default implementation of the logger.
- DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
- defaultMacroDirectory - Static variable in class org.jmol.viewer.JC
- defaultMessage - Variable in class org.jmol.console.GenericConsole
- defaultMode - Variable in class org.jmol.viewer.TransformManager
- DEFAULTNMRNORMALIZATION - Enum constant in enum class jspecview.common.ScriptToken
- defaultOffset - Variable in class org.jmol.shape.Labels
- defaultON - Static variable in class org.jmol.script.T
- defaultPaletteID - Variable in class org.jmol.shape.Labels
- defaultPlotColorNames - Static variable in class jspecview.common.ColorParameters
- defaultPlotColors - Static variable in class jspecview.common.ColorParameters
- defaultPointer - Variable in class org.jmol.shape.Labels
- defaultPrintHeight - Static variable in class jspecview.common.PanelData
- defaultPrintWidth - Static variable in class jspecview.common.PanelData
- defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultQuality - Variable in class javajs.img.JpgEncoder
- defaults - Static variable in class org.jmol.script.T
- defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
- defaultstructuredssp - Static variable in class org.jmol.script.T
- defaultTickInfo - Variable in class org.jmol.shape.Measures
- defaulttorsionlabel - Static variable in class org.jmol.script.T
- defaulttranslucent - Static variable in class org.jmol.script.T
- defaultvdw - Static variable in class org.jmol.script.T
- defaultZPos - Variable in class org.jmol.shape.Labels
- deferred - Variable in class org.jmol.awt.AwtSwingComponent
- define - Static variable in class org.jmol.script.T
- define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
-
called by the client to generate a set of measurements
- defineAtomSets(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- definedAtomSets - Variable in class org.jmol.viewer.Viewer
- definesStereo() - Method in class org.jmol.smiles.SmilesAtom
-
for InChI or any other system that self-defines stereochemistry.
- deflate(int) - Method in class com.jcraft.jzlib.Deflater
- deflate(int) - Method in class com.jcraft.jzlib.DeflaterOutputStream
- Deflate - Class in com.jcraft.jzlib
- deflater - Variable in class com.jcraft.jzlib.DeflaterOutputStream
- Deflater - Class in com.jcraft.jzlib
- Deflater() - Constructor for class com.jcraft.jzlib.Deflater
- DeflaterOutputStream - Class in com.jcraft.jzlib
- DeflaterOutputStream() - Constructor for class com.jcraft.jzlib.DeflaterOutputStream
- DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
- degreesPerRadian - Static variable in class org.jmol.export.___Exporter
- degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
- delay - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- delay - Static variable in class org.jmol.script.T
- delaymaximumms - Static variable in class org.jmol.script.T
- delayScript(int) - Method in class org.jmol.script.ScriptEval
- delete - Static variable in class org.jmol.script.T
- delete(BS) - Method in class org.jmol.modelset.Atom
- deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
- deleteAllBonds2() - Method in class org.jmol.modelset.BondCollection
- deleteAtom(Atom) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
- deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- deleteAtoms(int, BS, BS) - Method in class org.jmol.modelset.StateScript
- deleteAtoms(BS) - Method in class org.jmol.modelset.ModelSet
- deleteAtoms(BS, boolean) - Method in class org.jmol.viewer.Viewer
- deleteAtomsInVariables(BS) - Method in interface org.jmol.api.JmolScriptEvaluator
- deleteAtomsInVariables(BS) - Method in class org.jmol.script.ScriptEval
- deleteBits(BS, BS) - Static method in class org.jmol.util.BSUtil
-
this one slides deleted bits out of a pattern.
- deleteBonds(BS) - Method in class org.jmol.viewer.Viewer
- deleteBonds(BS, boolean) - Method in class org.jmol.modelset.ModelSet
- deleteConnections(float, float, int, BS, BS, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
- DELETED - Enum constant in enum class org.jmol.c.FIL
- deleteElements(Object, int, int) - Static method in class javajs.util.AU
- deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
- deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
- deleteMeshI(int) - Method in class org.jmol.shape.MeshCollection
- deleteMeshKey(String) - Method in class org.jmol.shape.MeshCollection
- deleteModelAtoms(int, int, int, BS) - Method in class org.jmol.viewer.Viewer
- deleteModelAtoms(int, int, BS) - Method in interface org.jmol.api.JmolDataManager
- deleteModelAtoms(int, int, BS) - Method in class org.jmol.modelset.AtomCollection
- deleteModelAtoms(int, int, BS) - Method in class org.jmol.viewer.DataManager
- deleteModelBonds(int) - Method in class org.jmol.modelset.ModelSet
- deleteModels(int) - Method in class org.jmol.shapecgo.CGO
- deleteModels(int, BS) - Method in class org.jmol.viewer.Viewer
-
called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
- deleteModels(BS) - Method in class org.jmol.modelset.ModelSet
- deleteNodes(Lst<JSVTreeNode>) - Method in interface jspecview.api.JSVTree
- deleteNodes(Lst<JSVTreeNode>) - Method in class jspecview.application.AwtTree
- deleteNodes(Lst<JSVTreeNode>) - Method in class jspecview.tree.SimpleTree
- deleteSaved(String) - Method in class org.jmol.viewer.StateManager
- deleteShapeAtoms(Object[], BS) - Method in class org.jmol.viewer.ShapeManager
- deltaX - Variable in class jspecview.export.AMLExporter
- deltaX - Variable in class jspecview.export.CMLExporter
- deltaX - Variable in class jspecview.source.AnIMLReader
- deltaX(double, double, int) - Static method in class jspecview.common.Coordinate
-
Returns the Delta X value
- density - Static variable in class org.jmol.script.T
- depict - Variable in class jme.JME
- depictBorder - Variable in class jme.JME
- deprecatedparam - Static variable in class org.jmol.script.T
- depth - Static variable in class org.jmol.script.T
- depth - Variable in class org.jmol.util.GData
- depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
- depthValue - Variable in class org.jmol.viewer.TransformManager
- depthZ - Variable in class org.jmol.export.___Exporter
- DESCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- descent - Variable in class org.jmol.modelset.Text
- descent - Variable in class org.jmol.render.LabelsRenderer
- desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- destroy() - Method in interface javajs.api.JSInterface
- destroy() - Method in class jspecview.appletjs.JSVApplet
- destroy() - Method in interface org.jmol.api.JmolAppletInterface
- destroy() - Method in class org.jmol.g3d.Graphics3D
- destroy() - Method in class org.jmol.util.GData
- destroy() - Method in class org.jmol.util.GenericApplet
- destroy() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- destroy() - Method in interface org.openscience.jmol.app.JmolPlugin
- destroyConsole() - Method in class org.jmol.console.GenericConsole
- DetachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
- Detailed Jmol SMARTS/Jmol bioSMARTS Specification - Search tag in package org.jmol.smiles
- Section
- Detailed Jmol SMILES/bioSMILES Specification - Search tag in package org.jmol.smiles
- Section
- detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
- determinant3() - Method in class javajs.util.M34
- determinant4() - Method in class javajs.util.M4
-
Computes the determinant of this matrix.
- determineAtomSetCollectionReader(Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
-
the main resolver method.
- determineSurfaceFileType(BufferedReader) - Static method in class org.jmol.viewer.FileManager
-
Try to determine a surface file type based on its header.
- DEVICE_PORT - Static variable in class com.sparshui.common.NetworkConfiguration
- DF - Class in javajs.util
-
created to remove ambiguities and make a simpler DecimalFormat
- DF() - Constructor for class javajs.util.DF
- dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- DgridReader - Class in org.jmol.adapter.readers.quantum
-
A reader for Dgrid BASISFILE data.
- DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
- dialog - Variable in class jspecview.dialog.JSVDialog
- Dialog - Class in org.jmol.dialog
- Dialog() - Constructor for class org.jmol.dialog.Dialog
- Dialog.ExportChoiceListener - Class in org.jmol.dialog
- Dialog.QualityListener - Class in org.jmol.dialog
- Dialog.TypeFilter - Class in org.jmol.dialog
- dialogAsk(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
Ask for new file name when saving or opening a file in Java and saving a file in JavaScript.
- DialogManager - Class in jspecview.dialog
-
Dialogs include Integration, PeakListing, Views, OverlayLegend, and Measurements These dialogs have been generalized for platform independence.' This manager is subclassed as AwtDialogManager and JsDialogManager, which apply their own interpretation of how to create the dialog and get its event callbacks.
- DialogManager() - Constructor for class jspecview.dialog.DialogManager
- DialogParams - Class in jspecview.dialog
-
DialogParams handles all the platform-independent needs of AwtAnnotationDialog and subclasses of it.
- DialogParams() - Constructor for class jspecview.dialog.DialogParams
- dialogsToFront(Spectrum) - Method in class jspecview.common.PanelData
- dialogType - Variable in class org.jmol.dialog.Dialog
- diameter - Variable in class org.jmol.jvxl.data.JvxlData
- diameter - Variable in class org.jmol.render.MeshRenderer
- diameter - Static variable in class org.jmol.script.T
- diameter - Variable in class org.jmol.shape.Mesh
- DIF - Enum constant in enum class jspecview.common.ExportType
- DIFDUP - Enum constant in enum class jspecview.common.ExportType
- diff - Variable in class org.openscience.jmol.app.janocchio.Measure
- diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
- diffusepercent - Static variable in class org.jmol.script.T
- dimension - Variable in class org.jmol.util.SimpleUnitCell
- Dimension - Class in org.jmol.awtjs.swing
- Dimension(int, int) - Constructor for class org.jmol.awtjs.swing.Dimension
- dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- dipole - Static variable in class org.jmol.script.T
- Dipole - Class in org.jmol.shapespecial
- Dipole() - Constructor for class org.jmol.shapespecial.Dipole
- dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
- dipoles - Variable in class org.jmol.shapespecial.Dipoles
- Dipoles - Class in org.jmol.shapespecial
- Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
- dipolescale - Static variable in class org.jmol.script.T
- DipolesRenderer - Class in org.jmol.renderspecial
- DipolesRenderer() - Constructor for class org.jmol.renderspecial.DipolesRenderer
- dipoleValue - Variable in class org.jmol.shapespecial.Dipole
- directedDistanceToPlane(P3, P4, P3) - Static method in class javajs.util.Measure
- direction - Static variable in class org.jmol.script.T
- dirLastExported - Variable in class jspecview.java.AwtFileHelper
- dirLastOpened - Variable in class jspecview.java.AwtFileHelper
- DISABLE - Static variable in class org.jmol.shapecgo.CGOMesh
- disablepopupmenu - Static variable in class org.jmol.script.T
- discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilContains(String) - Method in class jspecview.source.JDXReader
- discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilContains(String) - Method in interface org.jmol.api.JmolJDXMOLReader
- discardLinesUntilContains2(String, String) - Method in class jspecview.source.JDXReader
- discardLinesUntilContains2(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilContains2(String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
- discardLinesUntilNonBlank() - Method in class jspecview.source.JDXReader
- discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilNonBlank() - Method in interface org.jmol.api.JmolJDXMOLReader
- discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardPreviousAtoms() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
- discardTempDataSR(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- discrete - Static variable in class org.jmol.script.T
- dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.CmdExt
-
The command dispatcher for the set of commands extended by this class.
- dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.IsoExt
- dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.ScriptExt
- dispatchCommands(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- dispatchTouchEvent(JmolTouchSimulator.TouchData) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
-
protocol modified by Bob Hanson for Jmol to demonstrate extended SparshUI protocol to include a return from the server indicating whether or not to consume this event.
- displacement - Static variable in class org.jmol.script.T
- display - Variable in class jspecview.common.JSViewer
- display - Variable in class org.jmol.i18n.Language
- display - Static variable in class org.jmol.script.T
- display - Variable in class org.jmol.viewer.Viewer
- display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- display1D - Variable in class jspecview.common.PanelData
- DISPLAY1D - Enum constant in enum class jspecview.common.ScriptToken
- DISPLAY2D - Enum constant in enum class jspecview.common.ScriptToken
- displayAtoms(BS, boolean, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
- displayBonds(BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
- displaycellparameters - Static variable in class org.jmol.script.T
- displayConsole() - Method in class org.jmol.console.GenericConsole
- displayed - Static variable in class org.jmol.script.T
- displayFontName - Variable in class jspecview.common.ColorParameters
- DISPLAYFONTNAME - Enum constant in enum class jspecview.common.ScriptToken
- displayLoadErrors - Variable in class org.jmol.viewer.Viewer
- displayMaxX - Variable in class org.jmol.util.GData
- displayMaxX2 - Variable in class org.jmol.util.GData
- displayMaxY - Variable in class org.jmol.util.GData
- displayMaxY2 - Variable in class org.jmol.util.GData
- displayMinX - Variable in class org.jmol.util.GData
- displayMinX2 - Variable in class org.jmol.util.GData
- displayMinY - Variable in class org.jmol.util.GData
- displayMinY2 - Variable in class org.jmol.util.GData
- displayName - Variable in class org.jmol.symmetry.SpaceGroup
- DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
- DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
- DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
-
Action calling evalStringQuiet(<action> + CheckBoxState)
- DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
-
Action calling moveTo()
- DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
-
Action calling setStatus()
- DisplaySchemesProcessor - Class in jspecview.application
-
DisplaySchemesProcessor
loads and saves the display schemes of Jspecview. - DisplaySchemesProcessor() - Constructor for class jspecview.application.DisplaySchemesProcessor
-
Initialises the
DisplaySchemesProcessor
- displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- displayType - Variable in class org.jmol.shapesurface.Contact
- displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
- displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
- dispose() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- dispose() - Method in class com.sparshui.server.GestureServer
- dispose() - Method in interface jspecview.api.JSVViewPanel
- dispose() - Method in interface jspecview.api.PlatformDialog
- dispose() - Method in class jspecview.app.GenericMouse
- dispose() - Method in class jspecview.app.JSVApp
- dispose() - Method in class jspecview.common.IntegralData
- dispose() - Method in class jspecview.common.JSViewer
- dispose() - Method in class jspecview.common.PanelData
- dispose() - Method in class jspecview.common.PanelNode
- dispose() - Method in class jspecview.common.Spectrum
- dispose() - Method in class jspecview.dialog.JSVDialog
- dispose() - Method in class jspecview.java.AwtDialog
- dispose() - Method in class jspecview.java.AwtMainPanel
- dispose() - Method in class jspecview.java.AwtPanel
- dispose() - Method in class jspecview.java.FileDropperJmol
- dispose() - Method in class jspecview.js2d.JsDialog
- dispose() - Method in class jspecview.js2d.JsMainPanel
- dispose() - Method in class jspecview.js2d.JsPanel
- dispose() - Method in class jspecview.source.JDXSource
- dispose() - Method in interface org.jmol.api.GenericMouseInterface
- dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
- dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
- dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
- dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- dispose() - Method in class org.jmol.api.JmolViewer
- dispose() - Method in class org.jmol.awt.FileDropper
- dispose() - Method in class org.jmol.awtjs.swing.JDialog
- dispose() - Method in class org.jmol.awtjs2d.Mouse
- dispose() - Method in class org.jmol.console.GenericConsole
- dispose() - Method in class org.jmol.console.JmolConsole
- dispose() - Method in class org.jmol.console.ScriptEditor
- dispose() - Method in class org.jmol.consolejs.AppletConsole
- dispose() - Method in class org.jmol.modelkit.ModelKit
- dispose() - Method in class org.jmol.multitouch.ActionManagerMT
- dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
- dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- dispose() - Method in class org.jmol.viewer.ActionManager
- dispose() - Method in class org.jmol.viewer.Viewer
-
end of life for this viewer
- dispose() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- dispose() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
- dispose(SC) - Method in class org.jmol.awt.AwtPopupHelper
- dispose(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- dispose(SC) - Method in interface org.jmol.popup.PopupHelper
- dispose(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Remove this component's HTML5 equivalent and clear references to it.
- disposeGraphics(Object) - Method in class jspecview.java.AwtPlatform
- disposeGraphics(Object) - Method in class jspecview.js2d.JsPlatform
- disposeGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
- disposeGraphics(Object) - Method in class org.jmol.awt.Platform
- disposeGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
- disposeMenu() - Method in class org.jmol.awtjs.swing.JPopupMenu
- distance - Variable in class org.jmol.adapter.smarter.Bond
- distance - Static variable in class org.jmol.script.T
- distance(T3) - Method in class javajs.util.T3
-
Returns the distance between this point and point p1.
- distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
- distance2V(V3d, V3d) - Static method in class org.jmol.minimize.Util
- distance4(P4) - Method in class javajs.util.P4
-
Returns the distance between this point and point p1.
- distancefactor - Static variable in class org.jmol.script.T
- distanceMode - Variable in class org.jmol.quantum.MepCalculation
- distancePointToPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
- distances - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- distanceSquared(T3) - Method in class javajs.util.T3
-
Computes the square of the distance between this point and point p1.
- distanceToMappingPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
- distanceToPlane(P4, T3) - Static method in class javajs.util.Measure
- distanceToPlaneD(P4, float, P3) - Static method in class javajs.util.Measure
- distanceToPlaneV(V3, float, P3) - Static method in class javajs.util.Measure
- distinguishAndPropagateGroup(Chain, String, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.BioResolver
- div - Static variable in class org.jmol.script.T
- div(Quat) - Method in class javajs.util.Quat
- divide - Static variable in class org.jmol.script.T
- divLeft(Quat) - Method in class javajs.util.Quat
- dmesh - Variable in class org.jmol.renderspecial.DrawRenderer
- DmolReader - Class in org.jmol.adapter.readers.xtal
- DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
- dna - Static variable in class org.jmol.script.T
- DNA - Enum constant in enum class org.jmol.c.STR
- DNA_MASK - Static variable in class org.jmol.viewer.JC
- doAction() - Method in class jme.JME
- doAction(Object) - Method in class org.jmol.console.GenericConsole
- doAdvanced(String) - Method in class jspecview.app.JSVApp
-
called by Pro's popup window Advanced...
- doAjax(Object, String, Object, boolean) - Method in interface javajs.api.js.J2SObjectInterface
- doAjax(String, String, Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
- doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCentralize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCircle(int, int, int, boolean) - Method in class javajs.export.PDFCreator
- doClose - Variable in class javajs.img.ImageEncoder
- doClose(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- doClose(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- Document - Interface in org.jmol.awtjs.swing
- documentBase - Variable in class org.jmol.util.GenericApplet
- doDebug - Variable in class org.jmol.quantum.QuantumCalculation
- doDrop(PropertyChangeEvent) - Method in class jspecview.java.FileDropperJmol
- doDrop(PropertyChangeEvent) - Method in class org.jmol.awt.FileDropper
- doEval(String) - Method in class org.jmol.util.GenericApplet
-
return RAW JAVASCRIPT OBJECT, NOT A STRING
- doExitJmol() - Method in interface jspecview.api.AppletFrame
- doExitJmol() - Method in class jspecview.appletjs.JSVApplet
- doExitJmol() - Method in class jspecview.appletjs.JSVAppletPro
- doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- doFormatText - Variable in class org.jmol.modelset.Text
- doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
- doGetModel(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doIterate - Variable in class org.jmol.jvxl.data.VolumeData
- dollarsign - Static variable in class org.jmol.script.T
- doLogLevel(boolean) - Static method in class org.jmol.util.Logger
-
Indicates if the level is logged.
- domains - Static variable in class org.jmol.script.T
- doMenu - Variable in class jme.JME
- doMenuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
- doMenuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
- doMenuSelected() - Method in class jspecview.application.ApplicationMenu
- doMouseAtomAction() - Method in class jme.JME
- doMouseBondAction() - Method in class jme.JME
- doMouseClicked(int, int, boolean) - Method in class jspecview.common.PanelData
- doMouseDragged(int, int) - Method in class jspecview.common.PanelData
- doMouseMoved(int, int) - Method in class jspecview.common.PanelData
- doMousePressed(int, int) - Method in class jspecview.common.PanelData
- doMouseReleased(int, int, boolean) - Method in class jspecview.common.PanelData
- DOMReader - Class in org.jmol.io
- DOMReader() - Constructor for class org.jmol.io.DOMReader
- DOMResolve(Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
-
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
- done - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- done() - Method in class jspecview.dialog.JSVDialog
- doNewMoleculeAction(int, int) - Method in class jme.JME
- DONOR - Enum constant in enum class org.jmol.c.HB
- doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doPolygon(int[], int[], int, boolean) - Method in class javajs.export.PDFCreator
- doPreSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
- doPreSymmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- doPreSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doPreviewAction(boolean) - Method in class org.jmol.dialog.FilePreview
- doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doReadMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doRect(int, int, int, int, boolean) - Method in class javajs.export.PDFCreator
- doRepaint(boolean) - Method in interface jspecview.api.JSVPanel
- doRepaint(boolean) - Method in class jspecview.java.AwtPanel
- doRepaint(boolean) - Method in class jspecview.js2d.JsPanel
- doReport() - Method in class org.jmol.script.ScriptEval
- doResume() - Method in class org.jmol.console.ScriptEditor
- doSendCallback(CBK, Object, Object[], String) - Method in class org.jmol.util.GenericApplet
- doShowDocument(URL) - Method in class org.jmol.util.GenericApplet
- doShowStatus(String) - Method in class org.jmol.util.GenericApplet
- doSort - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- doStep() - Method in class org.jmol.console.ScriptEditor
- doStroke(Object, boolean) - Method in class jspecview.common.PDFWriter
- doStroke(Object, boolean) - Method in class jspecview.java.AwtG2D
- doStroke(Object, boolean) - Method in class jspecview.js2d.JsG2D
- doStroke(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
- doStroke(Object, boolean) - Method in class org.jmol.awt.AwtG2D
- doStroke(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
- dot - Static variable in class org.jmol.script.T
- dot(Quat) - Method in class javajs.util.Quat
- dot(T3) - Method in class javajs.util.T3
-
Vector dot product.
- dot(V3d) - Method in class javajs.util.V3d
-
Computes the dot product of the this vector and vector v.
- doTags - Variable in class jme.JME
- dotdensity - Static variable in class org.jmol.script.T
- dotProduct(double, double, double, double) - Static method in class jme.JMEUtil
- doTransform - Variable in class org.jmol.adapter.writers.CMLWriter
- doTransform4D - Variable in class org.jmol.viewer.TransformManager
- doTranslate - Variable in class org.jmol.util.GenericApplet
- dots - Static variable in class org.jmol.script.T
- Dots - Class in org.jmol.shapespecial
- Dots() - Constructor for class org.jmol.shapespecial.Dots
- dotscale - Static variable in class org.jmol.script.T
- dotsOrDashes - Variable in class org.jmol.render.FontLineShapeRenderer
- DotsRenderer - Class in org.jmol.renderspecial
- DotsRenderer() - Constructor for class org.jmol.renderspecial.DotsRenderer
- dotsselectedonly - Static variable in class org.jmol.script.T
- dotsurface - Static variable in class org.jmol.script.T
- dotted - Static variable in class org.jmol.script.T
- DOTWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
- DOUBLE - Enum constant in enum class org.jmol.c.STER
- DOUBLE - Static variable in class org.jmol.viewer.binding.Binding
- doubleLength(Object) - Static method in class javajs.util.AU
-
Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
- doubleLengthBool(boolean[]) - Static method in class javajs.util.AU
- doubleLengthByte(byte[]) - Static method in class javajs.util.AU
- doubleLengthF(float[]) - Static method in class javajs.util.AU
- doubleLengthI(int[]) - Static method in class javajs.util.AU
- doubleLengthS(String[]) - Static method in class javajs.util.AU
- doubleLengthShort(short[]) - Static method in class javajs.util.AU
- doubleprecision - Static variable in class org.jmol.script.T
- DOWN - Static variable in class org.jmol.viewer.binding.Binding
- downsample - Static variable in class org.jmol.script.T
- downsample2d(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
- downsampleFactor - Variable in class org.jmol.jvxl.readers.JvxlReader
- downsampleFactor - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- downsampleFactor - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- downsampleRemainders - Variable in class org.jmol.jvxl.readers.JvxlReader
- downsampleRemainders - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- downsampleRemainders - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- doZoomLinked(GraphSet, double, double, boolean, boolean, boolean) - Method in class jspecview.common.PanelData
- DRAG - Static variable in class org.jmol.viewer.binding.Binding
- DRAG_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- DRAG_EVENT - Static variable in class com.sparshui.GestureType
- DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- DRAG_GESTURE - Static variable in class com.sparshui.GestureType
- DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- DragBinding - Class in org.jmol.viewer.binding
- DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
- DRAGDROP - Enum constant in enum class org.jmol.c.CBK
- dragEnter(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
- dragEnter(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
- dragEnter(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
- DragEvent - Class in com.sparshui.common.messages.events
- DragEvent() - Constructor for class com.sparshui.common.messages.events.DragEvent
- DragEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.DragEvent
-
Constructs a dragEvent from a complete serialized version of the drag event.
- DragEvent(float, float, int, long) - Constructor for class com.sparshui.common.messages.events.DragEvent
- dragExit(DropTargetEvent) - Method in class jspecview.java.AwtFileDropper
- dragExit(DropTargetEvent) - Method in class jspecview.java.FileDropperJmol
- dragExit(DropTargetEvent) - Method in class org.jmol.awt.FileDropper
- dragged(long, int, int, int) - Method in class jspecview.app.GenericMouse
- DRAGGED - Static variable in class org.jmol.awtjs.Event
- dragOver(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
- dragOver(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
- dragOver(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
- dragselected - Static variable in class org.jmol.script.T
- draw - Static variable in class org.jmol.script.T
- draw(Graphics) - Method in class jme.AtomDisplayLabel
- draw(Graphics) - Method in class jme.JMEmol
- Draw - Class in org.jmol.shapespecial
- Draw() - Constructor for class org.jmol.shapespecial.Draw
- DRAW_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- Draw.EnumDrawType - Enum Class in org.jmol.shapespecial
- draw000 - Variable in class org.jmol.render.FontLineShapeRenderer
- drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
- drawAtom(Atom, float) - Method in interface org.jmol.api.JmolRendererInterface
- drawAtom(Atom, float) - Method in class org.jmol.export.Export3D
- drawAtom(Atom, float) - Method in class org.jmol.g3d.Graphics3D
- drawAxes(String, String) - Method in class org.jmol.modelkit.ModelKit
- drawBond(P3, P3, short, short, byte, short, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.export.Export3D
- drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
- drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
-
draws a simple circle (draw circle)
- drawCircle(Object, int, int, int) - Method in class jspecview.common.PDFWriter
- drawCircle(Object, int, int, int) - Method in class jspecview.java.AwtG2D
- drawCircle(Object, int, int, int) - Method in class jspecview.js2d.JsG2D
- drawCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawCoordinates(Object, int, int, int) - Method in class jspecview.common.PanelData
- drawDashedCylinder(JmolRendererInterface, int, int, int, int, int, int, int[], int, short, short, int, boolean, P3i) - Static method in class org.jmol.render.FontLineShapeRenderer
- drawDashedLineBits(int, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.export.Export3D
- drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawEdge(int, int, boolean, T3, T3, P3i, P3i) - Method in class org.jmol.render.MeshRenderer
- drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
- drawEllipse(P3, P3, P3, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.export.Export3D
- drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
- drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
draws a ring and filled circle (halos, draw CIRCLE, draw handles)
- drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
-
draws a screened circle ...
- drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawfontsize - Static variable in class org.jmol.script.T
- drawGraph(Object, Object, Object, int, int, boolean) - Method in class jspecview.common.PanelData
-
Draws the Spectrum to the panel
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.common.PDFWriter
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.java.AwtG2D
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.js2d.JsG2D
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawHermite4(int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
- drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in interface org.jmol.api.JmolRendererInterface
- drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.export.Export3D
- drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.g3d.Graphics3D
- drawHKL(Viewer, String, P4, P3[]) - Method in class org.jmol.util.BZone
- drawhover - Static variable in class org.jmol.script.T
- drawImage(Object, int, int, int, int, int, int, int, int) - Method in class javajs.export.PDFCreator
- drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
- drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class jspecview.java.AwtPlatform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class jspecview.js2d.JsPlatform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in interface org.jmol.api.GenericPlatform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awt.Platform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs.Platform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Platform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class jspecview.java.AwtPlatform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class jspecview.js2d.JsPlatform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
- drawing - Static variable in class org.jmol.script.T
- drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
- drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.MeasuresRenderer
- drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
- drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawLine(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
- drawLine(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
- drawLine(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
- drawLine(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawLine(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawLine(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawLine2(JmolRendererInterface, int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
- drawLineAB(P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawLineAB(P3, P3) - Method in class org.jmol.export.Export3D
- drawLineAB(P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawLineABBits(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
- drawLineBits(short, short, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawLineBits(short, short, P3, P3) - Method in class org.jmol.export.Export3D
- drawLineBits(short, short, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawLineBits(P3, P3, short, short) - Method in class org.jmol.export.Export3D
- drawLinePixels(P3i, P3i, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.export.Export3D
- drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.util.GData
- drawLineXYZ(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
- drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- DrawMesh - Class in org.jmol.shapespecial
- DrawMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
- drawpicking - Static variable in class org.jmol.script.T
- drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
- drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
- drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
- drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
- drawPolygon(Object, int[], int[], int) - Method in class jspecview.common.PDFWriter
- drawPolygon(Object, int[], int[], int) - Method in class jspecview.java.AwtG2D
- drawPolygon(Object, int[], int[], int) - Method in class jspecview.js2d.JsG2D
- drawPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
- drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
- drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
- drawQuadrilateralBits(JmolRendererInterface, short, P3, P3, P3, P3) - Method in class org.jmol.util.GData
- drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.util.Escape
- drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
draws a rectangle
- drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
-
draws a rectangle
- drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
draws a rectangle
- drawRect(Graphics) - Method in class jme.AtomDisplayLabel
- drawRect(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
- drawRect(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
- drawRect(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
- drawRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- DrawRenderer - Class in org.jmol.renderspecial
- DrawRenderer() - Constructor for class org.jmol.renderspecial.DrawRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.BackboneRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.CartoonRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.RibbonsRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.RocketsRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.StrandsRenderer
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.TraceRenderer
- drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.render.FontLineShapeRenderer
- drawString(Object, String, int, int) - Method in class jspecview.common.PDFWriter
- drawString(Object, String, int, int) - Method in class jspecview.java.AwtG2D
- drawString(Object, String, int, int) - Method in class jspecview.js2d.JsG2D
- drawString(Object, String, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawString(Object, String, int, int) - Method in class org.jmol.awt.AwtG2D
- drawString(Object, String, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawString(String, Font, int, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
-
draws the specified string in the current font.
- drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.export.Export3D
-
draws the specified string in the current font.
- drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
-
draws the specified string in the current font.
- drawStringNoSlab(String, Font, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
-
draws the specified string in the current font.
- drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.export.Export3D
-
draws the specified string in the current font.
- drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
-
draws the specified string in the current font.
- drawStringRotated(Object, String, int, int, double) - Method in class jspecview.common.PDFWriter
- drawStringRotated(Object, String, int, int, double) - Method in class jspecview.java.AwtG2D
- drawStringRotated(Object, String, int, int, double) - Method in class jspecview.js2d.JsG2D
- drawStringRotated(Object, String, int, int, double) - Method in interface org.jmol.api.GenericGraphics
- drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awt.AwtG2D
- drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awtjs2d.JsG2D
- drawStringRotated(String, int, int, int) - Method in class javajs.export.PDFCreator
- drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
- drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
- drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
- drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
- drawSymop(int, int) - Method in class org.jmol.modelkit.ModelKit
-
from set picking symop
- drawTicks(int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
- drawTitle(Object, int, int, String) - Method in class jspecview.common.PanelData
-
Draws Title
- drawTriangle(P3i, short, P3i, short, P3i, short, int, int) - Method in class org.jmol.render.MeshRenderer
- drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.export.Export3D
- drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.g3d.Graphics3D
- drawTriangleBits(JmolRendererInterface, P3, short, P3, short, P3, short, int) - Method in class org.jmol.util.GData
- drawTriangles - Variable in class org.jmol.shape.Mesh
- drawType - Variable in class org.jmol.shapespecial.DrawMesh
- drawUnitCell(String, T3, String) - Method in class org.jmol.modelkit.ModelKit
- drawXAxisLeftToRight - Variable in class jspecview.common.PanelData
- DRIVER_NONE - Static variable in class com.sparshui.common.messages.events.EventType
- DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
- drop(DropTargetDropEvent) - Method in class jspecview.java.AwtFileDropper
- drop(DropTargetDropEvent) - Method in class jspecview.java.FileDropperJmol
- drop(DropTargetDropEvent) - Method in class org.jmol.awt.FileDropper
- dropActionChanged(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
- dropActionChanged(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
- dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
- DS - Static variable in class org.jmol.quantum.QS
- dslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- dssp - Static variable in class org.jmol.script.T
- DSSP - Class in org.jmol.dssx
- DSSP() - Constructor for class org.jmol.dssx.DSSP
- dsspcalchydrogen - Static variable in class org.jmol.script.T
- dssr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- dssr - Static variable in class org.jmol.script.T
- DSSR0 - Class in org.jmol.dssx
-
The original non-JSON parser for output from 3DNA web service.
- DSSR0() - Constructor for class org.jmol.dssx.DSSR0
- DSSR1 - Class in org.jmol.dssx
-
A parser for output from 3DNA web service.
- DSSR1() - Constructor for class org.jmol.dssx.DSSR1
- dssrBox - Variable in class org.jmol.modelsetbio.NucleicMonomer
- dssrBoxHeight - Variable in class org.jmol.modelsetbio.NucleicMonomer
- dssrCache - Variable in class org.jmol.modelset.Model
- dssrFrame - Variable in class org.jmol.modelsetbio.NucleicMonomer
- dssrNT - Variable in class org.jmol.modelset.Group
- DTI - Enum constant in enum class org.jmol.c.STER
- dumpArray(String, float[][], int, int, int, int) - Static method in class javajs.util.AU
- dumpContainer(Container, String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- dumpInfo() - Method in class org.jmol.symmetry.SpaceGroup
- dumpIntArray(int[], int) - Static method in class javajs.util.AU
- dumpList - Static variable in class jspecview.popup.JSVGenericPopup
- dVal(String) - Static method in class javajs.util.PT
- dyMode - Variable in class jme.JME
- dynamicmeasurements - Static variable in class org.jmol.script.T
E
- e - Variable in class org.jmol.scriptext.ScriptExt
- e(Object) - Static method in class org.jmol.util.Escape
- E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
- E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
- eAD(double[]) - Static method in class org.jmol.util.Escape
- eAF(float[]) - Static method in class org.jmol.util.Escape
- eAI(int[]) - Static method in class org.jmol.util.Escape
- eAP(T3[]) - Static method in class org.jmol.util.Escape
- eAS(String[], boolean) - Static method in class org.jmol.util.Escape
- EAST - Static variable in class org.jmol.awtjs.swing.BorderLayout
- EAST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- eBond(BS) - Static method in class org.jmol.util.Escape
- eBS(BS) - Static method in class org.jmol.util.Escape
- ec - Variable in class org.jmol.shapespecial.Dots
- eccentricity - Static variable in class org.jmol.script.T
- eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
- eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
- eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
- eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
- echo - Static variable in class org.jmol.script.T
- Echo - Class in org.jmol.shape
- Echo() - Constructor for class org.jmol.shape.Echo
- ECHO - Enum constant in enum class org.jmol.c.CBK
- ECHO_BOTTOM - Static variable in class org.jmol.viewer.JC
- ECHO_MIDDLE - Static variable in class org.jmol.viewer.JC
- ECHO_TOP - Static variable in class org.jmol.viewer.JC
- ECHO_XY - Static variable in class org.jmol.viewer.JC
- ECHO_XYZ - Static variable in class org.jmol.viewer.JC
- EchoRenderer - Class in org.jmol.render
- EchoRenderer() - Constructor for class org.jmol.render.EchoRenderer
- ed - Static variable in class org.jmol.script.T
- Edge - Class in org.jmol.util
- Edge() - Constructor for class org.jmol.util.Edge
- EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
- edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
- edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
- edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
- edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edges - Static variable in class org.jmol.script.T
- edges - Static variable in class org.jmol.util.BoxInfo
- EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
- EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
- EDGES_ONLY - Static variable in class org.jmol.shapespecial.Polyhedra
- edgesonly - Static variable in class org.jmol.script.T
- edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexes - Static variable in class org.jmol.util.TriangleData
- edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- editButton - Variable in class org.jmol.console.GenericConsole
- editor - Variable in class org.jmol.console.ScriptEditor
- EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- editPane - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- eds - Static variable in class org.jmol.script.T
- edsdiff - Static variable in class org.jmol.script.T
- Eigen - Class in javajs.util
-
Eigenvalues and eigenvectors of a real matrix.
- Eigen() - Constructor for class javajs.util.Eigen
- EigenInterface - Interface in javajs.api
- eigenSignMask - Variable in class org.jmol.util.Tensor
- eigenValues - Variable in class org.jmol.util.Tensor
- eigenVectors - Variable in class org.jmol.util.Tensor
- element - Static variable in class org.jmol.script.T
- ELEMENT_NUMBER_MASK - Static variable in class org.jmol.util.Elements
- elementColors - Variable in class jspecview.common.ColorParameters
- elementCounts - Variable in class org.jmol.util.JmolMolecule
- elementkeys - Static variable in class org.jmol.script.T
- elementLabel - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
- elementNames - Static variable in class org.jmol.util.Elements
- elementNumber - Variable in class org.jmol.adapter.smarter.Atom
- elementNumberFromName(String) - Static method in class org.jmol.util.Elements
- elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
- elementNumberMax - Static variable in class org.jmol.util.Elements
-
one larger than the last elementNumber, same as elementSymbols.length
- elementNumberMax - Variable in class org.jmol.util.JmolMolecule
- Elements - Class in org.jmol.util
- Elements() - Constructor for class org.jmol.util.Elements
- elementsPresent - Variable in class org.jmol.modelset.ModelSet
- elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
- elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
- elementSymbols - Static variable in class org.jmol.util.Elements
-
The default elementSymbols.
- elemisono - Static variable in class org.jmol.script.T
- elemno - Static variable in class org.jmol.script.T
- elemNo - Variable in class org.jmol.quantum.SlaterData
- ellipsoid - Static variable in class org.jmol.script.T
- Ellipsoid - Class in org.jmol.shapespecial
- ELLIPSOID - Static variable in class org.jmol.shapecgo.CGOMesh
- ellipsoidarcs - Static variable in class org.jmol.script.T
- ellipsoidarrows - Static variable in class org.jmol.script.T
- ellipsoidaxes - Static variable in class org.jmol.script.T
- ellipsoidaxisdiameter - Static variable in class org.jmol.script.T
- ellipsoidball - Static variable in class org.jmol.script.T
- ellipsoiddotcount - Static variable in class org.jmol.script.T
- ellipsoiddots - Static variable in class org.jmol.script.T
- ellipsoidfill - Static variable in class org.jmol.script.T
- Ellipsoids - Class in org.jmol.shapespecial
- Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
- ellipsoidShades - Variable in class org.jmol.util.Shader
- EllipsoidsRenderer - Class in org.jmol.renderspecial
- EllipsoidsRenderer() - Constructor for class org.jmol.renderspecial.EllipsoidsRenderer
- elsecmd - Static variable in class org.jmol.script.T
- elseif - Static variable in class org.jmol.script.T
- embedded - Variable in class jme.JME
- EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JC
- embedScript(String) - Static method in class org.jmol.viewer.JC
- EMPTY - Static variable in interface javajs.api.GenericCifDataParser
- EMPTY - Static variable in class org.jmol.adapter.readers.cif.CifReader
- emptySet - Static variable in class org.jmol.util.BSUtil
- ENABLE - Static variable in class org.jmol.shapecgo.CGOMesh
- enabled - Variable in class org.jmol.awtjs.swing.Component
- enableShell(int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...
- enableStatus(boolean) - Method in class jspecview.application.MainFrame
- enableToolbar(boolean) - Method in class jspecview.application.MainFrame
- ENABLEZOOM - Enum constant in enum class jspecview.common.ScriptToken
- ENC_CALC_MAX_DIST - Static variable in class org.jmol.viewer.JC
- encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
- encodeColor(short) - Static method in class org.jmol.shape.Shape
- encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- Encoding - Enum Class in javajs.util
- end - Static variable in class org.jmol.script.T
- end() - Method in class com.jcraft.jzlib.Deflater
- end() - Method in class com.jcraft.jzlib.Inflater
- end() - Method in class org.jmol.util.PatternMatcher.JSPattern
- END - Static variable in class org.jmol.shapecgo.CGOMesh
- END_ELEMENT - Static variable in class jspecview.source.XMLParser
- endAssignment() - Method in class org.jmol.script.ScriptMathProcessor
- endcap - Variable in class org.jmol.render.FontLineShapeRenderer
- ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
- ENDCAPS_FLAT_TO_SPHERICAL - Static variable in class org.jmol.util.GData
- ENDCAPS_HIDDEN - Static variable in class org.jmol.util.GData
- ENDCAPS_NONE - Static variable in class org.jmol.util.GData
- ENDCAPS_OPEN_TO_SPHERICAL - Static variable in class org.jmol.util.GData
- ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
- endChainID - Variable in class org.jmol.adapter.smarter.Structure
- ENDCOM - Static variable in class javajs.api.GenericZipInputStream
- endDocument() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- endDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
- endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader
- endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- ENDHDR - Static variable in class javajs.api.GenericZipInputStream
- endifcmd - Static variable in class org.jmol.script.T
- endIndex - Variable in class jspecview.export.AMLExporter
- endIndex - Variable in class jspecview.export.CMLExporter
- ENDINDEX - Enum constant in enum class jspecview.common.ScriptToken
- endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
- endLayout() - Method in interface jspecview.api.PlatformDialog
- endLayout() - Method in class jspecview.java.AwtDialog
- endLayout() - Method in class jspecview.js2d.JsDialog
- endMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
- endOfData - Variable in class org.jmol.jvxl.readers.JvxlReader
- endOfData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- endOfData - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- ENDOFF - Static variable in class javajs.api.GenericZipInputStream
- endRecording() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- endRendering() - Method in class org.jmol.g3d.Graphics3D
- endRendering() - Method in class org.jmol.util.GData
- endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
- ENDSIG - Static variable in class javajs.api.GenericZipInputStream
- ENDSIZ - Static variable in class javajs.api.GenericZipInputStream
- ENDSUB - Static variable in class javajs.api.GenericZipInputStream
- ENDTOT - Static variable in class javajs.api.GenericZipInputStream
- energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- energy - Static variable in class org.jmol.script.T
- ENERGY - Enum constant in enum class org.jmol.c.PAL
- energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyunits - Static variable in class org.jmol.script.T
- energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
- energyUnits - Variable in class org.jmol.viewer.GlobalSettings
- ensureLength(Object, int) - Static method in class javajs.util.AU
-
Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
- ensureLengthA(float[], int) - Static method in class javajs.util.AU
- ensureLengthByte(byte[], int) - Static method in class javajs.util.AU
- ensureLengthI(int[], int) - Static method in class javajs.util.AU
- ensureLengthS(String[], int) - Static method in class javajs.util.AU
- ensureLengthShort(short[], int) - Static method in class javajs.util.AU
- ensureSignedBytes(byte[]) - Static method in class javajs.util.AU
-
Ensure that we have signed and not unsigned bytes coming out of any process, but particularly out of file reading.
- entered(long, int, int) - Method in class jspecview.app.GenericMouse
- enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- ENV_CALC_MAX_LEVEL - Static variable in class org.jmol.viewer.JC
- EnvelopeCalculation - Class in org.jmol.geodesic
- EnvelopeCalculation() - Constructor for class org.jmol.geodesic.EnvelopeCalculation
- eof - Variable in class com.jcraft.jzlib.InflaterInputStream
- EOF - Static variable in class jspecview.source.XMLParser
- eP(T3) - Static method in class org.jmol.util.Escape
-
must be its own, because of the possibility of being null
- eP4(P4) - Static method in class org.jmol.util.Escape
- equals(int[], int[]) - Static method in class jme.JMEUtil
- equals(Object) - Method in class javajs.util.A4
-
Returns true if the Object o is of type AxisAngle4f and all of the data members of o1 are equal to the corresponding data members in this AxisAngle4f.
- equals(Object) - Method in class javajs.util.BArray
- equals(Object) - Method in class javajs.util.BS
-
Compares this object against the specified object.
- equals(Object) - Method in class javajs.util.M3
-
Returns true if the Object o is of type Matrix3f and all of the data members of t1 are equal to the corresponding data members in this Matrix3f.
- equals(Object) - Method in class javajs.util.M4
-
Returns true if the Object o is of type Matrix4f and all of the data members of t1 are equal to the corresponding data members in this Matrix4f.
- equals(Object) - Method in class javajs.util.T3
-
Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this
- equals(Object) - Method in class javajs.util.T3d
-
Returns true if all of the data members of Tuple3d t1 are equal to the corresponding data members in this
- equals(Object) - Method in class javajs.util.T3i
-
Returns true if the Object o is of type Tuple3i and all of the data members of t are equal to the corresponding data members in this Tuple3i.
- equals(Object) - Method in class javajs.util.T4
-
Returns true if all of the data members of Object are equal to the corresponding data members in this
- equals(Object) - Method in class org.jmol.modelset.Atom
- equals(Object) - Method in class org.jmol.script.T
- equals(Coordinate) - Method in class jspecview.common.Coordinate
-
Indicates whether some other Coordinate is equal to this one
- err() - Method in class javajs.util.M34
- error - Variable in class org.jmol.script.ScriptError
- error - Variable in class org.jmol.script.ScriptParallelProcessor
- error - Static variable in class org.jmol.script.T
- error(int) - Method in class org.jmol.script.ScriptError
- error(int) - Method in class org.jmol.script.ScriptCompiler
- error(int) - Method in class org.jmol.scriptext.ScriptExt
- error(String) - Method in class org.jmol.util.DefaultLogger
- error(String) - Static method in class org.jmol.util.Logger
-
Writes a log at ERROR level.
- error(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at ERROR level.
- error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- ERROR - Enum constant in enum class org.jmol.c.CBK
- ERROR - Static variable in class jspecview.source.JDXDataObject
-
Error number that is returned when a min value is undefined
- ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptError
- ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_badContext - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptError
- ERROR_cannotSet - Static variable in class org.jmol.script.ScriptError
- ERROR_commandExpected - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptError
- ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptError
- ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
- ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptError
- ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptError
- ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptError
- ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptError
- ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_MESSAGE - Static variable in class jspecview.dialog.DialogManager
- ERROR_missingEnd - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptError
- ERROR_moIndex - Static variable in class org.jmol.script.ScriptError
- ERROR_moModelError - Static variable in class org.jmol.script.ScriptError
- ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptError
- ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptError
- ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptError
- ERROR_noData - Static variable in class org.jmol.script.ScriptError
- ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptError
- ERROR_numberExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_operationCanceled - Static variable in class org.jmol.script.ScriptError
- ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptCompiler
- ERROR_what - Static variable in class org.jmol.script.ScriptError
- ERROR_writeWhat - Static variable in class org.jmol.script.ScriptError
- errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
- errorEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at ERROR level with detail on exception.
- errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at ERROR level with detail on exception.
- errorIntStr2(int, String, String) - Method in class org.jmol.script.ScriptCompiler
- errorLine - Variable in class org.jmol.script.ScriptCompiler
- errorLog - Variable in class jspecview.source.AnIMLReader
- errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- errorMessage - Variable in class org.jmol.script.ScriptContext
- errorMessage - Variable in class org.jmol.script.ScriptError
- errorMessage - Variable in class org.jmol.script.ScriptCompiler
- errorMessageUntranslated - Variable in class org.jmol.script.ScriptError
- errorMessageUntranslated - Variable in class org.jmol.script.ScriptCompiler
- errorStr(int, String) - Method in class org.jmol.script.ScriptError
- errorStr(int, String) - Method in class org.jmol.script.ScriptCompiler
- errorStr2(int, String, String) - Method in class org.jmol.script.ScriptError
- errorStr2(String, String) - Method in class org.jmol.script.ScriptCompiler
- errorType - Variable in class org.jmol.script.ScriptContext
- errorType - Variable in class org.jmol.script.ScriptError
- errorType - Variable in class org.jmol.script.ScriptCompiler
- esc(String) - Static method in class javajs.util.PT
- escape() - Method in class org.jmol.script.SV
- escape(BS, char, char) - Static method in class javajs.util.BS
- Escape - Class in org.jmol.util
- Escape() - Constructor for class org.jmol.util.Escape
- escapeColor(int) - Static method in class org.jmol.util.Escape
- escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
- escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
- escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
- escapeHelical(String, int, P3, P3, T3[]) - Static method in class org.jmol.util.Escape
-
Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxis
- escapeHTML(String) - Static method in class org.jmol.i18n.GT
- escapeKeyPressed(boolean) - Method in class jspecview.common.PanelData
- escapeMap(Map<String, Object>) - Static method in class org.jmol.util.Escape
- escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
- escapeMultiplier(T3) - Static method in class org.jmol.util.SimpleUnitCell
-
Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
- escapeUrl(String) - Static method in class javajs.util.PT
- escF(float) - Static method in class javajs.util.PT
-
ensures that a float turned to string has a decimal point
- escUnicode(String) - Static method in class javajs.util.PT
- EspressoReader - Class in org.jmol.adapter.readers.xtal
- EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
- eta - Static variable in class org.jmol.script.T
- eV(Lst<SV>) - Static method in class org.jmol.util.Escape
- eval - Static variable in class org.jmol.script.T
- eval - Variable in class org.jmol.thread.JmolThread
- eval - Variable in class org.jmol.viewer.Viewer
- eval(String) - Method in interface org.jmol.api.JmolStatusListener
- eval(String) - Method in class org.jmol.util.GenericApplet
- eval(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- EVAL - Enum constant in enum class org.jmol.c.CBK
- evalCallback(String, Object[], boolean) - Method in interface org.jmol.api.JmolScriptManager
- evalCallback(String, Object[], boolean) - Method in class org.jmol.script.ScriptManager
- evalCallback(String, Object[], boolean) - Method in class org.jmol.viewer.Viewer
- evalError(String, String) - Method in class org.jmol.script.ScriptError
- evalFile(String) - Method in interface org.jmol.api.JmolScriptManager
- evalFile(String) - Method in class org.jmol.api.JmolViewer
- evalFile(String) - Method in class org.jmol.script.ScriptManager
- evalFile(String) - Method in class org.jmol.viewer.Viewer
- evalFileArgs(String, String) - Method in interface org.jmol.api.JmolScriptManager
- evalFileArgs(String, String) - Method in class org.jmol.api.JmolViewer
- evalFileArgs(String, String) - Method in class org.jmol.script.ScriptManager
- evalFileArgs(String, String) - Method in class org.jmol.viewer.Viewer
- evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.api.JmolScriptEvaluator
- evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
- evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEval
- evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
- evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.api.JmolScriptEvaluator
- evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptEval
- evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.scriptext.CmdExt
-
used for TRY command
- evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
- evalString(String) - Method in class org.jmol.api.JmolViewer
- evalString(String) - Method in class org.jmol.viewer.Viewer
- evalStringGUI(String) - Method in class org.jmol.viewer.Viewer
-
Run a script asynchronously, adding the GUI flag to indicate that we should fire the SELECT callback at the end if there is one.
- evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
- evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
- evalStringQuietSync(String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
- evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
- evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
- evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
- evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- evaluate(ScriptMathProcessor, T, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateCompiledScript(Object[], boolean, boolean, boolean, boolean, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- evaluateCompiledScript(Object[], boolean, boolean, boolean, boolean, SB, boolean) - Method in class org.jmol.script.ScriptEval
- evaluateExpression(Object) - Method in class org.jmol.api.JmolViewer
- evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
-
synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
- evaluateExpression(Object, boolean, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- evaluateExpression(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
-
a general-use method to evaluate a "SET" type expression.
- evaluateExpressionAsVariable(Object) - Method in class org.jmol.api.JmolViewer
- evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
- Event - Class in org.jmol.awtjs
- Event - Interface in com.sparshui.common
-
This interface must be implemented by all user-defined events.
- Event() - Constructor for class org.jmol.awtjs.Event
- EVENT - Static variable in class com.sparshui.common.ClientProtocol.MessageType
- eventApply() - Method in class jspecview.dialog.JSVDialog
- eventFocus() - Method in class jspecview.dialog.JSVDialog
- EventManager - Interface in org.jmol.api
- EventType - Class in com.sparshui.common.messages.events
-
This is an enumeration of all event types currently available.
- EventType() - Constructor for class com.sparshui.common.messages.events.EventType
- evspoints - Variable in class jspecview.source.AnIMLReader
- EX - Variable in class org.jmol.quantum.MOCalculation
- excludeAtoms(BS, boolean) - Method in class org.jmol.viewer.SelectionManager
- excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
- excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
- execHidden(boolean) - Method in class jspecview.application.MainFrame
- execLoad(String, String) - Method in class jspecview.common.JSViewer
- execute(String) - Method in class org.jmol.console.AppletConsole
- execute(String) - Method in class org.jmol.console.GenericConsole
- execute(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
- executionPaused - Variable in class org.jmol.script.ScriptContext
- executionStepping - Variable in class org.jmol.script.ScriptContext
- executor - Variable in class org.jmol.viewer.Viewer
- execView(String, boolean) - Method in class jspecview.common.JSViewer
- exit - Static variable in class org.jmol.script.T
- exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
- exitBondRotation() - Method in class org.jmol.awt.AwtModelKitPopup
- exitBondRotation() - Method in class org.jmol.modelkit.ModelKitPopup
- exitBondRotation(String) - Method in class org.jmol.modelkit.ModelKit
- exited(long, int, int) - Method in class jspecview.app.GenericMouse
- exitjmol - Static variable in class org.jmol.script.T
- exitJmol() - Method in class org.jmol.viewer.Viewer
- exitJSpecView(boolean, Object) - Method in class jspecview.app.JSVAppPro
- exitJSpecView(boolean, Object) - Method in class jspecview.application.JSpecView
- exitJSpecView(boolean, Object) - Method in interface org.jmol.api.JSVInterface
- exitJSpecView(boolean, Object) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- exitMeasurementMode(String) - Method in class org.jmol.viewer.ActionManager
- expandFloatArray(float[], int, boolean) - Method in class org.jmol.script.ScriptEval
-
Accepts a float array and expands [1 -3] to [1 2 3], for example.
- explicitID - Variable in class org.jmol.shape.MeshCollection
- export(String, int) - Method in class jspecview.appletjs.JSVApplet
-
Deprecated.
- export(String, int) - Method in class jspecview.common.JSViewer
- EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
- EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JC
- EXPORT_NOT - Static variable in class org.jmol.util.GData
- EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
- export3D - Variable in class org.jmol.export.___Exporter
- Export3D - Class in org.jmol.export
- Export3D() - Constructor for class org.jmol.export.Export3D
- exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
- exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExportChoiceListener() - Constructor for class org.jmol.dialog.Dialog.ExportChoiceListener
- exportCmd(JSVPanel, Lst<String>, boolean) - Method in interface jspecview.export.ExportInterface
-
from EXPORT command
- exporter - Variable in class org.jmol.export.Export3D
- Exporter - Class in jspecview.export
- Exporter() - Constructor for class jspecview.export.Exporter
- ExportInterface - Interface in jspecview.api
- ExportInterface - Interface in jspecview.export
- exportPass - Variable in class org.jmol.render.MeshRenderer
- exportPrecision - Variable in class jspecview.common.ScaleData
- exportscale - Static variable in class org.jmol.script.T
- exportScale - Variable in class org.jmol.export.___Exporter
- exportSpectrum(String, int) - Method in interface jspecview.api.JSVAppletInterface
-
Delivers spectrum coded as desired: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML, PDF(base64-encoded)
- exportSpectrum(String, int) - Method in class jspecview.app.JSVApp
-
Delivers spectrum coded as desired: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML
- exportSpectrum(String, int) - Method in class jspecview.appletjs.JSVApplet
- exportSpectrum(String, int) - Method in class jspecview.application.MainFrame
- exportSpectrum(JSViewer, String) - Method in interface jspecview.export.ExportInterface
- exportSurface(short) - Method in class org.jmol.render.MeshRenderer
- exportTheSpectrum(String, String, Spectrum, int, int) - Method in interface jspecview.export.ExportInterface
-
returns message if path is not null, otherwise full string of text (unsigned applet)
- exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in interface jspecview.api.JSVExporter
- exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.AMLExporter
-
Exports the Spectrum that is displayed by JSVPanel to a file given by fileName If display is zoomed then export the current view
- exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.CMLExporter
-
Exports the Spectrum that is displayed by JSVPanel to a file given by fileName If display is zoomed then export the current view
- exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.Exporter
- exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.JDXExporter
-
Exports spectrum in one of several formats
- exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.SVGExporter
-
Export a Graph as SVG to a file given by fileName
- exportType - Variable in class org.jmol.render.ShapeRenderer
- ExportType - Enum Class in jspecview.common
- expressionBegin - Static variable in class org.jmol.script.T
- expressionEnd - Static variable in class org.jmol.script.T
- EXTCRC - Static variable in class javajs.api.GenericZipInputStream
- extendGrid - Variable in class org.jmol.jvxl.readers.Parameters
- externalContainer - Variable in class org.jmol.console.JmolConsole
- EXTHDR - Static variable in class javajs.api.GenericZipInputStream
- EXTLEN - Static variable in class javajs.api.GenericZipInputStream
- extractMolData(String) - Method in class org.jmol.api.JmolViewer
- extractMolData(String) - Method in class org.jmol.viewer.Viewer
- extractProperty(Object, Object, int) - Method in class org.jmol.viewer.Viewer
- extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in class org.jmol.viewer.PropertyManager
- extractTagOnly(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
- EXTSIG - Static variable in class javajs.api.GenericZipInputStream
- EXTSIZ - Static variable in class javajs.api.GenericZipInputStream
- EY - Variable in class org.jmol.quantum.MOCalculation
- EZ - Variable in class org.jmol.quantum.MOCalculation
F
- facecenteroffset - Static variable in class org.jmol.script.T
- faceMap - Variable in class org.jmol.renderspecial.DotsRenderer
- faceOrder - Static variable in class org.jmol.util.BoxInfo
- facePoints - Static variable in class org.jmol.util.BoxInfo
- faces - Variable in class org.jmol.shapespecial.Polyhedron
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.AdfReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.AmsReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.DgridReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.AdfReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.AmsReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.DgridReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- fact_2n - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- FACTOR - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
- factorType - Variable in class org.jmol.atomdata.RadiusData
- FAHReader - Class in org.jmol.adapter.readers.simple
-
FoldingAtHome json reader.
- FAHReader() - Constructor for class org.jmol.adapter.readers.simple.FAHReader
- falsifyMesh() - Method in class org.jmol.shapebio.BioShape
- fatal(String) - Method in class org.jmol.util.DefaultLogger
- fatal(String) - Static method in class org.jmol.util.Logger
-
Writes a log at FATAL level.
- fatal(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at FATAL level.
- fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
- fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at FATAL level with detail on exception.
- fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at ERROR level with detail on exception.
- FC - Static variable in class org.jmol.quantum.QS
- fclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- fcoord(T3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- fcoord(T3, String) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Get string version of fraction
- FD_PROPERTY_INLINE - Static variable in class jspecview.java.FileDropperJmol
- fdup(String, int, int) - Static method in class javajs.util.PT
-
fdup duplicates p or q formats for formatCheck and the format() function.
- ffAtomType - Variable in class org.jmol.minimize.MinAtom
- fflistValue(T, int) - Static method in class org.jmol.script.SV
- fformat(double, int, int) - Static method in class jme.JMEUtil
-
Truncate to dec digits after the decimal place and left-pad to length len.
- FFParam - Class in org.jmol.minimize.forcefield
- FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
- ffParams - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- ffType - Variable in class org.jmol.minimize.MinAtom
- fid - Variable in class org.jmol.util.Font
- fids - Variable in class org.jmol.shape.Labels
- fieldProperty(int) - Method in class org.jmol.adapter.readers.cif.CifReader
- FIL - Enum Class in org.jmol.c
- file - Static variable in class org.jmol.script.T
- FILE_DROPPED - Static variable in interface org.jmol.api.JmolScriptManager
- FILE_OPEN_ALREADY - Static variable in class jspecview.common.JSViewer
- FILE_OPEN_ERROR - Static variable in class jspecview.common.JSViewer
- FILE_OPEN_NO_DATA - Static variable in class jspecview.common.JSViewer
- FILE_OPEN_OK - Static variable in class jspecview.common.JSViewer
- FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- fileAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- filecachedirectory - Static variable in class org.jmol.script.T
- filecaching - Static variable in class org.jmol.script.T
- FileChooser - Class in org.jmol.dialog
-
JFileChooser with possibility to fix size and location
- FileChooser() - Constructor for class org.jmol.dialog.FileChooser
- FileDropper - Class in org.jmol.awt
-
A simple Dropping class to allow files to be dragged onto a target.
- FileDropper(JmolStatusListener, Viewer, JmolDropEditor) - Constructor for class org.jmol.awt.FileDropper
- FileDropperJmol - Class in jspecview.java
-
A simple Dropping class to allow files to be dragged onto a target.
- FileDropperJmol(PlatformViewer) - Constructor for class jspecview.java.FileDropperJmol
- fileFirstX - Variable in class jspecview.source.JDXDataObject
-
JDXReader only
- fileHelper - Variable in class jspecview.common.JSViewer
- fileLastX - Variable in class jspecview.source.JDXDataObject
-
JDXReader only
- FileManager - Class in org.jmol.viewer
- filename - Variable in class org.jmol.console.ScriptEditor
- fileName - Variable in class jspecview.common.PanelNode
- fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fileName - Variable in class org.jmol.atomdata.AtomData
- fileName - Variable in class org.jmol.export.___Exporter
- fileName - Variable in class org.jmol.jvxl.readers.Parameters
- fileNPoints - Variable in class jspecview.source.JDXDataObject
-
JDXReader only
- fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filePath - Variable in class jspecview.source.AnIMLReader
- filePath - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- FilePreview - Class in org.jmol.dialog
-
File previsualisation before opening
- FilePreview(Viewer, JFileChooser, boolean, Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview
-
Constructor
- FileReader - Class in org.jmol.io
- FileReader(Viewer, String, String, String, String, Object, Map<String, Object>, boolean) - Constructor for class org.jmol.io.FileReader
- fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filesData - Variable in class org.jmol.jvxl.readers.Parameters
- FilesReader - Class in org.jmol.io
-
open a set of models residing in different files
- FilesReader() - Constructor for class org.jmol.io.FilesReader
- FileSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- fill - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- fill - Static variable in class org.jmol.script.T
- fill() - Method in class com.jcraft.jzlib.InflaterInputStream
- fill() - Method in class javajs.export.PDFCreator
- fill3x3(String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills a double[3][3]
- fillADa(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
- fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
- fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
- fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
- fillBackground(Object, GenericColor) - Method in class jspecview.common.PDFWriter
- fillBackground(Object, GenericColor) - Method in class jspecview.java.AwtG2D
- fillBackground(Object, GenericColor) - Method in class jspecview.js2d.JsG2D
- fillBackground(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
- fillBackground(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
- fillBackground(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
- fillCircle(Object, int, int, int) - Method in class jspecview.common.PDFWriter
- fillCircle(Object, int, int, int) - Method in class jspecview.java.AwtG2D
- fillCircle(Object, int, int, int) - Method in class jspecview.js2d.JsG2D
- fillCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- fillCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
- fillCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- fillConeScreen3f(byte, int, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.export.Export3D
- fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._PovrayExporter
- fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._TachyonExporter
- fillCylinder(byte, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.export.Export3D
- fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
- fillCylinder(JmolRendererInterface, short, short, byte, int, int, int, int, int, int, int, boolean) - Static method in class org.jmol.render.FontLineShapeRenderer
- fillCylinderBits(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
- fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- fillCylinderBits2(short, short, byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.export.Export3D
- fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.Export3D
- fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.g3d.Graphics3D
- fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
- fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
- fillDataBlockFixed(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format.
- fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in interface org.jmol.api.JmolRendererInterface
- fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.export.Export3D
- fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.Graphics3D
- fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills a float array with string data from a file
- fillFloatArrays(V3[], float[]) - Method in interface javajs.api.EigenInterface
- fillFloatArrays(V3[], float[]) - Method in class javajs.util.Eigen
-
Specifically for 3x3 systems, returns eigenVectors as V3[3] and values as float[3]; sorted from smallest to largest value.
- fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int, String[][]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Extracts a block of frequency data from a file.
- fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
- fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
- fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
- fillParams(V3, V3, V3, float[]) - Static method in class org.jmol.util.SimpleUnitCell
- fillPolygon(Object, int[], int[], int) - Method in class jspecview.common.PDFWriter
- fillPolygon(Object, int[], int[], int) - Method in class jspecview.java.AwtG2D
- fillPolygon(Object, int[], int[], int) - Method in class jspecview.js2d.JsG2D
- fillPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
- fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
- fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
- fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
- fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fillRect(Graphics) - Method in class jme.AtomDisplayLabel
- fillRect(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
- fillRect(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
- fillRect(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
- fillRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- fillRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- fillRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- fillSphereBits(int, P3) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphereBits(int, P3) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphereBits(int, P3) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillSphereI(int, P3i) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphereI(int, P3i) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphereI(int, P3i) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillSphereXYZ(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphereXYZ(int, int, int, int) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillTextRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
fills background rectangle for label
- fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
-
fills background rectangle for label
- fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
fills background rectangle for label
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.___Exporter
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__CartesianExporter
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export._PovrayExporter
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export._TachyonExporter
- fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.export.Export3D
- fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.g3d.Graphics3D
- fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.export.Export3D
- fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangle3f(P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
- fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.export.Export3D
- fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangles - Variable in class org.jmol.shape.Mesh
- fillTriangleTwoSided(short, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.export.Export3D
- fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filter - Static variable in class org.jmol.script.T
- FILTER_LAST - Static variable in class javajs.img.PngEncoder
- FILTER_NONE - Static variable in class javajs.img.PngEncoder
-
Constants for filters
- FILTER_SUB - Static variable in class javajs.img.PngEncoder
- FILTER_UP - Static variable in class javajs.img.PngEncoder
- filterAllHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterCased - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterCIFAtom(Atom, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
- filteredPrecision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
check line for filter options
- filterPDBAtom(Atom, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalize() - Method in class com.sparshui.server.GestureServer
- finalize() - Method in class org.jmol.viewer.Viewer
- finalizeAromatic(Lst<BS>) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
- finalizeAtoms(BS, boolean) - Method in class org.jmol.viewer.ShapeManager
- finalizeHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
- finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
- finalizeMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeModelSet() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
- finalizeModelSet() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeModulation() - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.
- finalizeModulation() - Method in interface org.jmol.adapter.smarter.MSInterface
- finalizeObject(int, int, float, int, boolean, Object, int, BS) - Method in class org.jmol.scriptext.ScriptExt
- finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
- finalizeOutput() - Method in class org.jmol.export.___Exporter
- finalizeOutput() - Method in class org.jmol.export._IdtfExporter
- finalizeOutput() - Method in class org.jmol.export._ObjExporter
- finalizeOutput() - Method in class org.jmol.export._PovrayExporter
- finalizeOutput() - Method in class org.jmol.export._StlExporter
- finalizeOutput() - Method in class org.jmol.export.Export3D
- finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
- finalizeOutput2() - Method in class org.jmol.export.___Exporter
- finalizeOutput2() - Method in class org.jmol.export._PovrayExporter
- finalizeOutput2() - Method in class org.jmol.export._TachyonExporter
- finalizeReader() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
PRIOR to symmetry application, process all internal symop/translation aspects.
- finalizeReaderASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeReaderMR() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- finalizeReaderPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- finalizeRingData() - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
- finalizeRna3d(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
- finalizeStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
- finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.BCIFReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.CifReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.P2nReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.InputReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
-
Fix connections to Fragments and Nicknames, adjust stereochemistry for wavy displays, flag invalid atoms, and adjust the scale to something more molecular.
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
Set final auxiliary info and symmetry, including "fileHeader", "magresUnits", and "interactionTensors"; note that print getProperty("auxiliaryInfo.models[1].magresUnits") should return a catalog of tensor types.
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
optional reader-specific method run first.
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Symmetry has been applied.
- finalizeTrajectoryAs(Lst<P3[]>, Lst<V3[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
- finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
- finalizeValidations(Viewer, Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
-
Create property_xxxx for each validation category.
- find - Static variable in class org.jmol.script.T
- find() - Method in class org.jmol.util.PatternMatcher.JSPattern
- find(double) - Method in class jspecview.common.MeasurementData
- find(String, int) - Method in class org.jmol.util.CommandHistory
- find(String, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- find(String, String, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Searches for all matches of a pattern within a SMILES string.
- find(Lst<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
- findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
- findAtomsInRectangle(Rectangle) - Method in class org.jmol.modelset.ModelSet
- findAtomsLike(String) - Method in class org.jmol.modelset.Atom
- findAtomsLike(String) - Method in class org.jmol.smiles.SmilesAtom
- findAtomsLike(String) - Method in interface org.jmol.util.Node
- findAxis(P3[], int, P3, V3, V3) - Static method in class javajs.util.Measure
- findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Have the vwr show a particular frame with frequencies if it can be found.
- findLineSeparator(String) - Static method in class jme.JMEUtil
- findMatchingPeakInfo(PeakInfo) - Method in class jspecview.common.PanelData
- findMatchingPeakInfo(PeakInfo) - Method in class jspecview.common.Spectrum
- findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
- findMonomer(BS, boolean) - Method in class org.jmol.modelsetbio.ProteinStructure
- findNearest2(int, int, Atom[], BS, int) - Method in class org.jmol.modelset.AtomCollection
- findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
- findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
- findNearestAtomIndex(int, int, BS, int) - Method in class org.jmol.modelset.ModelSet
- findNearestAtomIndex(int, int, Atom[], short[], int, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
- findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shape.Shape
- findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShape
- findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShapeCollection
- findNearestAtomIndexMovable(int, int, boolean) - Method in class org.jmol.viewer.Viewer
- findNearestShapeAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.viewer.ShapeManager
- findNode(String, int, P3) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Called from TLink and TAtom to find a node with the given symmetry.
- findNode(JSVPanel, Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
-
Returns the tree node that is associated with a panel
- findNodeById(String, Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
- findPeakByCoord(int, Coordinate) - Method in class jspecview.common.Spectrum
- findSeparator(String) - Static method in class jme.JMEmol
- findSourceByNameOrId(String, Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
- findSpaceGroup(SymmetryInterface, BS, String, float[], T3, T3[], int) - Method in class org.jmol.viewer.Viewer
- findSpaceGroup(Viewer, BS, String, float[], T3, T3[], int) - Method in interface org.jmol.api.SymmetryInterface
- findSpaceGroup(Viewer, BS, String, float[], T3, T3[], int) - Method in class org.jmol.symmetry.Symmetry
- findSpaceGroupFromXYZ(String) - Static method in class org.jmol.symmetry.SpaceGroup
- findX(Spectrum, double) - Method in class jspecview.common.PanelData
- FINDX - Enum constant in enum class jspecview.common.ScriptToken
- findXForPeakNearest(double) - Method in class jspecview.common.Spectrum
- findXForPeakNearest(Coordinate[], double, boolean) - Static method in class jspecview.common.Coordinate
- finish() - Method in class com.jcraft.jzlib.Deflater
- finish() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- finish(Object) - Method in class org.jmol.api.JmolAdapter
- FINISH - Static variable in class org.jmol.thread.JmolThread
- finished() - Method in class com.jcraft.jzlib.Deflater
- finished() - Method in class com.jcraft.jzlib.Inflater
- first - Variable in class org.jmol.modelset.TickInfo
- first - Static variable in class org.jmol.script.T
- firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
- firstAtomIndex - Variable in class org.jmol.modelset.Group
- firstAtomIndex - Variable in class org.jmol.modelset.Model
- firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
- firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
- firstAtomToBond - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- firstChar - Variable in class org.jmol.adapter.readers.cif.CifReader
- firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
- firstIsotope - Static variable in class org.jmol.util.Elements
-
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
- firstModelIndex - Variable in class org.jmol.atomdata.AtomData
- firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- firstX - Variable in class jspecview.export.AMLExporter
- firstX - Variable in class jspecview.export.CMLExporter
- firstX - Variable in class jspecview.source.AnIMLReader
- firstY - Variable in class jspecview.source.AnIMLReader
- FIX - Enum constant in enum class jspecview.common.ExportType
- fix2Stereo() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- fixAtoms(int, SV, BS, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
- fixAtoms(int, SV, BS, int, int) - Method in class org.jmol.dssx.AnnotationParser
-
Adjusts _atoms bitset to account for added hydrogen atoms.
- fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
- fixD(float, boolean) - Method in class org.jmol.modelset.BondCollection
- fixDataString(String) - Static method in class org.jmol.util.Parser
- fixDOSName(String) - Static method in class org.jmol.adapter.smarter.Resolver
- fixDOSName(String) - Static method in class org.jmol.viewer.FileManager
-
Switch \ for / only for DOS names such as C:\temp\t.xyz, not names like http://cactus.nci.nih.gov/chemical/structure/CC/C=C\CC
- fixDouble(double, double) - Static method in class javajs.util.PT
- fixDoubleA(double[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fixDSSRJSONMap(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
- fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
- fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
-
kissingLoops and coaxStacks use index arrays instead of duplication;
- fixed - Static variable in class org.jmol.script.T
- fixedLattice - Variable in class org.jmol.jvxl.data.JvxlData
- fixedOrigin - Variable in class org.jmol.shape.Axes
- fixedOriginUC - Variable in class org.jmol.shape.Axes
- fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
- fixedRotationCenter - Variable in class org.jmol.export.___Exporter
- fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
- fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
- fixedtemp - Static variable in class org.jmol.script.T
- FIXEDTEMP - Enum constant in enum class org.jmol.c.PAL
- fixedTranslation - Variable in class org.jmol.viewer.TransformManager
- fixedValue - Variable in class org.jmol.modelset.Measurement
- fixedValue - Variable in class org.jmol.modelset.MeasurementData
- fixFloat(float, double) - Static method in class javajs.util.PT
- fixFloatA(float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fixFloatPt(P3, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fixFormalCharges(BS) - Method in class org.jmol.modelset.AtomCollection
- fixIndices(int, int, BS) - Method in class org.jmol.modelset.Model
- fixIndices(int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
- fixIndices(int, BS) - Method in class org.jmol.modelset.Group
- fixIndicesM(int, int, BS) - Method in class org.jmol.modelset.Model
- fixInlineString(String, char) - Static method in class org.jmol.viewer.Viewer
- fixJMEFormalCharges(BS, String) - Method in interface org.jmol.api.JmolPropertyManager
- fixJMEFormalCharges(BS, String) - Method in class org.jmol.viewer.PropertyManager
-
Fix a JME string returned from NCI CIR to have the proper formal charges.
- fixKey(String) - Method in interface javajs.api.GenericCifDataParser
- fixKey(String) - Method in class javajs.util.CifDataParser
- fixPropertyValue(BS, Object, boolean) - Method in class org.jmol.modelsetbio.BioResolver
- fixPtFloats(T3, float) - Static method in class javajs.util.PT
- fixRadius(float) - Static method in class org.jmol.adapter.readers.pdb.PdbReader
- fixScreenZ(int) - Method in class org.jmol.export.___Exporter
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- fixTextImageRGB(int) - Static method in class org.jmol.g3d.Graphics3D
- fixTitle(String) - Static method in class jspecview.dialog.DialogManager
- fixUnitCell(float[]) - Method in interface org.jmol.api.SymmetryInterface
- fixUnitCell(float[]) - Method in class org.jmol.symmetry.Symmetry
- fixUnits(String) - Static method in class org.jmol.modelset.Measurement
- fixUTF(byte[]) - Static method in class javajs.util.Rdr
- fixUTF(byte[]) - Static method in class jspecview.common.JSVFileManager
- fixValue(String, boolean) - Method in class org.jmol.modelset.Measurement
- fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- flat - Static variable in class org.jmol.script.T
- FLICK_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- FLICK_EVENT - Static variable in class com.sparshui.GestureType
- FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- FLICK_GESTURE - Static variable in class com.sparshui.GestureType
- FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- FlickEvent - Class in com.sparshui.common.messages.events
- FlickEvent() - Constructor for class com.sparshui.common.messages.events.FlickEvent
- FlickEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.FlickEvent
-
Constructs a flickEvent from a complete serialized version of the drag event.
- FlickEvent(float, float) - Constructor for class com.sparshui.common.messages.events.FlickEvent
- FlickEvent(int, int, int) - Constructor for class com.sparshui.common.messages.events.FlickEvent
- flistValue(T, int) - Static method in class org.jmol.script.SV
- FLOAT_MIN_SAFE - Static variable in class org.jmol.viewer.JC
- floatifyJavaDouble - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- floatparam - Static variable in class org.jmol.script.T
- floatParameter(int) - Method in class org.jmol.script.ScriptParam
- floatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- floatParameterRange(int, float, float) - Method in class org.jmol.script.ScriptParam
- floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptParam
-
process a general string or set of parameters as an array of floats, allowing for relatively free form input
- floatproperty - Static variable in class org.jmol.script.T
- floatToByteArray(byte[], int, float) - Static method in class com.sparshui.common.utils.Converter
- floatToIntBits(float) - Static method in class javajs.util.T3
- flowCommand - Static variable in class org.jmol.script.T
- FlowLayout - Class in org.jmol.awtjs.swing
- FlowLayout() - Constructor for class org.jmol.awtjs.swing.FlowLayout
- flush() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- flushBytes() - Method in class javajs.img.GifEncoder
- flushImage(Object) - Method in class jspecview.java.AwtPlatform
- flushImage(Object) - Method in class jspecview.js2d.JsPlatform
- flushImage(Object) - Method in interface org.jmol.api.GenericPlatform
- flushImage(Object) - Method in class org.jmol.awt.Platform
- flushImage(Object) - Method in class org.jmol.awtjs2d.Platform
- fm - Variable in class org.jmol.adapter.readers.spartan.SpartanUtil
- fm - Variable in class org.jmol.viewer.Viewer
- fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- foccupancy - Variable in class org.jmol.adapter.smarter.Atom
- focusGained(FocusEvent) - Method in class jspecview.java.AwtDialogManager
- focusLost(FocusEvent) - Method in class jspecview.java.AwtDialogManager
- FoldingXyzReader - Class in org.jmol.adapter.readers.simple
-
This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
- FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
- font - Variable in class jspecview.common.PrintLayout
-
The font of the elements
- font - Variable in class org.jmol.modelset.Text
- font - Static variable in class org.jmol.script.T
- font - Variable in class org.jmol.util.Font
- Font - Class in org.jmol.util
-
Provides font support using a int fid (Font ID) as an index into font table.
- FONT - Static variable in class org.jmol.shapecgo.CGOMesh
- FONT_AXES - Static variable in class org.jmol.shapecgo.CGOMesh
- FONT_FACE_MONO - Static variable in class org.jmol.util.Font
- FONT_FACE_SANS - Static variable in class org.jmol.util.Font
- FONT_FACE_SERIF - Static variable in class org.jmol.util.Font
- FONT_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
- FONT_STYLE_BOLD - Static variable in class org.jmol.util.Font
- FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.util.Font
- FONT_STYLE_ITALIC - Static variable in class org.jmol.util.Font
- FONT_STYLE_PLAIN - Static variable in class org.jmol.util.Font
- FONT_VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
- font3d - Variable in class org.jmol.render.FontLineShapeRenderer
- font3d - Variable in class org.jmol.shape.FontLineShape
- font3d - Variable in class org.jmol.shape.Frank
- font3d - Variable in class org.jmol.shape.Measures
- fontcaching - Static variable in class org.jmol.script.T
- fontChild - Variable in class org.jmol.export._VrmlExporter
- fontFace - Variable in class org.jmol.export._VrmlExporter
- fontFace - Variable in class org.jmol.util.Font
- fontID - Variable in class org.jmol.shapespecial.DrawMesh
- FontLineShape - Class in org.jmol.shape
- FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
- FontLineShapeRenderer - Class in org.jmol.render
- FontLineShapeRenderer() - Constructor for class org.jmol.render.FontLineShapeRenderer
- FontManager - Interface in org.jmol.api
-
A generic interface for font queries.
- fontScale - Variable in class org.jmol.modelset.Text
- fontscaling - Static variable in class org.jmol.script.T
- fontsize - Static variable in class org.jmol.script.T
- fontSize - Variable in class org.jmol.export._VrmlExporter
- fontSize - Variable in class org.jmol.util.Font
- fontSizeNominal - Variable in class org.jmol.util.Font
- fontStringWidth(Font, String) - Method in class jspecview.java.AwtPlatform
- fontStringWidth(Font, String) - Method in class jspecview.js2d.JsPlatform
- fontStringWidth(Font, String) - Method in interface org.jmol.api.FontManager
- fontStringWidth(Font, String) - Method in class org.jmol.awt.Platform
- fontStringWidth(Font, String) - Method in class org.jmol.awtjs2d.Platform
- fontStyle - Variable in class org.jmol.export._VrmlExporter
- fontStyle - Variable in class org.jmol.util.Font
- force - Variable in class org.jmol.minimize.MinAtom
- forceAsyncLoad(String) - Method in class jspecview.java.AwtPlatform
- forceAsyncLoad(String) - Method in class jspecview.js2d.JsPlatform
- forceAsyncLoad(String) - Method in interface org.jmol.api.GenericPlatform
- forceAsyncLoad(String) - Method in class org.jmol.awt.Platform
- forceAsyncLoad(String) - Method in class org.jmol.awtjs2d.Platform
- forceautobond - Static variable in class org.jmol.script.T
- forcefield - Static variable in class org.jmol.script.T
- ForceField - Class in org.jmol.minimize.forcefield
- ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
- ForceFieldMMFF - Class in org.jmol.minimize.forcefield
-
MMFF94 implementation 5/14/2012 - fully validated for atom types and charges - reasonably well validated for energies (see below) - TODO: add UFF for preliminary/backup calculation
- ForceFieldMMFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldMMFF
- ForceFieldReader - Class in org.jmol.adapter.readers.more
- ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
- ForceFieldUFF - Class in org.jmol.minimize.forcefield
- ForceFieldUFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
- forceMOPAC - Variable in class org.jmol.adapter.readers.quantum.MOReader
- forcePacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- forceShowTriangles - Variable in class org.jmol.render.MeshRenderer
- forceSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- forcmd - Static variable in class org.jmol.script.T
- FORMAL_CHARGE - Enum constant in enum class org.jmol.c.PAL
- FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
- FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
- FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
-
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber invalid input: '<'invalid input: '<' 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
- formalcharge - Static variable in class org.jmol.script.T
- formalCharge - Variable in class org.jmol.adapter.smarter.Atom
- format - Static variable in class org.jmol.script.T
- format(SV[], int) - Static method in class org.jmol.script.SV
-
Accepts arguments from the format() function First argument is a format string.
- formatCheck(String) - Static method in class javajs.util.PT
-
formatCheck checks p and q formats and duplicates if necessary "%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
- formatD(double, int, int, boolean, boolean) - Static method in class javajs.util.PT
- formatDecimal(double, int) - Static method in class javajs.util.DF
-
a simple alternative to DecimalFormat (which Java2Script does not have and which is quite too complex for our use here.)
- formatDecimalDbl(double, int) - Static method in class javajs.util.DF
- formatDecimalTrimmed(double, int) - Static method in class javajs.util.DF
-
an alternative to DecimalFormat "0.#"
- formatDecimalTrimmed0(double, int) - Static method in class javajs.util.DF
-
an alternative to DecimalFormat "0.0"
- formatDistance(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatExpNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatF(float, int, int, boolean, boolean) - Static method in class javajs.util.PT
- formatJ(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatLabel(Viewer, Atom, String, P3) - Method in class org.jmol.modelset.LabelToken
- formatLabelAtomArray(Viewer, Atom, LabelToken[], char, int[], P3) - Static method in class org.jmol.modelset.LabelToken
-
returns a formatted string based on the precompiled label tokens
- formatLabelBond(Viewer, Bond, LabelToken[], Map<String, Object>, int[], P3) - Static method in class org.jmol.modelset.LabelToken
- formatLabelMeasure(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
- formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
- formatMeasurementAs(String, String, boolean) - Method in class org.jmol.modelset.Measurement
- formatNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formats - Variable in class org.jmol.shape.Labels
- formatS(String, int, int, boolean, boolean) - Static method in class javajs.util.PT
- formatStringF(String, String, float) - Static method in class javajs.util.PT
- formatStringI(String, String, int) - Static method in class javajs.util.PT
- formatStringS(String, String, String) - Static method in class javajs.util.PT
- formatText(String) - Method in class org.jmol.viewer.Viewer
- forThermalEllipsoid - Variable in class org.jmol.util.Tensor
- foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
- foundDistance2() - Method in class org.jmol.bspt.CubeIterator
-
After calling nextElement(), allows one to find out the value of the distance squared.
- foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- foundDistance2() - Method in class org.jmol.symmetry.UnitCellIterator
- fourdots - Static variable in class org.jmol.render.FontLineShapeRenderer
- fps - Static variable in class org.jmol.script.T
- FRACTIONAL_PRECISION - Static variable in class javajs.util.PT
- fractionalizeCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fractionalPoint - Variable in class org.jmol.script.ScriptParam
-
set in getPointOrPlane
- fractionalrelative - Static variable in class org.jmol.script.T
- fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- fracx - Static variable in class org.jmol.script.T
- fracxyz - Static variable in class org.jmol.script.T
- fracy - Static variable in class org.jmol.script.T
- fracz - Static variable in class org.jmol.script.T
- frame - Static variable in class org.jmol.script.T
- frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- frameCounter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- FrameCounter - Class in org.openscience.jmol.app.janocchio
- FrameCounter(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameCounter
-
Constructor
- frameDelay - Variable in class org.jmol.modelset.Model
- frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- FrameDeltaDisplay - Class in org.openscience.jmol.app.janocchio
- FrameDeltaDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
-
Constructor
- frameTitle - Variable in class jspecview.common.PanelNode
- frameTitles - Variable in class org.jmol.modelset.ModelSet
- frank - Static variable in class org.jmol.script.T
- Frank - Class in org.jmol.shape
- Frank() - Constructor for class org.jmol.shape.Frank
- frankAscent - Variable in class org.jmol.shape.Frank
- frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
- frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
- frankDescent - Variable in class org.jmol.shape.Frank
- frankMargin - Static variable in class org.jmol.shape.Frank
- frankOn - Variable in class org.jmol.viewer.Viewer
- frankPopup - Variable in class org.jmol.popup.JmolGenericPopup
- FrankRenderer - Class in org.jmol.render
- FrankRenderer() - Constructor for class org.jmol.render.FrankRenderer
- frankString - Variable in class org.jmol.shape.Frank
- frankWidth - Variable in class org.jmol.shape.Frank
- freeBonds - Variable in class org.jmol.modelset.BondCollection
- freeTempEnum(STR[]) - Method in class org.jmol.util.TempArray
- freeTempEnum(STR[]) - Method in class org.jmol.viewer.Viewer
- freeTempPoints(P3[]) - Method in class org.jmol.util.TempArray
- freeTempPoints(P3[]) - Method in class org.jmol.viewer.Viewer
- freeTempScreens(P3i[]) - Method in class org.jmol.util.TempArray
- freeTempScreens(P3i[]) - Method in class org.jmol.viewer.Viewer
- freeze() - Method in class org.jmol.modelset.Model
- freeze() - Method in class org.jmol.modelsetbio.BioModel
- freezeM() - Method in class org.jmol.modelset.Model
- freq2dX - Variable in class jspecview.source.JDXDataObject
- freq2dY - Variable in class jspecview.source.JDXDataObject
- fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
- FRIENDLY - Static variable in class org.jmol.util.ColorEncoder
- from - Static variable in class org.jmol.script.T
- from3D() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- fromASC(AtomSetCollection) - Static method in class org.jmol.adapter.writers.CDXMLWriter
- fromCDX(GenericBinaryDocument) - Static method in class org.jmol.adapter.writers.CDXMLWriter
- fromOABC(T3[], boolean) - Static method in class org.jmol.symmetry.UnitCell
-
A special constructor for spacially defined unit cells.
- fromParams(float[], boolean, float) - Static method in class org.jmol.symmetry.UnitCell
- fromString(Viewer, String, String) - Static method in class org.jmol.adapter.writers.CDXMLWriter
- fromUnits(float, String) - Static method in class org.jmol.modelset.Measurement
- front - Static variable in class org.jmol.script.T
- frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- frontedges - Static variable in class org.jmol.script.T
- frontlit - Static variable in class org.jmol.script.T
- frontonly - Static variable in class org.jmol.script.T
- frontOnly - Variable in class org.jmol.render.MeshRenderer
- frontOnly - Variable in class org.jmol.shape.Mesh
- FS - Static variable in class org.jmol.quantum.QS
- fScrPt - Variable in class org.jmol.viewer.TransformManager
- fslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- full - Static variable in class org.jmol.script.T
- fullAtomWidthLabel - Variable in class jme.AtomDisplayLabel
- fullCommand - Variable in class org.jmol.script.ScriptEval
- fullCubeCorners - Static variable in class org.jmol.util.Triangulator
-
For each corner 0-7: {c c c t} where c c c are the connected corners, arranged clockwise and t is the bitset of triangles associated with faces intersecting at this corner.
- fullCubePolygon - Static variable in class org.jmol.util.Triangulator
- fullName - Variable in class jspecview.common.JSViewer
- fullName - Variable in class org.jmol.util.GenericApplet
- fullName - Variable in class org.jmol.viewer.Viewer
- fullplane - Static variable in class org.jmol.script.T
- fullTrim(Object) - Static method in class org.jmol.adapter.readers.cif.CifReader
- fullTrim(String) - Method in interface javajs.api.GenericCifDataParser
- fullTrim(String) - Method in class javajs.util.CifDataParser
-
Used especially for data that might be multi-line data that might have unwanted white space at start or end.
- fullylit - Static variable in class org.jmol.script.T
- fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
- func - Variable in class org.jmol.jvxl.readers.Parameters
- function - Static variable in class org.jmol.script.T
- functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
- functionName - Variable in class org.jmol.script.ScriptContext
- functionName - Variable in class org.jmol.script.ScriptEval
- functionxy - Static variable in class org.jmol.script.T
- functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
-
for isosurface FUNCTIONXY
- functionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
- functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
-
fills an array with data -- if nX invalid input: '<' 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
- functionXY(String, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
this is just a test method for isosurface FUNCTIONXY
- functionxyz - Static variable in class org.jmol.script.T
- functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
-
for isosurface FUNCTIONXYZ
- functionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
- functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
- functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- fux - Static variable in class org.jmol.script.T
- fuxyz - Static variable in class org.jmol.script.T
- fuy - Static variable in class org.jmol.script.T
- fuz - Static variable in class org.jmol.script.T
- fVal(String) - Static method in class javajs.util.PT
- fValue(T) - Static method in class org.jmol.script.SV
G
- g - Variable in class org.jmol.util.Rgb16
- g - Variable in class org.jmol.viewer.Viewer
- g(String) - Method in class javajs.export.PDFCreator
- G_SIZE - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- g2d - Variable in class jspecview.common.JSViewer
- g2d - Variable in class jspecview.common.PanelData
- g2d0 - Variable in class jspecview.common.PanelData
- g3d - Variable in class org.jmol.modelset.AtomCollection
- g3d - Variable in class org.jmol.render.ShapeRenderer
-
could be vwr.gdata or an exporter
- G3DRenderer - Interface in org.jmol.g3d
- GamessReader - Class in org.jmol.adapter.readers.quantum
- GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
- GamessUKReader - Class in org.jmol.adapter.readers.quantum
- GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
- GamessUSReader - Class in org.jmol.adapter.readers.quantum
- GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
- gamma - Variable in class org.jmol.util.SimpleUnitCell
- gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
- gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
- gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
- GaussianDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
- GaussianFchkReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
- GaussianFchkReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianFchkReader
- gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
- GaussianReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian 94/98/03/09 output files.
- GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
- gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
- gaussians - Variable in class org.jmol.quantum.MOCalculation
- GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian Wfn files -- not implemented yet
- GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
- GC - Static variable in class org.jmol.quantum.QS
- gdata - Variable in class org.jmol.export.___Exporter
- gdata - Variable in class org.jmol.viewer.Viewer
- GData - Class in org.jmol.util
- GData() - Constructor for class org.jmol.util.GData
-
It is possible to instantiate this class with no Graphics3D.
- generate() - Method in class javajs.img.GifEncoder
- generate() - Method in class javajs.img.ImageEncoder
- generate() - Method in class javajs.img.Jpg64Encoder
- generate() - Method in class javajs.img.JpgEncoder
- generate() - Method in class javajs.img.PdfEncoder
- generate() - Method in class javajs.img.PngEncoder
- generate() - Method in class javajs.img.PpmEncoder
- generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- generateCrystalClass(int, P3) - Method in class org.jmol.modelset.AtomCollection
- generateCrystalClass(P3) - Method in interface org.jmol.api.SymmetryInterface
- generateCrystalClass(P3) - Method in class org.jmol.symmetry.Symmetry
- generateOutputForExport(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
-
for POV-Ray
- generateOutputForExport(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- generatePrimes(int) - Static method in class jme.JMEUtil
- generateScene(Map<String, Object>) - Method in interface org.jmol.api.JmolSceneGenerator
- GenericApplet - Class in org.jmol.util
-
A collection of all methods necessary for initialization of and communication with the applet.
- GenericApplet() - Constructor for class org.jmol.util.GenericApplet
- GenericBinaryDocument - Interface in javajs.api
- GenericBinaryDocumentReader - Interface in javajs.api
- GenericCifDataParser - Interface in javajs.api
- GenericColor - Interface in javajs.api
-
GenericColor allows both java.awt.Color and org.jmol.awtjs.swing.Color to be handled by methods that need not distinguish between them.
- GenericConsole - Class in org.jmol.console
- GenericConsole() - Constructor for class org.jmol.console.GenericConsole
- GenericConsoleTextArea - Interface in org.jmol.api.js
- GenericFileInterface - Interface in org.jmol.api
- GenericGraphics - Interface in org.jmol.api
- GenericImageDialog - Interface in org.jmol.api
- GenericImageEncoder - Interface in javajs.api
- GenericLineReader - Interface in javajs.api
- GenericMenuInterface - Interface in org.jmol.api
- GenericMouse - Class in jspecview.app
- GenericMouse(JSVPanel) - Constructor for class jspecview.app.GenericMouse
- GenericMouseInterface - Interface in org.jmol.api
- GenericOutputChannel - Interface in javajs.api
- GenericPlatform - Interface in org.jmol.api
- GenericPopup - Class in org.jmol.popup
-
The overall parent of all popup classes in Jmol and JSmol.
- GenericPopup() - Constructor for class org.jmol.popup.GenericPopup
- GenericTextArea - Interface in org.jmol.console
- GenericZipInputStream - Class in javajs.api
- GenericZipInputStream(InputStream) - Constructor for class javajs.api.GenericZipInputStream
- GenericZipTools - Interface in javajs.api
-
Class abandoned as unnecessary in SwingJS
- GenNBOReader - Class in org.jmol.adapter.readers.quantum
-
NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure
- GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
- Geodesic - Class in org.jmol.util
-
J2SRequireImport is needed because we use ArrayUtil in a static method
- Geodesic() - Constructor for class org.jmol.util.Geodesic
- geosurface - Static variable in class org.jmol.script.T
- GeoSurface - Class in org.jmol.shapespecial
- GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
- GeoSurfaceRenderer - Class in org.jmol.renderspecial
- GeoSurfaceRenderer() - Constructor for class org.jmol.renderspecial.GeoSurfaceRenderer
- Gesture - Interface in com.sparshui.gestures
-
Defines the interface that all user-defined gestures must implement.
- GestureServer - Class in com.sparshui.server
-
The main gesture server class.
- GestureServer() - Constructor for class com.sparshui.server.GestureServer
- GestureServer(int, GestureServer) - Constructor for class com.sparshui.server.GestureServer
- gestureswipefactor - Static variable in class org.jmol.script.T
- GestureType - Class in com.sparshui
-
This class is a place for the enum GestureType to stand.
- GestureType(int) - Constructor for class com.sparshui.GestureType
- GestureType(String) - Constructor for class com.sparshui.GestureType
- get(int) - Method in class javajs.util.BS
-
Returns the value of the bit with the specified index.
- get(int) - Method in class org.jmol.util.Int2IntHash
- get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- GET_ALLOWED_GESTURES - Static variable in class com.sparshui.common.ClientProtocol.MessageType
- GET_GROUP_ID - Static variable in class com.sparshui.common.ClientProtocol.MessageType
- get1(int) - Static method in class org.jmol.awtjs.swing.Color
- get2SidedNormix(V3, BS) - Static method in class org.jmol.util.Normix
- get3(int, int, int) - Method in class jspecview.java.AwtColor
- get3(int, int, int) - Method in class org.jmol.awt.AwtColor
- get3(int, int, int) - Static method in class org.jmol.awtjs.swing.Color
- get33(int, int) - Method in class javajs.util.M34
- get3dProjection(V3) - Method in class javajs.util.Quat
- get4(int, int, int, int) - Method in class jspecview.java.AwtColor
- get4(int, int, int, int) - Method in class org.jmol.awt.AwtColor
- get4(int, int, int, int) - Static method in class org.jmol.awtjs.swing.Color
- getAbbrSimulationFileName(String) - Static method in class jspecview.common.JSVFileManager
-
In the case of applet-based simulations with file names that involve mol=..., we want to abbreviate those names for display
- getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Fetch the action that was created for the given command.
- getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- getActionCommand() - Method in interface org.jmol.api.SC
- getActionCommand() - Method in class org.jmol.awt.AwtSwingComponent
- getActionCommand() - Method in class org.jmol.awtjs.swing.JComponent
- getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
- getActionName(int) - Static method in class org.jmol.viewer.ActionManager
- getActiveMenu() - Method in class org.jmol.modelkit.ModelKit
-
for the thin box on the top left of the window
- getAdditionalHydrogens(BS, Lst<Atom>, int) - Method in class org.jmol.viewer.Viewer
- getAdditionalOperations() - Method in interface org.jmol.api.SymmetryInterface
- getAdditionalOperations() - Method in class org.jmol.symmetry.Symmetry
- getAdditionalOperations(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
- getAdditionalOperationsCount() - Method in interface org.jmol.api.SymmetryInterface
- getAdditionalOperationsCount() - Method in class org.jmol.symmetry.Symmetry
- getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
- getAlignment(int) - Static method in class org.jmol.viewer.JC
- getAllAtomInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getAllAtoms() - Method in class org.jmol.viewer.Viewer
- getAllAtomTensors(String) - Method in class org.jmol.modelset.AtomCollection
- getAllBondInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getAllChainInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getAllChimeInfo(SB) - Method in class org.jmol.viewer.ChimeMessenger
- getAllChimeInfo(SB) - Method in interface org.jmol.viewer.JmolChimeMessenger
- getAllCifData() - Method in interface javajs.api.GenericCifDataParser
- getAllCifData() - Method in class javajs.util.CifDataParser
-
Parses all CIF data for a reader defined in the constructor into a standard Map structure and close the BufferedReader if it exists.
- getAllCifDataType(String...) - Method in class javajs.util.CifDataParser
- getAllData() - Method in class javajs.util.CompoundDocument
- getAllDataFiles(String, String) - Method in interface javajs.api.GenericBinaryDocument
- getAllDataFiles(String, String) - Method in class javajs.util.BinaryDocument
- getAllDataFiles(String, String) - Method in class javajs.util.CompoundDocument
- getAllDataMapped(String, String, Map<String, String>) - Method in interface javajs.api.GenericBinaryDocument
- getAllDataMapped(String, String, Map<String, String>) - Method in class javajs.util.BinaryDocument
- getAllDataMapped(String, String, Map<String, String>) - Method in class javajs.util.CompoundDocument
-
reads a compound document directory and saves all data in a Hashtable so that the files may be organized later in a different order.
- getAllDefaultStructures(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAlleneAtoms(boolean, SmilesAtom, SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
- getAllHeteroList(int) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllOperators() - Method in class org.jmol.modelkit.ModelKit
- getAllowedGestures(int) - Method in interface com.sparshui.client.SparshClient
-
This method must return the allowed Gestures for the specified group.
- getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
- getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
- getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- getAllowJSThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
- getAllowJSThreads() - Method in class org.jmol.script.ScriptEval
- getAllPoints(int, int) - Method in class org.jmol.scriptext.ScriptExt
- getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
- getAllSequenceBits(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllSettings(String) - Method in class org.jmol.viewer.Viewer
- getAllStructures(String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- getAllZipData(InputStream, String[], String, String, String, Map<String, String>) - Method in interface javajs.api.GenericZipTools
- getAllZipData(InputStream, String[], String, String, String, Map<String, String>) - Method in class javajs.util.ZipTools
-
Deprecated.
- getAltLoc() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
- getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelSet
- getAmbientPercent() - Method in class org.jmol.util.GData
- getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioModelSet
- getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
- getAndRegisterPlugin(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getAndSetNewVariable(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
- getAngles() - Method in class org.jmol.minimize.Minimizer
- getAnnotationInfo(SV, String, int) - Method in class org.jmol.viewer.Viewer
- getAnnotationInfo(Viewer, SV, String, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
- getAnnotationInfo(Viewer, SV, String, int, int) - Method in class org.jmol.dssx.AnnotationParser
-
Get a string report of annotation data
- getAnnotationParser(boolean) - Method in class org.jmol.viewer.Viewer
- getApiPlatform() - Method in interface jspecview.api.JSVPanel
- getApiPlatform() - Method in class jspecview.java.AwtPanel
- getApiPlatform() - Method in class jspecview.js2d.JsPanel
- getApp() - Method in interface jspecview.api.AppletFrame
- getApp() - Method in class jspecview.appletjs.JSVApplet
- getApplet() - Method in class jspecview.common.JSViewer
- getAppletFrame() - Method in class jspecview.app.JSVApp
- getAppletInfo() - Method in interface jspecview.api.AppletFrame
- getAppletInfo() - Static method in class jspecview.app.JSVApp
- getAppletInfo() - Method in class jspecview.appletjs.JSVApplet
-
Get Applet information
- getAppletInfo() - Method in class jspecview.appletjs.JSVAppletPro
- getAppletInfo() - Method in interface org.jmol.api.JmolAppletInterface
- getAppletInfo() - Method in class org.jmol.util.GenericApplet
- getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- getArgb() - Method in class org.jmol.util.Rgb16
- getArgb(float) - Method in class org.jmol.util.ColorEncoder
- getArgb(short) - Static method in class org.jmol.util.C
- getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
- getArgbFromString(String) - Static method in class javajs.util.CU
-
accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or [red,green,blue] or a valid JavaScript color
- getArgbGreyscale(short) - Static method in class org.jmol.util.C
- getArgbHbondType(int) - Static method in class org.jmol.util.Edge
- getArgbMinMax(float, float, float) - Method in class org.jmol.util.ColorEncoder
- getArgbParam(int) - Method in class org.jmol.script.ScriptParam
- getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptParam
- getArgbParamOrNone(int, boolean) - Method in class org.jmol.script.ScriptParam
- getArgbs(int) - Method in class org.jmol.modelsetbio.BioResolver
- getArray() - Method in class javajs.util.Matrix
-
Access the internal two-dimensional array.
- getArrayCopy() - Method in class javajs.util.Matrix
-
Copy the internal two-dimensional array.
- getArrayDepth(T) - Static method in class org.jmol.script.SV
- getArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
turn "[1,2,3]" into [1.0,2.0,3.0] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
- getAscent() - Method in class org.jmol.util.Font
- getAsciiFileOrNull(String) - Method in class org.jmol.viewer.Viewer
- getAssocArray(int) - Method in class org.jmol.script.ScriptEval
- getAssociatedAtoms(ModelSet) - Method in class org.jmol.modelset.BondSet
- getAssociatedPeakInfo(int, Coordinate) - Method in class jspecview.common.Spectrum
- getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getAtom(int) - Method in class org.jmol.modelset.AtomCollection
- getAtom(int) - Method in class org.jmol.modelset.Bond
- getAtom(int) - Method in class org.jmol.modelset.Measurement
- getAtom(int) - Method in class org.jmol.smiles.SmilesBond
- getAtom(int) - Method in interface org.jmol.util.SimpleEdge
-
Get the respective atom, 0 or 1
- getAtom1() - Method in class org.jmol.smiles.SmilesBond
- getAtomAt(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomBits(int, Object) - Method in class org.jmol.script.ScriptEval
- getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in interface org.jmol.api.JmolAnnotationParser
- getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.AnnotationParser
- getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.DSSR1
- getAtomBitsBS(int, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAtomBitSet(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
- getAtomBitSet(Object) - Method in class org.jmol.script.ScriptEval
-
A general method to evaluate a string representing an atom set.
- getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
- getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in interface org.jmol.api.JmolScriptManager
- getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.script.ScriptManager
- getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelSet
- getAtomBitsMDa(int, Object, BS) - Method in class org.jmol.modelset.AtomCollection
-
general unqualified lookup of atom set type
- getAtomBitsMDb(int, Object) - Method in class org.jmol.modelset.BondCollection
- getAtomBitsStr(int, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAtomCIPChiralityCode(Atom) - Method in class org.jmol.modelset.ModelSet
-
Determine the Cahn-Ingold-Prelog R/S chirality of an atom
- getAtomCount() - Method in class jme.JMEmol
- getAtomCount() - Method in class org.jmol.modelset.ModelLoader
- getAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomCount(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomCount(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the number of atoms contained in the file.
- getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getAtomData(String, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getAtomData(String, String, boolean) - Method in class org.jmol.viewer.PropertyManager
-
use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.
- getAtomDefs(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- getAtomFromName(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- getAtomFromName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
- getAtomGroupQuaternions(BS, int) - Method in class org.jmol.viewer.Viewer
- getAtomGroupQuaternions(BS, int, char) - Method in class org.jmol.modelset.ModelSet
- getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
- getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
- getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.Node
- getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
- getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
- getAtomicDSSRData(float[], String) - Method in class org.jmol.modelsetbio.BioModel
- getAtomicDSSRData(int) - Method in class org.jmol.modelset.ModelSet
- getAtomicDSSRData(ModelSet, int, float[], String) - Method in interface org.jmol.api.JmolAnnotationParser
- getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.AnnotationParser
- getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.DSSR1
- getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atomic mass of the atom.
- getAtomicMass(int) - Static method in class org.jmol.util.Elements
- getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
- getAtomIdentityInfo(int, Map<String, Object>, P3) - Method in class org.jmol.modelset.AtomCollection
- getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
- getAtomIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomIndex(String, int) - Method in class org.jmol.modelset.Group
- getAtomIndex(String, int) - Method in class org.jmol.modelsetbio.Monomer
- getAtomIndex1() - Method in class org.jmol.modelset.Bond
- getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
- getAtomIndex1() - Method in class org.jmol.util.Edge
- getAtomIndex2() - Method in class org.jmol.modelset.Bond
- getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
- getAtomIndex2() - Method in class org.jmol.util.Edge
- getAtomIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
- getAtomIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getAtomIndices(BS) - Method in class org.jmol.modelset.AtomCollection
- getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
- getAtomInfo(int, String, P3) - Method in class org.jmol.modelset.AtomCollection
- getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get an AtomIterator for retrieval of all atoms in the file.
- getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
- getAtomName() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAtomName() - Method in class org.jmol.modelset.Atom
- getAtomName() - Method in class org.jmol.smiles.SmilesAtom
- getAtomName() - Method in interface org.jmol.util.Node
- getAtomName() - Method in interface org.jmol.util.SimpleNode
- getAtomName(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomNumber() - Method in class org.jmol.modelset.Atom
- getAtomNumber() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the Jmol atom number
- getAtomNumber() - Method in interface org.jmol.util.Node
- getAtomNumber(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
- getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getAtomPointVector(BS) - Method in class org.jmol.modelset.AtomCollection
- getAtomPropertiesLike(String) - Static method in class org.jmol.script.T
- getAtoms() - Method in class jspecview.common.PeakInfo
- getAtoms(int, Object) - Method in class org.jmol.modelset.ModelSet
-
general lookup for integer type -- from Eval
- getAtoms(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- getAtoms(String) - Method in class org.jmol.smiles.SmilesMatcher
- getAtomsConnected(float, float, int, BS) - Method in class org.jmol.modelset.BondCollection
- getAtomSetAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetAtomIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the auxiliary information for a particular atomSet.
- getAtomSetAuxiliaryInfoValue(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetBondCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetCenter(BS) - Method in class org.jmol.modelset.ModelSet
- getAtomSetCollection() - Method in interface org.jmol.api.JmolFilesReaderInterface
- getAtomSetCollection() - Method in class org.jmol.io.FileReader
- getAtomSetCollection() - Method in class org.jmol.io.FilesReader
- getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Create the AtomSetCollection and return it
- getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the auxiliary information for this atomSetCollection.
- getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Direct DOM HTML4 page reading; Egon was interested in this at one point.
- getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionFromReaderType(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
all in one -- for TestSmarterJmolAdapter
- getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
- getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the name of the atom set collection, if known.
- getAtomSetCollectionOrBufferedReaderFromZip(Viewer, InputStream, String, String[], Map<String, Object>, int, boolean) - Method in class org.jmol.io.JmolUtil
-
A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
- getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
Read an atomSetCollection object from a bufferedReader and close the reader.
- getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
- getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
-
Associate an atomSetCollection object with an array of BufferedReader.
- getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get number of atomSets in the file or specific model index in file
- getAtomSetIndex() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the name of an atomSet.
- getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the number identifying each atomSet.
- getAtomsFromAtomNumberInFrame(int) - Method in class org.jmol.modelset.AtomCollection
- getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.JmolStateCreator
- getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.StateCreator
- getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
- getAtomsInFrame(BS) - Method in class org.jmol.modelset.AtomCollection
- getAtomSite() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAtomSite() - Method in class org.jmol.modelset.Atom
- getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
- getAtomSite() - Method in interface org.jmol.util.Node
- getAtomsNearPlane(float, P4) - Method in class org.jmol.modelset.AtomCollection
- getAtomsNearPt(float, P3, BS) - Method in class org.jmol.viewer.Viewer
- getAtomsStartingAt(int) - Method in class org.jmol.script.ScriptParam
- getAtomsWithin(float, T3, BS, int) - Method in class org.jmol.modelset.ModelSet
- getAtomsWithinRadius(float, BS, boolean, RadiusData, BS) - Method in class org.jmol.modelset.ModelSet
-
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
- getAtomSymmetry(Atom, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.
- getAtomSymmetry(Atom, XtalSymmetry.FileSymmetry) - Method in interface org.jmol.adapter.smarter.MSInterface
- getAtomTensor(int, String) - Method in class org.jmol.modelset.AtomCollection
- getAtomTensorList(int) - Method in class org.jmol.modelset.AtomCollection
- getAtomType() - Method in class org.jmol.modelset.Atom
- getAtomType() - Method in class org.jmol.smiles.SmilesAtom
- getAtomType() - Method in interface org.jmol.util.Node
- getAtomTypeDescriptions() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getAtomTypeDescs(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
- getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapterBondIterator
- getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapterBondIterator
- getAtomValidation(String, Atom) - Method in class org.jmol.viewer.Viewer
- getAtomValidation(Viewer, String, Atom) - Method in interface org.jmol.api.JmolAnnotationParser
- getAtomValidation(Viewer, String, Atom) - Method in class org.jmol.dssx.AnnotationParser
-
Get all validation values corresponding to a specific validation type.
- getAtropicStereoFlag(Node[]) - Static method in class org.jmol.smiles.SmilesStereo
- getAtropismNode(int, Node, boolean) - Static method in class org.jmol.util.Edge
- getAtropismOrder(int, int) - Static method in class org.jmol.util.Edge
- getAtropismOrder12(int) - Static method in class org.jmol.util.Edge
- getAtropisomerKeys(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
called by SmilesParser to get nn in ^nn- base on match to actual structure
- getAttachedAtomForPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
-
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
- getAttribute(String, String) - Method in interface org.jmol.api.JmolJDXMOLParser
- getAttribute(String, String) - Method in class org.jmol.jsv.JDXMOLParser
- getAttributeList() - Method in class jspecview.source.XMLParser
- getAttrValue(String) - Method in class jspecview.source.XMLParser
- getAttrValueLC(String) - Method in class jspecview.source.XMLParser
- getAType() - Method in interface jspecview.api.AnnotationData
- getAType() - Method in class jspecview.common.MeasurementData
- getAType() - Method in class jspecview.dialog.JSVDialog
- getAvailIn() - Method in class com.jcraft.jzlib.InflaterInputStream
- getAvailIn() - Method in class com.jcraft.jzlib.ZStream
- getAverageAtomPoint() - Method in class org.jmol.modelset.ModelSet
- getAxesState(SB) - Method in class org.jmol.shape.Axes
- getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
- getAxisLabel(boolean) - Method in class jspecview.common.Spectrum
-
checks in order: (1) Peaks tag attribute xUnits/yUnits, then (2) ##XLABEL/##YLABEL, then (3) ##XUNITS/##YUNITS
- getAxisPoint(int, boolean, P3) - Method in class org.jmol.shape.Axes
-
get actual point or 1/2 vector from origin to this point
- getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
- getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
- getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
- getBackgroundColor() - Method in class jspecview.java.AwtPanel
- getBase64() - Method in class javajs.util.OC
- getBase64(byte[]) - Static method in class javajs.util.Base64
- getBaseModelBitSet() - Method in class org.jmol.viewer.Viewer
- getBaseModelIndex(int) - Method in interface org.jmol.api.JmolJSpecView
- getBaseModelIndex(int) - Method in class org.jmol.jsv.JSpecView
- getBasePairs() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getBasePairs(Viewer, int) - Method in interface org.jmol.api.JmolAnnotationParser
- getBasePairs(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
- getBasePairs(Viewer, int) - Method in class org.jmol.dssx.DSSR1
- getBasePeakInfo() - Method in class jspecview.common.Spectrum
- getBaseRing6Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getBaseSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
Get the symmetry that was in place prior to any supercell business.
- getBasisAtom(int) - Method in class org.jmol.modelkit.ModelKit
- getBasisAtom(int, boolean) - Method in class org.jmol.modelset.ModelSet
- getBBoxVertices() - Method in class org.jmol.modelset.ModelSet
- getBestLineThroughPoints(P3[], int) - Static method in class javajs.util.Measure
-
Get the endpoints of the best line through N points, where N >= 2
- getBfactor() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getBfactor100() - Method in class org.jmol.modelset.Atom
- getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
- getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
- getBFactors() - Method in class org.jmol.modelset.AtomCollection
- getBgContrast(int) - Static method in class org.jmol.util.C
- getBinaryType(InputStream) - Static method in class org.jmol.adapter.smarter.Resolver
- getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
- getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
- getBindingInfo(String[], String[], String) - Method in class org.jmol.viewer.binding.Binding
- getBindings() - Method in class org.jmol.viewer.binding.Binding
- getBioBranches(Lst<BS>) - Method in class org.jmol.modelsetbio.BioModel
- getBioModel(int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelsetbio.BioResolver
- getBioModelSet(ModelSet) - Method in class org.jmol.modelsetbio.BioResolver
- getBioPolymerCount() - Method in class org.jmol.modelsetbio.BioModel
- getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getBioPolymerCountInModel(int) - Method in class org.jmol.modelsetbio.BioModelSet
- getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
- getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
- getBioPolymerLength() - Method in class org.jmol.modelset.Group
- getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
- getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
- getBioSmiles(BS) - Method in class org.jmol.viewer.Viewer
- getBioSmilesType() - Method in class org.jmol.modelset.Atom
- getBioSmilesType() - Method in class org.jmol.smiles.SmilesAtom
- getBioSmilesType() - Method in interface org.jmol.util.Node
- getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
- getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
- getBioStructureTypeName() - Method in interface org.jmol.util.Node
- getBioStructureTypeName(boolean) - Method in enum class org.jmol.c.STR
- getBIS(byte[]) - Static method in class javajs.util.Rdr
- getBisectingPlane(P3, V3, T3, V3, P4) - Static method in class javajs.util.Measure
- getBitSet() - Method in class jspecview.common.IntegralData
- getBitSet(SV, boolean) - Static method in class org.jmol.script.SV
- getBitSetForMF(Atom[], BS, String) - Static method in class org.jmol.util.JmolMolecule
- getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in class org.jmol.scriptext.CmdExt
- getBitsetIdentFull(BS, String, boolean, int, boolean, String[]) - Method in class org.jmol.scriptext.CmdExt
- getBitsetProperty(BS, Lst<SV>, int, P3, P4, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEval
- getBitsetPropertyFloat(BS, int, String, float, float) - Method in class org.jmol.scriptext.CmdExt
- getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
- getBond(int) - Method in class org.jmol.smiles.SmilesAtom
-
Returns the bond at index
number
. - getBond(Atom) - Method in class org.jmol.modelset.Atom
- getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
- getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
- getBondCount() - Method in class jme.JMEmol
- getBondCount() - Method in class org.jmol.modelset.Atom
- getBondCount() - Method in class org.jmol.modelset.Model
- getBondCount() - Method in class org.jmol.smiles.SmilesAtom
- getBondCount() - Method in interface org.jmol.util.SimpleNode
-
Get the total number of bonds, including hydrogen bonds.
- getBondCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
-
for general use
- getBondCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
- getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
- getBondedAtomIndex(int) - Method in interface org.jmol.util.Node
- getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
- getBondIndex(int) - Method in class org.jmol.minimize.MinAtom
- getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
- getBondingRadii() - Method in class org.jmol.modelset.AtomCollection
- getBondingRadius() - Method in class org.jmol.modelset.Atom
- getBondingRadius(int, int) - Static method in class org.jmol.api.JmolAdapter
- getBondingRadius(int, int) - Static method in class org.jmol.util.Elements
-
This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.
- getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get a BondIterator for retrieval of all bonds in the file.
- getBondIterator(BS) - Method in class org.jmol.modelset.BondCollection
- getBondIteratorForType(int, BS) - Method in class org.jmol.modelset.BondCollection
- getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
- getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getBondList(Object) - Method in class org.jmol.api.JmolAdapter
- getBondOrder(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- getBondOrderFromFloat(float) - Static method in class org.jmol.util.Edge
- getBondOrderFromString(String) - Static method in class org.jmol.util.Edge
-
Encode name such as 1 2 3 2.1 3.1 single double triple atropisomer_12 or "partial 1.3"
- getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.Edge
- getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.Edge
-
used for formatting labels and in the connect PARTIAL command
- getBondPickingMode() - Method in class org.jmol.viewer.ActionManager
- getBondProperties(int) - Method in class jme.JMEmol
- getBondRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getBondsForSelectedAtoms(BS) - Method in class org.jmol.viewer.Viewer
- getBondsForSelectedAtoms(BS, boolean) - Method in class org.jmol.modelset.BondCollection
- getBondTo(int) - Method in class org.jmol.minimize.MinAtom
- getBondType() - Method in class org.jmol.util.Edge
- getBondType() - Method in interface org.jmol.util.SimpleEdge
-
Get the order of the bond.
- getBoolean(boolean) - Static method in class org.jmol.script.SV
- getBoolean(int) - Method in class org.jmol.api.JmolViewer
- getBoolean(int) - Method in class org.jmol.viewer.Viewer
- getBoolean(ScriptToken) - Method in class jspecview.common.PanelData
- getBoolean(ScriptToken) - Method in class jspecview.common.Parameters
- getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
- getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
- getBooleans() - Method in class jspecview.common.Parameters
- getBooleanValue(String, boolean) - Method in class org.jmol.util.GenericApplet
- getBoolName(int) - Static method in class org.jmol.viewer.JC
- getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
- getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
- getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
- getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelSet
- getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
- getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
- getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelSet
- getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
- getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelSet
- getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
- getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
- getBoundBoxOrientation(int, BS, P3[]) - Method in class org.jmol.modelset.ModelSet
- getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
-
Return basic info on boundbox in the form of an array.
- getBoundBoxVertices() - Method in class org.jmol.util.BoxInfo
- getBoundingBox() - Method in class org.jmol.shape.Mesh
- getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getBox(int) - Method in class org.jmol.shape.Labels
- getBoxFacesFromOABC(P3[]) - Static method in class org.jmol.util.BoxInfo
- getBoxInfo() - Method in class org.jmol.modelset.ModelSet
- getBoxInfo(BS, float) - Method in class org.jmol.modelset.ModelSet
- getBR(String) - Static method in class javajs.util.Rdr
- getBranchBitSet(int, int, boolean) - Method in class org.jmol.viewer.Viewer
-
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.
- getBranchBitSet(Node[], int, BS, Lst<BS>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
-
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
- getBranchesForInversion(Node[], int, BS) - Static method in class org.jmol.util.JmolMolecule
- getBSAll() - Method in class org.jmol.adapter.smarter.StructureIterator
- getBSAll() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getBSAtoms(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Create bsAtoms if it is null, and set bits if desired.
- getBsBranches(float[]) - Method in class org.jmol.modelset.ModelSet
- getBSSideChain() - Method in class org.jmol.modelset.Group
- getBSSideChain() - Method in class org.jmol.modelsetbio.AminoMonomer
- getBsSurfaceClone() - Method in interface org.jmol.api.JmolEnvCalc
- getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getBufferData() - Method in class jspecview.source.XMLParser
- getBufferedFileInputStream(String) - Method in class jspecview.java.AwtPlatform
- getBufferedFileInputStream(String) - Method in class jspecview.js2d.JsPlatform
- getBufferedFileInputStream(String) - Method in interface org.jmol.api.GenericPlatform
- getBufferedFileInputStream(String) - Method in class org.jmol.awt.Platform
- getBufferedFileInputStream(String) - Method in class org.jmol.awtjs2d.Platform
- getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
- getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
- getBufferedInputStreamOrErrorMessageFromName(String, String, boolean, boolean, byte[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getBufferedReader() - Method in class javajs.util.DataReader
- getBufferedReader(BufferedInputStream, String) - Static method in class javajs.util.Rdr
-
Read an input stream fully, saving a byte array, then return a buffered reader to those bytes converted to string form.
- getBufferedReader(String) - Method in class org.jmol.minimize.forcefield.ForceField
- getBufferedReaderForInputStream(InputStream) - Static method in class jspecview.common.JSVFileManager
- getBufferedReaderForResource(Viewer, Object, String, String) - Static method in class org.jmol.viewer.FileManager
- getBufferedReaderForStringOrBytes(Object) - Static method in class jspecview.common.JSVFileManager
- getBufferedReaderFromName(String, String) - Static method in class jspecview.common.JSVFileManager
- getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
- getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.io.FilesReader
-
called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
- getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getBundle(String) - Method in class org.jmol.modelkit.ModelKitPopup
- getBundle(String) - Method in class org.jmol.popup.JmolGenericPopup
- getBundle(String) - Method in class org.jmol.popup.JmolPopup
- getButtonCount() - Method in class org.jmol.awtjs.swing.ButtonGroup
- getButtonGroup() - Method in class org.jmol.awt.AwtPopupHelper
- getButtonGroup() - Method in class org.jmol.awtjs2d.JSPopupHelper
- getButtonGroup() - Method in interface org.jmol.popup.PopupHelper
- getButtonMods(int) - Static method in class org.jmol.viewer.binding.Binding
- getByteCount() - Method in class javajs.util.OC
- getByteCount() - Method in class org.jmol.export.___Exporter
- getBytes() - Method in class javajs.img.PngEncoder
- getBytes(String) - Static method in class com.jcraft.jzlib.ZStream
-
added by Bob Hanson
- getBytes64(byte[]) - Static method in class javajs.util.Base64
- getBytesFromSB(SB) - Static method in class javajs.util.Rdr
-
Allow for base64-encoding check.
- getBytesRead() - Method in class com.jcraft.jzlib.Deflate
- getBytesRead() - Method in class com.jcraft.jzlib.Deflater
- getBytesWritten() - Method in class com.jcraft.jzlib.Deflate
- getBytesWritten() - Method in class com.jcraft.jzlib.Deflater
- getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getCachedPngjBytes(FileManager, String) - Method in class org.jmol.io.JmolUtil
- getCalcType(Atom[], String[], int) - Static method in class org.jmol.quantum.NMRCalculation
- getCalcValue() - Method in class org.openscience.jmol.app.janocchio.Measure
- getCallback(String) - Static method in enum class org.jmol.c.CBK
- getCallbackParameter(int) - Method in class org.jmol.script.ScriptParam
- getCameraDepth() - Method in class org.jmol.viewer.TransformManager
- getCameraFactors() - Method in class org.jmol.viewer.TransformManager
-
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
- getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
- getCanonicalCopy(float, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.Symmetry
- getCanonicalCopy(P3[], float) - Static method in class org.jmol.util.BoxInfo
-
Change points references to canonical form used in Triangulator, while also scaling.
- getCanonicalCopyTrimmed(P3, float) - Method in class org.jmol.symmetry.UnitCell
- getCanonicalName(String) - Method in class org.jmol.viewer.FileManager
- getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
- getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
- getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getCaretPosition() - Method in interface org.jmol.api.js.GenericConsoleTextArea
- getCaretPosition() - Method in interface org.jmol.console.GenericTextArea
- getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
- getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
- getCartoonType(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getCartoonType(int) - Method in interface org.jmol.api.PymolAtomReader
- getCel() - Method in class org.jmol.util.GData
- getCellRange() - Method in interface org.jmol.api.SymmetryInterface
- getCellRange() - Method in class org.jmol.symmetry.Symmetry
- getCellRange(T3, P3[]) - Static method in class org.jmol.util.SimpleUnitCell
- getCellStyle(int, int, GridBagConstraints) - Method in interface org.jmol.awtjs.swing.TableCellRenderer
- getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
-
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
- getCellWeight(P3) - Method in interface org.jmol.api.SymmetryInterface
- getCellWeight(P3) - Method in class org.jmol.symmetry.Symmetry
- getCellWeights(BS) - Method in class org.jmol.modelset.ModelSet
- getCelPower() - Method in class org.jmol.util.GData
- getCenter() - Method in class com.sparshui.common.messages.events.RotateEvent
- getCenter() - Method in class com.sparshui.common.messages.events.ZoomEvent
- getCenter(Location, Location) - Static method in class com.sparshui.common.Location
- getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.modelset.ModelSet
- getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.viewer.Viewer
- getCenterAndPoints(Lst<P3>) - Static method in class javajs.util.Measure
-
from a list of points, create an array that includes the center point as the first point.
- getCenterText() - Method in class org.jmol.modelkit.ModelKit
- getCentroid(Location, Location, float) - Static method in class com.sparshui.common.Location
-
get weighted average location.
- getChainAt(int) - Method in class org.jmol.modelset.Model
- getChainBits(int) - Method in class org.jmol.modelset.AtomCollection
- getChainCount(boolean) - Method in class org.jmol.modelset.Model
- getChainCountInModelWater(int, boolean) - Method in class org.jmol.modelset.ModelSet
- getChainID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getChainID() - Method in class org.jmol.modelset.Atom
- getChainID() - Method in class org.jmol.smiles.SmilesAtom
- getChainID() - Method in interface org.jmol.util.Node
- getChainID(String, boolean) - Method in class org.jmol.viewer.Viewer
-
Create a unique integer for any chain string.
- getChainIDStr() - Method in class org.jmol.modelset.Atom
- getChainIDStr() - Method in class org.jmol.smiles.SmilesAtom
- getChainIDStr() - Method in interface org.jmol.util.Node
- getChainIDStr(int) - Method in class org.jmol.viewer.Viewer
- getChangeableColix(int, int) - Method in class org.jmol.util.GData
- getChangeableColixIndex(short) - Static method in class org.jmol.util.C
- getChangeInX() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
- getChangeInY() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
- getCharacters() - Method in class jspecview.source.XMLParser
- getCharge() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the charge of the atom.
- getCharge(int) - Method in class jme.JMEmol
- getCheckBox(String) - Method in class org.jmol.awt.AwtPopupHelper
- getCheckBox(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getCheckBox(String) - Method in interface org.jmol.popup.PopupHelper
- getChemicalInfo(String, String, BS) - Method in class org.jmol.viewer.Viewer
- getChemicalShift(Atom) - Method in interface org.jmol.api.JmolNMRInterface
-
If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
- getChemicalShift(Atom) - Method in class org.jmol.quantum.NMRCalculation
- getChildCount() - Method in interface jspecview.api.JSVTreeNode
- getChildCount() - Method in class jspecview.tree.SimpleTreeNode
- getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
- getChimeInfo(int, BS) - Method in interface org.jmol.api.JmolPropertyManager
- getChimeInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
- getChimeMessenger() - Method in class org.jmol.viewer.Viewer
- getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
- getChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
- getChiralityForAtoms(CIPData) - Method in class org.jmol.symmetry.CIPChirality
-
A general determination of chirality that involves ultimately all of Rules 1-6.
- getCifData(int) - Method in class org.jmol.viewer.Viewer
- getCifDataParser() - Method in class org.jmol.adapter.readers.cif.BCIFReader
- getCifDataParser() - Method in class org.jmol.adapter.readers.cif.Cif2Reader
- getCifDataParser() - Method in class org.jmol.adapter.readers.cif.CifReader
- getCIPChirality(boolean) - Method in class org.jmol.modelset.Atom
-
Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
- getCIPChirality(boolean) - Method in class org.jmol.modelset.Bond
-
Not implemented.
- getCIPChirality(boolean) - Method in class org.jmol.smiles.SmilesAtom
- getCIPChirality(boolean) - Method in class org.jmol.util.Edge
- getCIPChirality(boolean) - Method in interface org.jmol.util.Node
- getCIPChiralityCode() - Method in class org.jmol.modelset.Atom
- getCIPChiralityCode() - Method in class org.jmol.smiles.SmilesAtom
- getCIPChiralityCode() - Method in interface org.jmol.util.Node
- getCIPChiralityCode(char) - Static method in class org.jmol.viewer.JC
- getCIPChiralityName(int) - Static method in class org.jmol.viewer.JC
- getCIPChiralityRule() - Method in class org.jmol.modelset.Atom
- getCIPRuleName(int) - Static method in class org.jmol.viewer.JC
- getClegId() - Method in interface org.jmol.api.SymmetryInterface
- getClegId() - Method in class org.jmol.symmetry.Symmetry
- getClickableSet(boolean) - Method in class org.jmol.modelset.AtomCollection
- getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
- getClickedCoordinate() - Method in class jspecview.common.PanelData
-
Returns the spectrum coordinate of the point on the display that was clicked
- getClipboardText() - Static method in class jspecview.java.AwtClipboard
-
Get the String residing on the clipboard.
- getClipboardText() - Method in class org.jmol.api.JmolViewer
- getClipboardText() - Static method in class org.jmol.awt.AwtClipboard
-
Get the String residing on the clipboard.
- getClipboardText() - Method in class org.jmol.viewer.Viewer
- getClone() - Method in class org.jmol.adapter.smarter.Atom
- getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
- getCmdExt() - Method in class org.jmol.script.ScriptEval
- getCmlBondOrder(int) - Static method in class org.jmol.util.Edge
- getCode() - Method in enum class org.jmol.c.FIL
- getCode() - Method in class org.jmol.symmetry.SymmetryOperation
- getColix() - Method in class org.jmol.api.JmolAdapterBondIterator
- getColix(int) - Static method in class org.jmol.util.C
- getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
- getColix2(int, Atom, boolean) - Method in class org.jmol.shape.Labels
- getColixA(short, byte, Atom) - Method in class org.jmol.shape.Shape
- getColixArray(String) - Static method in class org.jmol.util.C
- getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
- getColixB(short, int, Bond) - Method in class org.jmol.shape.Shape
- getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
- getColixI(short, byte, int) - Method in class org.jmol.shape.Shape
- getColixInherited(short, short) - Static method in class org.jmol.util.C
- getColixO(Object) - Static method in class org.jmol.util.C
- getColixS(String) - Static method in class org.jmol.util.C
- getColixTranslucencyFractional(short) - Static method in class org.jmol.util.C
- getColixTranslucencyLabel(short) - Static method in class org.jmol.util.C
- getColixTranslucencyLevel(short) - Static method in class org.jmol.util.C
- getColixTranslucent(int) - Static method in class org.jmol.util.C
- getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.C
- getColor() - Method in class jme.JME
- getColor() - Method in class jspecview.common.ColoredAnnotation
- getColor() - Method in enum class org.jmol.c.STR
- getColor(ScriptToken) - Method in class jspecview.common.PanelData
- getColor1(int) - Method in class jspecview.common.ColorParameters
- getColor1(int) - Method in class jspecview.common.PDFWriter
- getColor1(int) - Method in class jspecview.java.AwtG2D
- getColor1(int) - Method in class jspecview.java.AwtParameters
- getColor1(int) - Method in class jspecview.js2d.JsG2D
- getColor1(int) - Method in class jspecview.js2d.JsParameters
- getColor1(int) - Method in interface org.jmol.api.GenericGraphics
- getColor1(int) - Method in class org.jmol.awt.AwtG2D
- getColor1(int) - Method in class org.jmol.awtjs2d.JsG2D
- getColor3(int, int, int) - Method in class jspecview.common.ColorParameters
- getColor3(int, int, int) - Method in class jspecview.common.PDFWriter
- getColor3(int, int, int) - Method in class jspecview.java.AwtG2D
- getColor3(int, int, int) - Method in class jspecview.java.AwtParameters
- getColor3(int, int, int) - Method in class jspecview.js2d.JsG2D
- getColor3(int, int, int) - Method in class jspecview.js2d.JsParameters
- getColor3(int, int, int) - Method in interface org.jmol.api.GenericGraphics
- getColor3(int, int, int) - Method in class org.jmol.awt.AwtG2D
- getColor3(int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- getColor4(int, int, int, int) - Method in class jspecview.common.PDFWriter
- getColor4(int, int, int, int) - Method in class jspecview.java.AwtG2D
- getColor4(int, int, int, int) - Method in class jspecview.js2d.JsG2D
- getColor4(int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- getColor4(int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- getColor4(int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- getColorArgbOrGray(short) - Method in class org.jmol.util.GData
- getColorCommand(String, byte, short, boolean) - Static method in class org.jmol.shape.Shape
- getColorCommandUnk(String, short, boolean) - Static method in class org.jmol.shape.Shape
- getColoredAnnotation(GenericGraphics, Spectrum, Lst<String>, Annotation) - Static method in class jspecview.common.Annotation
- getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
- getColorFromString(String) - Method in class jspecview.common.ColorParameters
- getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
- getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
- getColorKey() - Method in class org.jmol.util.ColorEncoder
- getColorList(int, short[], int, BS, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
-
input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
- getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
- getColorRange(int) - Method in class org.jmol.script.ScriptEval
- getColorScheme() - Method in class org.jmol.util.ColorEncoder
- getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
- getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
- getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
- getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
- getColorTrans(ScriptEval, int, boolean, int[]) - Method in class org.jmol.scriptext.ScriptExt
-
Checks color, translucent, opaque parameters.
- getColour(Spectrum, boolean) - Method in interface jspecview.api.VisibleInterface
- getColour(Spectrum, boolean) - Method in class jspecview.common.Visible
-
Returns the integer color of a solution based on its visible spectrum.
- getColumn(int) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
- getColumn(int) - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
- getColumn(int) - Method in class org.jmol.awtjs.swing.JTable
- getColumn(int, float[]) - Method in class javajs.util.M3
-
Copies the matrix values in the specified column into the array parameter.
- getColumn(int, float[]) - Method in class javajs.util.M4
-
Copies the matrix values in the specified column into the array parameter.
- getColumn33(int, float[]) - Method in class javajs.util.M34
- getColumnCentering(int) - Method in class jspecview.java.AwtDialog
- getColumnCentering(int) - Method in class jspecview.js2d.JsDialog
- getColumnClass(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getColumnCount() - Method in interface javajs.api.GenericCifDataParser
- getColumnCount() - Method in class javajs.util.CifDataParser
- getColumnCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getColumnData(int) - Method in interface javajs.api.GenericCifDataParser
- getColumnData(int) - Method in class javajs.util.CifDataParser
- getColumnDimension() - Method in class javajs.util.Matrix
-
Get column dimension.
- getColumnModel() - Method in class org.jmol.awtjs.swing.JTable
- getColumnName(int) - Method in interface javajs.api.GenericCifDataParser
- getColumnName(int) - Method in class javajs.util.CifDataParser
- getColumnName(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getColumnV(int, T3) - Method in class javajs.util.M3
-
Copies the matrix values in the specified column into the vector parameter.
- getCommand(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- getCommandDown() - Method in class org.jmol.util.CommandHistory
-
Retrieves the following command from the top of the list, updates list position.
- getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Generates a commandline from the options set for povray path etc and sets in the textField.
- getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.Viewer
- getCommandSet(String) - Static method in class org.jmol.script.T
-
retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
- getCommandUp() - Method in class org.jmol.util.CommandHistory
-
Retrieves the following command from the bottom of the list, updates list position.
- getComment() - Method in class com.jcraft.jzlib.GZIPHeader
- getComparator(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getComponent(int) - Method in interface org.jmol.api.SC
- getComponent(int) - Method in class org.jmol.awt.AwtSwingComponent
- getComponent(int) - Method in class org.jmol.awtjs.swing.Container
- getComponentCount() - Method in interface org.jmol.api.SC
- getComponentCount() - Method in class org.jmol.awt.AwtSwingComponent
- getComponentCount() - Method in class org.jmol.awtjs.swing.Container
- getComponents() - Method in interface org.jmol.api.SC
- getComponents() - Method in class org.jmol.awt.AwtSwingComponent
- getComponents() - Method in class org.jmol.awtjs.swing.Container
- getConeMesh(P3, M3, short) - Static method in class org.jmol.export.___Exporter
- getConformation(int, boolean, BS, BS) - Method in class org.jmol.modelsetbio.BioModel
- getConformation(int, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
- getConnectingAtoms(BS, BS) - Method in class org.jmol.modelset.ModelSet
- getConsole() - Method in class org.jmol.viewer.Viewer
- getConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getConsoleFontScale() - Method in class org.jmol.viewer.Viewer
- getContentPane() - Method in class org.jmol.awtjs.swing.JDialog
- getContents() - Method in class javajs.util.AjaxURLConnection
- getContext(String) - Method in class org.jmol.viewer.StateManager
- getContextVariableAsVariable(String, boolean) - Method in class org.jmol.script.ScriptParam
- getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
create a set of contour data.
- getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
-
NWCHEM only
- getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.AlphaPolymer
- getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.BioPolymer
- getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
- getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.UnitCell
-
return a conventional lattice from a primitive
- getConversionFactor(Map<String, Object>, String, String) - Static method in class org.qcschema.QCSchemaUnits
-
Get the necessary conversion factor to the desired units from a key_units or atomic units
- getConversionFactorTo(ArrayList<Object>, String) - Static method in class org.qcschema.QCSchemaUnits
-
For a reader, use the JSON [units, factor] along with a desired unit to get the conversion factor from file values to desired units.
- getConvertedSpectrum() - Method in class jspecview.common.Spectrum
- getCoord() - Method in class jspecview.common.PeakPickEvent
- getCoordinate() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript to return the coordinate of clicked point in the plot area of the
JSVPanel
- getCoordinate() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript to return the coordinate of clicked point in the plot area of the
JSVPanel
- getCoordinate() - Method in class jspecview.appletjs.JSVApplet
- getCoordinate() - Method in class jspecview.application.MainFrame
- getCoordinate() - Method in class jspecview.common.JSViewer
- getCoordinateMap(T3[], int[], BS) - Method in class org.jmol.export.__CartesianExporter
- getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
- getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
- getCoordinateState(BS) - Method in class org.jmol.viewer.Viewer
- getCorrelationMaps(String, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getCorrelationMaps(String, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
- getCorrelationTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
get the correlation time in seconds
- getCorrelationTimeTauPS() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get the correlation time in picoseconds
- getCouples() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getCoupleWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- getCovalentBondCount() - Method in class org.jmol.modelset.Atom
- getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the number of bonds of this atom.
- getCovalentBondCount() - Method in interface org.jmol.util.Node
- getCovalentBondCount() - Method in interface org.jmol.util.SimpleNode
-
Get the total number of covalent bonds, thus not including hydrogen bonds.
- getCovalentBondCountPlusMissingH() - Method in class org.jmol.modelset.Atom
- getCovalentBondCountPlusMissingH() - Method in class org.jmol.smiles.SmilesAtom
- getCovalentBondCountPlusMissingH() - Method in interface org.jmol.util.Node
-
includes actual + missing
- getCovalentBondOrder(int) - Static method in class org.jmol.util.Edge
- getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
- getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getCovalentHydrogenCount() - Method in interface org.jmol.util.Node
- getCovalentOrder() - Method in class org.jmol.modelset.Bond
- getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
- getCovalentOrder() - Method in class org.jmol.util.Edge
- getCovalentOrder() - Method in interface org.jmol.util.SimpleEdge
- getCovalentOrPartialBondCount() - Method in class org.jmol.modelset.Atom
- getCovalentRadius(int) - Static method in class org.jmol.util.Elements
-
Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR
- getCRC() - Method in class com.jcraft.jzlib.GZIPHeader
- getCrcValue(byte[]) - Method in interface javajs.api.GenericZipTools
- getCrcValue(byte[]) - Method in class javajs.util.ZipTools
- getCrossLinkGroup(int, Lst<Integer>, Group, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Atom
-
Used by SMILES to get vector of cross-links
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Group
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.smiles.SmilesAtom
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in interface org.jmol.util.Node
- getCSSstyle(int, int) - Method in class org.jmol.awtjs.swing.Component
- getCSVString(String, int[]) - Static method in class javajs.util.PT
-
CSV format -- escaped quote is "" WITHIN "..."
- getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
- getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
- getCurrentColorSchemeName() - Method in class org.jmol.util.ColorEncoder
- getCurrentFileAsString(String) - Method in class org.jmol.viewer.Viewer
- getCurrentGraphSet() - Method in class jspecview.common.PanelData
- getCurrentModelAuxInfo() - Method in class org.jmol.viewer.Viewer
- getCurrentModelFileAsString(String) - Method in class org.jmol.script.ScriptEval
- getCurrentModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getCurrentPanelIndex() - Method in interface jspecview.api.JSVMainPanel
- getCurrentPanelIndex() - Method in class jspecview.java.AwtMainPanel
- getCurrentPanelIndex() - Method in class jspecview.js2d.JsMainPanel
- getCurrentPlotColor(int) - Method in class jspecview.common.PanelData
- getCurrentSpectrumIndex() - Method in class jspecview.common.PanelData
- getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
- getCurrentStructureFile() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getCurrentSubSpectrum() - Method in class jspecview.common.Spectrum
- getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
- getCursorX() - Method in class org.jmol.viewer.Viewer
- getCursorY() - Method in class org.jmol.viewer.Viewer
- getCutoff() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
get the cutoff distance
- getCutoffAng() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get the cutoff distance
- getCutoffField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getData() - Method in interface javajs.api.GenericCifDataParser
- getData() - Method in class javajs.util.CifDataParser
-
The work horse; a general reader for loop data.
- getData() - Method in interface jspecview.api.AnnotationData
- getData() - Method in class jspecview.common.MeasurementData
- getData() - Method in class jspecview.dialog.JSVDialog
- getData(InputStream, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
called by SmarterJmolAdapter via JmolUtil to open a Spartan directory and get all the needed data as a string.
- getData(String, String) - Method in class org.jmol.api.JmolViewer
- getData(String, String) - Method in class org.jmol.viewer.Viewer
- getData(String, BS, int) - Method in interface org.jmol.api.JmolDataManager
- getData(String, BS, int) - Method in class org.jmol.viewer.DataManager
- getDataClass() - Method in class jspecview.source.JDXHeader
-
Returns the data class spectrum only
- getDataHeader() - Method in class jspecview.common.IntegralData
- getDataHeader() - Method in class jspecview.common.MeasurementData
- getDataHeader() - Method in class jspecview.common.PeakData
- getDataObj(String, BS, int) - Method in class org.jmol.viewer.Viewer
-
Retrieve a data object
- getDataState(JmolStateCreator, SB) - Method in interface org.jmol.api.JmolDataManager
- getDataState(JmolStateCreator, SB) - Method in class org.jmol.viewer.DataManager
- getDataType() - Method in class jspecview.source.JDXHeader
-
Getter for property dataType.
- getDate() - Method in class jspecview.source.JDXHeader
-
Getter for property date.
- getDateFormat(String) - Method in class jspecview.java.AwtPlatform
- getDateFormat(String) - Method in class jspecview.js2d.JsPlatform
- getDateFormat(String) - Method in interface org.jmol.api.GenericPlatform
- getDateFormat(String) - Method in class org.jmol.awt.Platform
- getDateFormat(String) - Method in class org.jmol.awtjs2d.Platform
- getDef(String) - Method in class org.jmol.export._VrmlExporter
- getDefaultAnnotationInfo(Annotation.AType) - Method in class jspecview.source.JDXDataObject
- getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
- getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelsetbio.BioModel
- getDefaultLattice() - Method in class org.jmol.viewer.Viewer
- getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
-
When creating a new bond, determine bond diameter from order
- getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
- getDefaultModel() - Method in class org.jmol.modelkit.ModelKit
- getDefaultPropertyParam(int) - Method in interface org.jmol.api.JmolPropertyManager
- getDefaultPropertyParam(int) - Method in class org.jmol.viewer.PropertyManager
- getDefaultPropertyParam(int) - Method in class org.jmol.viewer.Viewer
- getDefaultScheme() - Method in class jspecview.application.DisplaySchemesProcessor
- getDefaultStructure(BS, BS) - Method in class org.jmol.modelset.ModelSet
- getDefaultUnitPrecision() - Method in class jspecview.source.JDXDataObject
- getDefaultVdwNameOrData(int, VDW, BS) - Method in class org.jmol.viewer.Viewer
- getDefaultVdwNameOrData(VDW, BS) - Method in interface org.jmol.api.JmolDataManager
- getDefaultVdwNameOrData(VDW, BS) - Method in class org.jmol.viewer.DataManager
- getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelSet
- getDefinedAtomSet(String) - Method in class org.jmol.viewer.Viewer
- getDeflater() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- getDegrees(float, boolean) - Method in class org.jmol.multitouch.ActionManagerMT
- getDegrees(float, boolean) - Method in class org.jmol.viewer.ActionManager
-
Transform a screen pixel change to an angular change such that a full sweep of the dimension (up to 500 pixels) corresponds to 180 degrees of rotation.
- getDelayMaximumMs() - Method in class org.jmol.viewer.Viewer
- getDeltaX() - Method in class jspecview.source.JDXDataObject
-
Returns the delta X
- getDescent() - Method in class org.jmol.util.Font
- getDescription() - Method in enum class jspecview.common.ScriptToken
- getDescription() - Method in class jspecview.java.AwtDialogFileFilter
-
Returns the JSpecViewFileFilter description
- getDescription() - Method in class org.jmol.dialog.Dialog.TypeFilter
- getDescription() - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getDFMap(String, String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
finds the position in the Jmol-required list of function types.
- getDialog() - Method in class org.jmol.dialog.FileChooser
- getDialog(Annotation.AType) - Method in class jspecview.common.PanelData
- getDialog(Annotation.AType, Spectrum) - Method in class jspecview.common.JSViewer
- getDialog(JSVDialog) - Method in class jspecview.dialog.DialogManager
- getDialog(JSVDialog) - Method in class jspecview.java.AwtDialogManager
- getDialog(JSVDialog) - Method in class jspecview.js2d.JsDialogManager
- getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.dialog.DialogManager
- getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.java.AwtDialogManager
- getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.js2d.JsDialogManager
- getDialogManager() - Method in class jspecview.common.JSViewer
- getDialogPrint(boolean) - Method in class jspecview.common.JSViewer
- getDialogs() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getDiameter(int, int) - Method in class org.jmol.render.FontLineShapeRenderer
- getDiff() - Method in class org.openscience.jmol.app.janocchio.Measure
- getDiffusePercent() - Method in class org.jmol.util.GData
- getDihedralCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getDihedralMap(int[]) - Method in class org.jmol.modelset.ModelSet
- getDimensionFromParams(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- getDimensionValue(int) - Method in class org.jmol.modelset.Atom
- getDipolarConstantHz(Atom, Atom) - Method in interface org.jmol.api.JmolNMRInterface
- getDipolarConstantHz(Atom, Atom) - Method in class org.jmol.quantum.NMRCalculation
- getDipolarCouplingHz(Atom, Atom, V3) - Method in interface org.jmol.api.JmolNMRInterface
- getDipolarCouplingHz(Atom, Atom, V3) - Method in class org.jmol.quantum.NMRCalculation
- getDirectedNormalThroughPoints(T3, T3, T3, T3, V3, V3) - Static method in class javajs.util.Measure
- getDirectory() - Method in class javajs.util.CompoundDocument
- getDirectoryListing(String) - Method in class javajs.util.CompoundDocument
- getDisplay1D() - Method in class jspecview.common.PanelData
- getDisplayModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getDisplayName() - Method in class org.jmol.symmetry.SpaceGroup
- getDisplaySchemes() - Method in class jspecview.application.DisplaySchemesProcessor
-
Returns the list of
DisplayScheme
s that were loaded - getDisplaySchemesProcessor(JSVInterface) - Method in class jspecview.application.JSpecView
- getDistance(Location) - Method in class com.sparshui.common.Location
- getDistanceFormatForState() - Method in class org.jmol.modelset.Measurement
- getDistances() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
- getDocument() - Method in class org.jmol.awtjs.swing.JTextPane
- getDocumentBase() - Method in interface jspecview.api.AppletFrame
- getDocumentBase() - Method in class jspecview.appletjs.JSVApplet
- getDoTranslate() - Static method in class org.jmol.i18n.GT
- getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getDouble(Map<String, Object>, String) - Method in class org.molecularplayground.MPJmolApp
- getDouble(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getDouble(Map<String, Object>, String, String) - Static method in class org.qcschema.QCSchemaUnits
-
Reads a value from an associative array, converting it to the desired units.
- getDoubleArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
-
Retrieve a double array, possibly unpacking it if it is run-length encoded.
- getDrawHover() - Method in class org.jmol.viewer.Viewer
- getDrawTitle(boolean) - Method in class jspecview.common.PanelData
- getDSSRFrame(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
- getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
- getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
- getDSSRFrame(Viewer) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getDx() - Method in class com.sparshui.common.messages.events.DragEvent
- getDy() - Method in class com.sparshui.common.messages.events.DragEvent
- getEchoName(int) - Static method in class org.jmol.viewer.JC
- getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
- getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
- getEdgePoints(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getEdges() - Method in class org.jmol.modelset.Atom
- getEdges() - Method in class org.jmol.smiles.SmilesAtom
- getEdges() - Method in interface org.jmol.util.Node
- getEdges() - Method in interface org.jmol.util.SimpleNode
-
Get the bond array, including hydrogen bonds.
- getEigenvalues() - Method in interface javajs.api.EigenInterface
- getEigenvalues() - Method in class javajs.util.Eigen
-
return values sorted from smallest to largest value.
- getEigenvectorsFloatTransposed() - Method in interface javajs.api.EigenInterface
- getEigenvectorsFloatTransposed() - Method in class javajs.util.Eigen
-
Transpose V and turn into floats; sorted from smallest to largest value.
- getElement() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getElement(int, int) - Method in class javajs.util.M3
-
Retrieves the value at the specified row and column of this matrix.
- getElement(int, int) - Method in class javajs.util.M4
-
Retrieves the value at the specified row and column of this matrix.
- getElement(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
-
allow for any number of characters, for which the first one or two are an element symbol.
- getElementColor(ScriptToken) - Method in class jspecview.common.ColorParameters
-
Gets the color of an element in the scheme
- getElementFromUser() - Method in class org.jmol.modelkit.ModelKit
- getElementKey(int) - Static method in class org.jmol.modelkit.ModelKit
- getElementName(int) - Method in class org.jmol.modelset.AtomCollection
- getElementNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getElementNumber() - Method in class org.jmol.modelset.Atom
- getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atomic number of the element or 0
- getElementNumber() - Method in interface org.jmol.util.Node
- getElementNumber() - Method in interface org.jmol.util.SimpleNode
- getElementNumber(int) - Static method in class org.jmol.util.Elements
- getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
- getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
- getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelSet
- getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
- getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
- getElementSymbol() - Method in class org.jmol.modelset.Atom
- getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
- getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
- getElementSymbolIso(boolean) - Method in class org.jmol.modelset.Atom
- getElemNos() - Method in class org.jmol.shapespecial.Polyhedron
- getEllipsoidForAtomTensor(Tensor, Atom) - Static method in class org.jmol.shapespecial.Ellipsoid
- getEllipsoidShade(float, float, float, int, M4) - Method in class org.jmol.util.Shader
- getEmbeddedFileState(String, boolean, String) - Method in class org.jmol.viewer.FileManager
-
Get the specified SPT file of a Jmol zip collection or the embedded script for any other file that is embeddable.
- getEmbeddedScript(String) - Static method in class org.jmol.viewer.FileManager
-
Extract a Jmol script embedded using JC.EMBEDDED_SCRIPT_TAG.
- getEmptyEllipsoid(String, int) - Static method in class org.jmol.shapespecial.Ellipsoid
- getEmptyPanel(JSViewer) - Static method in class jspecview.java.AwtPanel
-
Constructs a new JSVPanel
- getEmptyPanel(JSViewer) - Static method in class jspecview.js2d.JsPanel
-
Constructs a new JSVPanel
- getEncodedOrder() - Method in class org.jmol.api.JmolAdapterBondIterator
- getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within
element - getEndChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getEndChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getEndingPointIndex(int) - Method in class jspecview.common.PanelData
- getEndingPointIndex(int) - Method in class jspecview.common.ViewData
-
in some cases, there is only one scaleData, but there are more than that number of spectra this is no problem -- we just use mod to set this to 0
- getEndInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
- getEndInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
- getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getEndTag() - Method in class jspecview.source.XMLParser
- getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
- getEnergy() - Method in class org.jmol.modelset.Bond
- getEnergy() - Method in class org.jmol.modelset.HBond
- getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
- getEntryIcon(String[]) - Method in class org.jmol.popup.GenericPopup
- getEquationForQuadricWithCenter(float, float, float, M3, V3, M3, double[], M4) - Static method in class org.jmol.shapespecial.Ellipsoid
- getEquivPointList(Lst<P3>, int, String, M4[]) - Method in interface org.jmol.api.SymmetryInterface
- getEquivPointList(Lst<P3>, int, String, M4[]) - Method in class org.jmol.symmetry.Symmetry
- getEquivPoints(Lst<P3>, P3, String) - Method in interface org.jmol.api.SymmetryInterface
- getEquivPoints(Lst<P3>, P3, String) - Method in class org.jmol.symmetry.Symmetry
- getErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptError
- getErrorLineMessage2() - Method in class org.jmol.script.ScriptEval
- getErrorLog() - Method in class jspecview.source.JDXSource
-
Returns the error log for this source
- getErrorMessage() - Method in interface org.jmol.api.JmolScriptEvaluator
- getErrorMessage() - Method in class org.jmol.api.JmolViewer
- getErrorMessage() - Method in class org.jmol.script.ScriptError
- getErrorMessage() - Method in class org.jmol.viewer.Viewer
- getErrorMessageUn() - Method in class org.jmol.api.JmolViewer
- getErrorMessageUn() - Method in class org.jmol.viewer.Viewer
- getErrorMessageUntranslated() - Method in interface org.jmol.api.JmolScriptEvaluator
- getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptError
- getErrorMessageUntranslated() - Method in exception class org.jmol.script.ScriptException
- getEulerZXZ() - Method in class javajs.util.Quat
- getEulerZYZ() - Method in class javajs.util.Quat
- getEvalContextAndHoldQueue(JmolScriptEvaluator) - Method in class org.jmol.viewer.Viewer
- getEventType() - Method in interface com.sparshui.common.Event
-
Returns the integer value of this event type.
- getEventType() - Method in class com.sparshui.common.messages.events.DragEvent
- getEventType() - Method in class com.sparshui.common.messages.events.FlickEvent
- getEventType() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
- getEventType() - Method in class com.sparshui.common.messages.events.RotateEvent
- getEventType() - Method in class com.sparshui.common.messages.events.SpinEvent
- getEventType() - Method in class com.sparshui.common.messages.events.TouchEvent
- getEventType() - Method in class com.sparshui.common.messages.events.ZoomEvent
- getExecutor() - Method in interface org.jmol.api.JmolParallelProcessor
- getExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
- getExpCouple(int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getExpDist(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getExplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
- getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getExplicitHydrogenCount() - Method in interface org.jmol.util.Node
-
[CH2] for example
- getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
- getExpNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getExportDate() - Method in class org.jmol.export.___Exporter
- getExportDriverList() - Method in class org.jmol.viewer.Viewer
- getExportName() - Method in interface org.jmol.api.JmolRendererInterface
- getExportName() - Method in class org.jmol.export.Export3D
- getExportName() - Method in class org.jmol.g3d.Graphics3D
- getExportType() - Method in interface org.jmol.api.JmolRendererInterface
- getExportType() - Method in class org.jmol.export.Export3D
- getExportType() - Method in class org.jmol.g3d.Graphics3D
- getExpValue() - Method in class org.openscience.jmol.app.janocchio.Measure
- getExtension(File) - Method in class jspecview.java.AwtDialogFileFilter
-
Returns the extension of a file
- getF2C() - Method in class org.jmol.symmetry.UnitCell
- getFaces() - Method in class org.jmol.util.MeshSurface
- getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
- getFactoredValue(int) - Method in class org.jmol.util.Tensor
-
Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor
- getFactorToAU(String) - Static method in class org.qcschema.QCSchemaUnits
-
Get the standard conversion factor to atomic units for this unit.
- getFieldString(byte) - Method in class org.jmol.adapter.readers.cif.CifReader
- getFile() - Method in class org.openscience.jmol.app.HistoryFile
- getFile(String, Object, boolean) - Method in interface jspecview.api.JSVFileHelper
- getFile(String, Object, boolean) - Method in class jspecview.java.AwtFileHelper
- getFile(String, Object, boolean) - Method in class jspecview.js2d.JsFileHelper
- getFileAsBytes(String, OC) - Method in class org.jmol.viewer.FileManager
- getFileAsMap(String, String, boolean) - Method in class org.jmol.viewer.FileManager
-
create a PNG or ZIP file and return it as a map or, optionally, as a byte[]
- getFileAsString(String) - Method in class javajs.util.CompoundDocument
- getFileAsString(String) - Static method in class jspecview.common.JSVFileManager
- getFileAsString(String) - Method in class org.jmol.viewer.Viewer
- getFileAsString3(String, boolean, String) - Method in class org.jmol.viewer.Viewer
- getFileAsString4(String, int, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
- getFileData(int) - Method in class org.jmol.modelset.ModelSet
- getFileDataAsString(String[], int, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getFileHeader() - Method in interface javajs.api.GenericCifDataParser
- getFileHeader() - Method in class javajs.util.CifDataParser
- getFileHeader(int) - Method in class org.jmol.modelset.ModelSet
- getFileInfo() - Method in class org.jmol.viewer.FileManager
- getFileList(String, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
get a complete critical file list for a spartan file Mac directory based on file extension ".spardir.zip" or ".spardir"
- getFileName() - Method in class javajs.util.OC
- getFileName() - Method in class org.jmol.viewer.FileManager
- getFileName() - Method in exception class org.jmol.viewer.JmolAsyncException
- getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
- getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
- getFilePath() - Method in class jspecview.common.PeakInfo
- getFilePath() - Method in class jspecview.source.JDXDataObject
-
The path to the file
- getFilePath() - Method in class jspecview.source.JDXSource
- getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getFilePathForwardSlash() - Method in class jspecview.source.JDXDataObject
- getFileReferences(String, Lst<String>, Lst<String>) - Static method in class org.jmol.viewer.FileManager
- getFileType() - Method in class org.jmol.viewer.FileManager
- getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
-
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
- getFileTypefromFilter(String) - Static method in class org.jmol.adapter.smarter.Resolver
- getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Just get the resolved file type; if a file, does NOT close the reader
- getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the type of this file or molecular model, if known.
- getFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getFilterWithCase(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getFinalOperationCount() - Method in interface org.jmol.api.SymmetryInterface
- getFinalOperationCount() - Method in class org.jmol.symmetry.Symmetry
- getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
- getFirstAtomIndexFromAtomNumber(int, BS) - Method in class org.jmol.modelset.AtomCollection
- getFirstX() - Method in class jspecview.source.JDXDataObject
-
Returns the first X value
- getFirstY() - Method in class jspecview.source.JDXDataObject
-
Returns the first Y value
- getFlexFitList(BS, BS, String, boolean) - Method in class org.jmol.scriptext.SmilesExt
- getFloat(int) - Method in class org.jmol.api.JmolViewer
- getFloat(int) - Method in class org.jmol.shapecgo.CGOMesh
- getFloat(int) - Method in class org.jmol.viewer.Viewer
- getFloatColumnData(int) - Method in class org.jmol.adapter.readers.cif.BCIFReader
-
Called by processAtomSites to retrieve individual matrix elements and set them by name.
- getFloatColumnData(int) - Method in class org.jmol.adapter.readers.cif.CifReader
- getFloatEncodedInt(String) - Static method in class org.jmol.util.Edge
-
Encodes a string such as "2.10" as an integer instead of a double so as to distinguish "2.1" from "2.10".
- getFloatProperty(String) - Method in class org.jmol.modelset.Atom
- getFloatProperty(String) - Method in class org.jmol.smiles.SmilesAtom
- getFloatProperty(String) - Method in interface org.jmol.util.Node
- getFloats(byte[], int, float) - Static method in class javajs.util.MessagePackReader
-
mmtf type 1 and 11 byte[4] to float32
- getFocusNow(boolean) - Method in interface jspecview.api.JSVPanel
- getFocusNow(boolean) - Method in class jspecview.java.AwtPanel
- getFocusNow(boolean) - Method in class jspecview.js2d.JsPanel
- getFont(float) - Method in class org.jmol.shape.Frank
- getFont3D(float) - Method in class org.jmol.util.GData
- getFont3D(int) - Static method in class org.jmol.util.Font
- getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
- getFont3DCurrent() - Method in class org.jmol.util.GData
- getFont3DFS(String, float) - Method in class org.jmol.util.GData
- getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
- getFont3DScaled(Font, float) - Method in class org.jmol.util.GData
- getFontAscent(Object) - Method in class jspecview.java.AwtPlatform
- getFontAscent(Object) - Method in class jspecview.js2d.JsPlatform
- getFontAscent(Object) - Method in interface org.jmol.api.FontManager
- getFontAscent(Object) - Method in class org.jmol.awt.Platform
- getFontAscent(Object) - Method in class org.jmol.awtjs2d.Platform
- getFontCommand(String, Font) - Static method in class org.jmol.shape.Shape
- getFontDescent(Object) - Method in class jspecview.java.AwtPlatform
- getFontDescent(Object) - Method in class jspecview.js2d.JsPlatform
- getFontDescent(Object) - Method in interface org.jmol.api.FontManager
- getFontDescent(Object) - Method in class org.jmol.awt.Platform
- getFontDescent(Object) - Method in class org.jmol.awtjs2d.Platform
- getFontFaceID(String) - Method in interface jspecview.api.JSVPanel
- getFontFaceID(String) - Method in class jspecview.java.AwtPanel
- getFontFaceID(String) - Method in class jspecview.js2d.JsPanel
- getFontFaceID(String) - Static method in class org.jmol.util.Font
- getFontFidFS(String, float) - Method in class org.jmol.util.GData
- getFontFidI(float) - Method in class org.jmol.util.GData
- getFontMetrics() - Method in class org.jmol.util.Font
- getFontMetrics(Font, Object) - Method in class jspecview.java.AwtPlatform
- getFontMetrics(Font, Object) - Method in class jspecview.js2d.JsPlatform
- getFontMetrics(Font, Object) - Method in interface org.jmol.api.FontManager
- getFontMetrics(Font, Object) - Method in class org.jmol.awt.Platform
- getFontMetrics(Font, Object) - Method in class org.jmol.awtjs2d.Platform
- getFontName(ScriptToken, String) - Method in class jspecview.common.ColorParameters
- getFontStyleID(String) - Static method in class org.jmol.util.Font
- getForceField(String) - Method in class org.jmol.minimize.Minimizer
- getForceFieldUsed() - Method in class org.jmol.minimize.Minimizer
- getFormalCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getFormalCharge() - Method in class org.jmol.modelset.Atom
- getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
- getFormalCharge() - Method in interface org.jmol.util.Node
- getFormalCharge() - Method in interface org.jmol.util.SimpleNode
- getFormatType(String) - Static method in class org.jmol.script.SV
- getFormulaForAtoms(BS, String, boolean) - Method in class org.jmol.viewer.Viewer
-
Get formula -- MF or CELLFORMULA, possibly empirical
- getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
get all integers after letters negative entries are spaces (1Xn)
- getFractional(Atom, P3) - Method in class org.jmol.modelset.Trajectory
- getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
- getFractionalCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
- getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
- getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
- getFractionalOrigin() - Method in interface org.jmol.api.SymmetryInterface
- getFractionalOrigin() - Method in class org.jmol.symmetry.Symmetry
- getFractionalOrigin() - Method in class org.jmol.util.SimpleUnitCell
-
Get the fractional origin for the UccageRenderer.
- getFractionalPoint(int) - Method in class org.jmol.script.ScriptParam
-
Could return a P4 for large 1100100100 type indicators
- getFrame() - Method in interface jspecview.java.JmolFrame
- getFrame() - Method in interface org.jmol.awt.JmolFrame
- getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- getFrameActions() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getFrameActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getFrameAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getFrameAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getFrameAtoms() - Method in class org.jmol.viewer.Viewer
- getFrameBase(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getFrameCount() - Method in class org.jmol.viewer.AnimationManager
- getFrameDelayMs(int) - Method in class org.jmol.modelset.ModelSet
- getFrameModelInfo(String) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- getFrameOffsets(BS, boolean) - Method in class org.jmol.modelset.ModelSet
- getFrameTitle() - Method in class org.jmol.viewer.Viewer
- getFrameTitle(int) - Method in class org.jmol.modelset.ModelSet
- getFreqField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getFullMap() - Method in class org.jmol.script.ScriptContext
- getFullName() - Method in interface javajs.api.JSInterface
- getFullName() - Method in class jspecview.appletjs.JSVApplet
- getFullName() - Method in class org.jmol.util.GenericApplet
- getFullPath() - Method in interface org.jmol.api.GenericFileInterface
- getFullPathName(boolean) - Method in class org.jmol.script.ScriptEval
- getFullPathName(boolean) - Method in class org.jmol.viewer.FileManager
- getFullPathName(String) - Static method in class jspecview.common.JSVFileManager
-
FileManager.classifyName follow this with .replace('\\','/') and Escape.escape() to match Jmol's file name in
- getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
- getFullPDBHeader() - Method in class org.jmol.modelsetbio.BioModel
- getFullProteinStructureState(BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
- getFullScreenDimensions(Object, int[]) - Method in class jspecview.java.AwtPlatform
- getFullScreenDimensions(Object, int[]) - Method in class jspecview.js2d.JsPlatform
- getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.GenericPlatform
- getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
- getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awtjs2d.Platform
- getFunction(String) - Method in class org.jmol.script.ScriptEval
- getFunction(String) - Method in class org.jmol.viewer.Viewer
- getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
- getFunctions(boolean) - Method in class org.jmol.viewer.Viewer
- getGestures(int) - Method in class com.sparshui.server.ServerToClientProtocol
-
Retrieve a list of allowed gestures for the provided group id.
- getGestureType() - Method in interface com.sparshui.gestures.Gesture
-
Get the integer value of this gesture type.
- getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
- getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- getGlideFromTrans(T3, T3) - Static method in class org.jmol.symmetry.SymmetryOperation
- getGLmolView() - Method in class org.jmol.util.GenericApplet
-
This method is only called by JmolGLmol applet._refresh();
- getGLmolView() - Method in class org.jmol.viewer.Viewer
-
This method is only called by JmolGLmol applet._refresh();
- getGraphics(Object) - Method in class jspecview.java.AwtPlatform
- getGraphics(Object) - Method in class jspecview.js2d.JsPlatform
- getGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
- getGraphics(Object) - Method in class org.jmol.awt.Platform
- getGraphics(Object) - Method in class org.jmol.awtjs.Platform
- getGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
- getGraphSetKey() - Method in interface jspecview.api.AnnotationData
- getGraphSetKey() - Method in class jspecview.common.MeasurementData
- getGraphSetKey() - Method in class jspecview.dialog.JSVDialog
- getGroup1() - Method in class org.jmol.modelset.Group
- getGroup1() - Method in class org.jmol.modelsetbio.Monomer
- getGroup1(char) - Method in class org.jmol.modelset.Atom
- getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
- getGroup1(char) - Method in interface org.jmol.util.Node
- getGroup1b() - Method in class org.jmol.modelsetbio.Monomer
- getGroup1b() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getGroup3() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getGroup3() - Method in class org.jmol.modelset.Group
- getGroup3(boolean) - Method in class org.jmol.modelset.Atom
- getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
- getGroup3(boolean) - Method in interface org.jmol.util.Node
- getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
- getGroupBits(BS) - Method in class org.jmol.modelset.Atom
- getGroupBits(BS) - Method in class org.jmol.smiles.SmilesAtom
- getGroupBits(BS) - Method in interface org.jmol.util.Node
- getGroupCount() - Method in class org.jmol.modelset.Model
- getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
- getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
- getGroupID(Location) - Method in interface com.sparshui.client.SparshClient
-
This method must return an ID for a group of points that should be processed together.
- getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- getGroupID(TouchPoint) - Method in class com.sparshui.server.ServerToClientProtocol
-
Retrieve a list of allowed gestures for the provided group id.
- getGroupID(String) - Method in class org.jmol.modelsetbio.BioResolver
- getGroupInfo(int, P3) - Method in class org.jmol.modelset.Group
- getGroupParameter(int) - Method in class org.jmol.modelset.Group
-
Monomers only
- getGroupParameter(int) - Method in class org.jmol.modelsetbio.Monomer
- getGroups() - Method in class org.jmol.modelset.ModelSet
-
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
- getGroupsWithin(int, BS) - Method in class org.jmol.modelset.ModelSet
- getGroupsWithin(int, BS) - Method in class org.jmol.viewer.Viewer
- getGroupsWithinAll(int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getGyromagneticRatio(String) - Static method in class jspecview.source.JDXDataObject
- getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in interface org.jmol.api.JmolAnnotationParser
- getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.AnnotationParser
- getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.DSSR1
- getHCount() - Method in class org.jmol.minimize.MinAtom
- getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getHeader(int) - Method in class javajs.util.LimitedLineReader
- getHeaderMap(InputStream, Map<String, String>) - Static method in class jspecview.source.JDXReader
- getHeaderMapS(InputStream, Map<String, String>, String) - Static method in class jspecview.source.JDXReader
- getHeaderRendererIcon(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getHeaderRowDataAsArray() - Method in class jspecview.source.JDXDataObject
- getHeaderRowDataAsArray(boolean, int) - Method in class jspecview.source.JDXHeader
- getHeaderRowDataAsArray(boolean, String[][]) - Method in class jspecview.source.JDXSource
- getHeaderTable() - Method in class jspecview.source.JDXHeader
-
Returns the table of headers
- getHeight() - Method in interface jspecview.api.JSVViewPanel
- getHeight() - Method in class jspecview.common.JSViewer
- getHeight() - Method in class jspecview.js2d.JsMainPanel
- getHeight() - Method in class jspecview.js2d.JsPanel
- getHeight() - Method in class org.jmol.awtjs.swing.Component
- getHeight() - Method in class org.jmol.util.Font
- getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
- getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
- getHelp(String) - Method in class org.jmol.viewer.Viewer
- getHermiteLevel() - Method in class org.jmol.viewer.Viewer
- getHermiteList(int, T3, T3, T3, T3, T3, T3[], int, int, boolean) - Static method in class org.jmol.util.GData
-
Used by Navigator, BioShapeRenderer, and DrawRenderer
- getHeteroList(int) - Method in class org.jmol.modelset.ModelSet
- getHexCode(short) - Static method in class org.jmol.util.C
- getHexCodes(short[]) - Static method in class org.jmol.util.C
- getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
- getHexitValue(char) - Static method in class org.jmol.util.Escape
- getHiddenCanvas(JSAppletObject, String, int, int) - Method in interface javajs.api.js.J2SObjectInterface
- getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
- getHistoryWindowPosition(String) - Method in interface org.jmol.api.JmolAppAPI
- getHistoryWindowPosition(String) - Method in class org.openscience.jmol.app.JmolApp
- getHistoryWindowSize(String) - Method in interface org.jmol.api.JmolAppAPI
- getHistoryWindowSize(String) - Method in class org.openscience.jmol.app.JmolApp
- getHklPlane(T3, float, Lst<P3>) - Method in class org.jmol.script.ScriptParam
- getHorizAlignmentName(int) - Static method in class org.jmol.viewer.JC
- getHoverDelay() - Method in class org.jmol.viewer.Viewer
- getHtmlDisabled() - Method in class org.jmol.awtjs.swing.AbstractButton
- getHtmlDisabled() - Method in class org.jmol.awtjs.swing.JMenuItem
- getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getHybridizationAndAxes(int, int, V3, V3, String, boolean, boolean, boolean, T3) - Method in class org.jmol.modelset.AtomCollection
- getHybridizationAndAxes(int, V3, V3, String) - Method in class org.jmol.viewer.Viewer
- getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the hydrogen atom count -- for ligand files
- getHydrogenCount() - Method in class jspecview.source.JDXDataObject
- getHydrogenCount(int) - Method in class jme.JMEmol
- getHydrophobicity() - Method in class org.jmol.modelset.Atom
- getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
- getHydrophobicity(int) - Static method in class org.jmol.util.Elements
- getIcon() - Method in interface org.jmol.api.SC
- getIcon() - Method in class org.jmol.awt.AwtSwingComponent
- getIcon() - Method in class org.jmol.awtjs.swing.AbstractButton
- getIconX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getIconX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getIconX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getId() - Method in enum class org.jmol.c.STR
- getID() - Method in class com.sparshui.server.Group
- getID() - Method in class com.sparshui.server.TouchPoint
-
Get the touch point ID.
- getIdentifierOrNull(String) - Method in class org.jmol.modelsetbio.BioModelSet
- getIdentity() - Method in class org.jmol.minimize.MinAtom
- getIdentity() - Method in class org.jmol.modelset.Bond
- getIdentityXYZ(P3, int) - Method in class org.jmol.modelset.Atom
- getIDStr() - Method in class org.jmol.modelset.Chain
- getImage(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- getImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
- getImage(Viewer, Object, String, boolean) - Method in class org.jmol.io.JmolUtil
- getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.api.JmolViewer
- getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in class jspecview.java.AwtPlatform
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in class jspecview.js2d.JsPlatform
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.GenericPlatform
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awt.Platform
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awtjs2d.Platform
- getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
- getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in class org.jmol.dialog.Dialog
- getImageHeight(Object) - Method in class jspecview.java.AwtPlatform
- getImageHeight(Object) - Method in class jspecview.js2d.JsPlatform
- getImageHeight(Object) - Method in interface org.jmol.api.GenericPlatform
- getImageHeight(Object) - Method in class org.jmol.awt.Platform
- getImageHeight(Object) - Method in class org.jmol.awtjs2d.Platform
- getImageIcon(String) - Method in class jspecview.java.AwtPopup
- getImageIcon(String) - Method in class jspecview.js2d.JsPopup
- getImageIcon(String) - Method in class org.jmol.awt.AwtJmolPopup
- getImageIcon(String) - Method in class org.jmol.awt.AwtModelKitPopup
- getImageIcon(String) - Method in class org.jmol.awtjs2d.JSJmolPopup
- getImageIcon(String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- getImageIcon(String) - Method in class org.jmol.popup.GenericPopup
- getImagEigenvalues() - Method in class javajs.util.Eigen
-
Return the imaginary parts of the eigenvalues
- getImageURL(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getImageWidth(Object) - Method in class jspecview.java.AwtPlatform
- getImageWidth(Object) - Method in class jspecview.js2d.JsPlatform
- getImageWidth(Object) - Method in interface org.jmol.api.GenericPlatform
- getImageWidth(Object) - Method in class org.jmol.awt.Platform
- getImageWidth(Object) - Method in class org.jmol.awtjs2d.Platform
- getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
- getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getImplicitHydrogenCount() - Method in interface org.jmol.util.Node
-
can be > 0 for PDB model with no H atoms or for SMILES string CCC
- getInchi(BS, Object, String) - Method in class org.jmol.viewer.Viewer
-
Get an InChI or InChIKey for a set of atoms or MOL data.
- getInchi(Viewer, BS, Object, String) - Method in interface org.jmol.api.JmolInChI
- getInchi(Viewer, BS, Object, String) - Method in class org.jmol.inchi.InChIJNI
- getInchi(Viewer, BS, Object, String) - Method in class org.jmol.inchi.InChIJS
- getInChI() - Method in class jspecview.java.AwtPlatform
- getInChI() - Method in class jspecview.js2d.JsPlatform
- getInChI() - Method in interface org.jmol.api.GenericPlatform
- getInChI() - Method in class org.jmol.awt.Platform
- getInChI() - Method in class org.jmol.awtjs2d.Platform
- getIndex() - Method in interface jspecview.api.JSVTreeNode
- getIndex() - Method in class jspecview.application.AwtTreeNode
- getIndex() - Method in class jspecview.common.PeakInfo
- getIndex() - Method in class jspecview.tree.SimpleTreeNode
- getIndex() - Method in class org.jmol.modelset.Atom
- getIndex() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atom index of the atom.
- getIndex() - Method in class org.jmol.symmetry.SpaceGroup
- getIndex() - Method in interface org.jmol.util.Node
- getIndex() - Method in interface org.jmol.util.SimpleNode
- getIndex(int, int, int, int) - Method in class org.jmol.modelsetbio.BioPolymer
- getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
- getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
- getIndexFromName(String) - Method in class org.jmol.shape.Shape
- getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
- getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
- getIndexFromName(String) - Method in class org.jmol.shapespecial.Polyhedra
- getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
- getInflater() - Method in class com.jcraft.jzlib.InflaterInputStream
- getInfo() - Method in class org.jmol.modelset.Atom
- getInfo() - Method in class org.jmol.symmetry.SymmetryOperation
- getInfo() - Method in class org.jmol.util.Font
- getInfo() - Method in class org.jmol.util.Modulation
- getInfo(boolean) - Method in class org.jmol.shape.Mesh
- getInfo(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getInfo(boolean, String) - Method in class jspecview.common.PanelData
- getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
- getInfo(int, String) - Method in class org.jmol.modelset.ModelSet
- getInfo(String) - Method in class jspecview.common.Spectrum
- getInfo(String) - Method in interface org.jmol.api.JmolNMRInterface
- getInfo(String) - Method in class org.jmol.quantum.NMRCalculation
- getInfo(String) - Method in class org.jmol.util.BoxInfo
-
for {*}.boundbox("info"|"volume"|"center"|null)
- getInfo(String) - Method in class org.jmol.util.Tensor
-
returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
- getInfo(Map<String, Object>) - Method in class jspecview.common.IntegralData
- getInfo(Map<String, Object>) - Method in class jspecview.common.PeakData
- getInfo(Map<String, Object>) - Method in class org.jmol.util.ModulationSet
- getInfo(Map<String, Object>) - Method in class org.jmol.util.Vibration
- getInfoAsString(int) - Method in class org.jmol.shape.Measures
- getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
- getInfoB(int, String) - Method in class org.jmol.modelset.ModelSet
- getInfoI(int, String) - Method in class org.jmol.modelset.ModelSet
- getInfoM(String) - Method in class org.jmol.modelset.ModelSet
- getInfoXYZ(Atom) - Method in class org.jmol.viewer.ChimeMessenger
-
called when an atom is picked
- getInfoXYZ(Atom) - Method in interface org.jmol.viewer.JmolChimeMessenger
- getInlineChar() - Method in class org.jmol.viewer.Viewer
- getInlineData() - Method in class jspecview.source.JDXDataObject
- getInlineData(int) - Method in class org.jmol.modelset.ModelSet
- getInlineData(SB, String, boolean, Integer, String) - Method in class org.jmol.viewer.StateCreator
- getInMotion(boolean) - Method in class org.jmol.viewer.Viewer
- getInput(String, String, String) - Method in interface jspecview.api.JSVPanel
- getInput(String, String, String) - Method in class jspecview.java.AwtPanel
- getInput(String, String, String) - Method in class jspecview.js2d.JsPanel
- getInputStream() - Method in interface javajs.api.GenericBinaryDocument
- getInputStream() - Method in class javajs.util.AjaxURLConnection
- getInputStream() - Method in class javajs.util.BinaryDocument
- getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- getInputStream(String, boolean, byte[]) - Static method in class jspecview.common.JSVFileManager
- getInsCode() - Method in class org.jmol.modelset.Group
- getInsertedCommand() - Method in class org.jmol.viewer.Viewer
- getInsertionCode() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getInsertionCode() - Method in class org.jmol.modelset.Atom
- getInsertionCode() - Method in class org.jmol.modelset.Group
- getInsertionCode() - Method in class org.jmol.smiles.SmilesAtom
- getInsertionCode() - Method in interface org.jmol.util.Node
- getInsertionCodeChar(int) - Static method in class org.jmol.modelset.Group
- getInsertionCodeFor(int) - Static method in class org.jmol.modelset.Group
- getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
- getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getInstance() - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getInstanceWithParams(String, Class<?>[], Object...) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getInt(int) - Method in class org.jmol.api.JmolViewer
- getInt(int) - Method in class org.jmol.shapecgo.CGOMesh
- getInt(int) - Method in class org.jmol.viewer.Viewer
- getInt(Map<String, Object>, String) - Method in class org.molecularplayground.MPJmolApp
- getInt(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getInt4(int, byte[]) - Static method in class javajs.img.PngEncoder
- getIntArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
-
Retrieve an int array, possibly unpacking it if it is run-length encoded.
- getIntArray2(int) - Method in class org.jmol.scriptext.ScriptExt
- getIntArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
turn "[1,2,3]" into [1,2,3] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
- getIntegralFactor() - Method in class jspecview.common.IntegralData
- getIntegration() - Method in class org.jmol.quantum.QuantumCalculation
- getIntegrationRatiosFromString(Spectrum, String) - Static method in class jspecview.common.IntegralData
-
Parses x-coordinates and values from a string and returns them as
IntegrationRatio
objects - getInterface(String) - Static method in class javajs.api.Interface
- getInterface(String) - Static method in class jspecview.common.JSViewer
- getInterface(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getInterface(String, Viewer, String) - Static method in class org.jmol.api.Interface
- getIntersection(float, P4, P3[], Lst<P3[]>, float[], BS, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSlicer
- getIntersection(P3, V3, P4, P3, V3, V3) - Static method in class javajs.util.Measure
-
Calculate the intersection of a line with a plane.
- getIntersectionPP(P4, P4) - Static method in class javajs.util.Measure
-
Calculate the line that is the intersection of two planes.
- getInts(byte[], int) - Static method in class javajs.util.MessagePackReader
-
mmtf types 2-4 Decode a byte array into a byte, short, or int array.
- getIntTableIndex() - Method in interface org.jmol.api.SymmetryInterface
- getIntTableIndex() - Method in class org.jmol.symmetry.Symmetry
- getIntTableNumber() - Method in interface org.jmol.api.SymmetryInterface
- getIntTableNumber() - Method in class org.jmol.symmetry.Symmetry
- getIntTableNumberFull() - Method in interface org.jmol.api.SymmetryInterface
- getIntTableNumberFull() - Method in class org.jmol.symmetry.Symmetry
- getIntTableTransform() - Method in interface org.jmol.api.SymmetryInterface
- getIntTableTransform() - Method in class org.jmol.symmetry.Symmetry
- getInvariantSymops(P3, int[]) - Method in interface org.jmol.api.SymmetryInterface
- getInvariantSymops(P3, int[]) - Method in class org.jmol.symmetry.Symmetry
- getInverseNormix(short) - Static method in class org.jmol.util.Normix
- getIsHetero() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getIsoExt() - Method in class org.jmol.script.ScriptEval
- getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in interface org.jmol.api.JmolNMRInterface
-
If t is null, then a1, a2, and type are used to find the appropriate tensor.
- getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
- getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
- getIsotope() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getIsotopeNumber() - Method in class org.jmol.modelset.Atom
- getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
- getIsotopeNumber() - Method in interface org.jmol.util.Node
- getIsotopeNumber() - Method in interface org.jmol.util.SimpleNode
- getIsotopeNumber(int) - Static method in class org.jmol.util.Elements
- getItaIndex() - Method in class org.jmol.symmetry.SpaceGroup
- getITASettingValue(Viewer, String, String) - Method in interface org.jmol.api.SymmetryInterface
- getITASettingValue(Viewer, String, String) - Method in class org.jmol.symmetry.Symmetry
- getItem(int) - Method in class org.jmol.awtjs.swing.JMenu
- getItem(int) - Static method in class org.jmol.quantum.QS
- getItemCount() - Method in class org.jmol.awtjs.swing.JMenu
- getItemType(SC) - Method in class org.jmol.awt.AwtPopupHelper
- getItemType(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getItemType(SC) - Method in interface org.jmol.popup.PopupHelper
- getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelSet
-
only some models can be iterated through.
- getIterator(Viewer, Atom, BS, float) - Method in interface org.jmol.api.SymmetryInterface
- getIterator(Viewer, Atom, BS, float) - Method in class org.jmol.symmetry.Symmetry
- getJavaConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getJavaConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Deprecated.
- getJBR() - Method in class org.jmol.viewer.Viewer
- getJcampdx() - Method in class jspecview.source.JDXHeader
-
Getter for property jcampdx.
- getJCouplingHz(Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
- getJDXBaseModelIndex(int) - Method in class org.jmol.viewer.Viewer
-
get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
- getJDXSpectrum(int) - Method in class jspecview.source.JDXSource
-
Returns the Spectrum at a given index in the list
- getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
- getJmol(JFrame, int, int, Map<String, Object>) - Static method in class org.openscience.jmol.app.Jmol
- getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.Jmol
- getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelSet
- getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelSet
- getJmolDistance(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
- getJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Calc using Jmol atom index
- getJmolFilePath(String) - Static method in class jspecview.common.JSVFileManager
- getJmolFrameType(int) - Method in class org.jmol.modelset.ModelSet
- getJmolNoe(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
- getJmolNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getJmolParameter(String) - Method in class org.jmol.util.GenericApplet
- getJmolPerspective() - Method in class org.jmol.export.___Exporter
- getJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getJmolValueAsString(Viewer, String) - Static method in class org.molecularplayground.MPJmolApp
- getJmolVersion() - Static method in class org.jmol.api.JmolViewer
- getJmolVersion() - Static method in class org.jmol.viewer.Viewer
- getJmolVersionNoDate() - Static method in class org.jmol.api.JmolViewer
- getJsObjectInfo(Object[], String, Object[]) - Method in class jspecview.java.AwtPlatform
- getJsObjectInfo(Object[], String, Object[]) - Method in class jspecview.js2d.JsPlatform
- getJsObjectInfo(Object[], String, Object[]) - Method in interface org.jmol.api.GenericPlatform
- getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awt.Platform
- getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awtjs2d.Platform
- getJsonNioServer() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getJspecViewProperties(Object) - Method in class org.jmol.viewer.Viewer
- getJSpecViewProperty(String) - Method in class jspecview.application.MainFrame
- getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolStatusListener
- getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolSyncInterface
- getJSpecViewProperty(String) - Method in class org.jmol.util.GenericApplet
-
JSpecView shares the JmolSyncInterface; used to get JSpecView
- getJSpecViewProperty(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- getJSVPanel(JSViewer, Lst<Spectrum>) - Method in interface jspecview.api.AppletFrame
- getJSVPanel(JSViewer, Lst<Spectrum>) - Method in class jspecview.appletjs.JSVApplet
- getJVXLCutoff() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getJVXLCutoff() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getJzt() - Method in class org.jmol.viewer.Viewer
- getJzu() - Method in class org.jmol.viewer.FileManager
- getKey() - Method in interface org.jmol.api.JmolAbstractButton
- getKey() - Method in class org.jmol.console.JmolButton
- getKey() - Method in class org.jmol.console.JmolLabel
- getKey() - Method in class org.jmol.console.JmolToggleButton
- getKey() - Method in class org.jmol.console.KeyJCheckBox
- getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
- getKey() - Method in class org.jmol.console.KeyJMenu
- getKey() - Method in class org.jmol.console.KeyJMenuItem
- getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
- getKey(int, int, int, int, int) - Static method in class org.jmol.minimize.MinObject
- getKey(ScriptTokenizer) - Static method in enum class jspecview.common.ScriptToken
- getKeyMap() - Static method in class org.jmol.shapecgo.CGOMesh
- getKeys(boolean) - Method in class org.jmol.script.SV
- getLabel(int) - Method in class org.jmol.shape.Labels
- getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
- getLabel(String) - Static method in class org.jmol.console.GenericConsole
- getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
- getLabel1() - Method in class org.jmol.console.AppletConsole
- getLabel1() - Method in class org.jmol.console.GenericConsole
- getLabelArray() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- getLabeler() - Method in class org.jmol.modelset.AtomCollection
- getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.GenericConsole
- getLanguage() - Static method in class org.jmol.i18n.GT
- getLanguageList() - Static method in class org.jmol.i18n.Language
-
This is the place to put the list of supported languages.
- getLanguageList(GT) - Static method in class org.jmol.i18n.GT
- getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getLastError() - Static method in exception class org.jmol.smiles.InvalidSmilesException
- getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
- getLastException() - Method in class org.jmol.smiles.SmilesMatcher
- getLastFileFirstNode(Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
- getLastIndex() - Method in class org.jmol.modelset.Measurement
- getLastPathComponent() - Method in interface jspecview.api.JSVTreePath
- getLastPathComponent() - Method in class jspecview.tree.SimpleTreePath
- getLastVibrationVector(int, int) - Method in class org.jmol.modelset.ModelSet
- getLastX() - Method in class jspecview.source.JDXDataObject
-
Returns the last X value
- getLastY() - Method in class jspecview.source.JDXDataObject
-
Returns the last Y value
- getLatticeCentering() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeCentering() - Method in class org.jmol.symmetry.Symmetry
- getLatticeCentering(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
- getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
- getLatticeOp() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeOp() - Method in class org.jmol.symmetry.Symmetry
- getLatticePoints(Lst<P3>, int, int, int) - Static method in class javajs.util.Measure
-
Based on a set of centering points, creates a list of lattice points in place.
- getLatticeType() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeType() - Method in class org.jmol.symmetry.Symmetry
- getLeadAtom() - Method in class org.jmol.modelset.Group
- getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
- getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
- getLeadAtomOr(Atom) - Method in class org.jmol.modelset.Group
- getLeadColix(int) - Method in class org.jmol.renderbio.BackboneRenderer
- getLeadColix(int) - Method in class org.jmol.renderbio.CartoonRenderer
- getLeadColix(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- getLeadColix(int) - Method in class org.jmol.renderbio.RibbonsRenderer
- getLeadColix(int) - Method in class org.jmol.renderbio.RocketsRenderer
- getLeadColix(int) - Method in class org.jmol.renderbio.StrandsRenderer
- getLeadColix(int) - Method in class org.jmol.renderbio.TraceRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.BackboneRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.CartoonRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.RibbonsRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.RocketsRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.StrandsRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.TraceRenderer
- getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
- getLength(int) - Method in class org.jmol.shapespecial.Ellipsoid
- getLength(Object) - Static method in class javajs.util.AU
- getLevel(int) - Static method in class org.jmol.util.Logger
-
Returns the text corresponding to a level.
- getlexpNoes() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getLigandInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
- getLigandInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getLigandModel(String, String, String, String) - Method in class org.jmol.viewer.Viewer
-
obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state
- getLightingState() - Method in class org.jmol.viewer.Viewer
- getLightSource() - Method in class org.jmol.util.GData
- getLimitedStreamBytes(InputStream, long) - Static method in class javajs.util.Rdr
-
Read a possibly limited number of bytes (when n > 0) from a stream, leaving the stream open.
- getLine() - Method in class org.jmol.jvxl.readers.XmlReader
- getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEval
- getList() - Method in class org.jmol.script.SV
- getList(Object, String) - Static method in class org.qcschema.QCSchemaUnits
-
Retrieve an array of any sort as a list of objects, possibly unpacking it if it is run-length encoded.
- getList(String) - Method in class org.jmol.symmetry.CIPData
-
Retrieve an array of bit sets that match a given SMARTS
- getList(String) - Method in class org.jmol.symmetry.CIPDataSmiles
- getLoadSymmetryParams(int, SB, Map<String, Object>) - Method in class org.jmol.scriptext.CmdExt
- getLocalDirectory(Viewer, boolean) - Static method in class org.jmol.viewer.FileManager
- getLocalPathForWritingFile(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
- getLocalUrl(String) - Method in class jspecview.java.AwtPlatform
- getLocalUrl(String) - Method in class jspecview.js2d.JsPlatform
- getLocalUrl(String) - Method in interface org.jmol.api.GenericPlatform
- getLocalUrl(String) - Method in class org.jmol.awt.Platform
- getLocalUrl(String) - Method in class org.jmol.awtjs2d.Platform
- getLocalUrl(String) - Method in class org.jmol.viewer.Viewer
- getLocation() - Method in class com.sparshui.server.TouchPoint
-
Get the touch point location.
- getLocationOnScreen(Object) - Method in class jspecview.dialog.DialogManager
- getLocationOnScreen(Object) - Method in class jspecview.java.AwtDialogManager
- getLocationOnScreen(Object) - Method in class jspecview.js2d.JsDialogManager
- getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
- getLogFileName() - Method in class org.jmol.viewer.Viewer
- getLogLevel() - Static method in class org.jmol.util.Logger
- getLogPath(String) - Method in class org.jmol.viewer.OutputManagerAwt
- getLogPath(String) - Method in class org.jmol.viewer.OutputManagerJS
- getLong(Map<String, Object>, String) - Method in class org.molecularplayground.MPJmolApp
- getLong(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getLongDate() - Method in class jspecview.source.JDXHeader
-
Getter for property longDate.
- getMacro(String) - Method in class org.jmol.viewer.Viewer
-
retrieve macros.json from the directory
- getMadBond() - Method in class org.jmol.api.JmolViewer
- getMadBond() - Method in class org.jmol.viewer.Viewer
- getMadParameter() - Method in class org.jmol.script.ScriptParam
- getMagic(InputStream, int) - Static method in class javajs.util.Rdr
- getMagneticShielding(Atom) - Method in interface org.jmol.api.JmolNMRInterface
- getMagneticShielding(Atom) - Method in class org.jmol.quantum.NMRCalculation
- getManifestScriptPath(String) - Static method in class org.jmol.viewer.FileManager
-
check a JmolManifest for a reference to a script file (.spt)
- getMap() - Method in class org.jmol.script.SV
- getMapForJME(String, Atom[], BS) - Method in interface org.jmol.api.SmilesMatcherInterface
- getMapForJME(String, Atom[], BS) - Method in class org.jmol.smiles.SmilesMatcher
- getMapForStream(BufferedInputStream) - Method in class javajs.util.MessagePackReader
- getMapKeys(int, boolean) - Method in class org.jmol.script.SV
- getMapValueNoCase(Map<String, ?>, String) - Static method in class javajs.util.PT
- getMass() - Method in class org.jmol.modelset.Atom
- getMass() - Method in class org.jmol.smiles.SmilesAtom
- getMass() - Method in interface org.jmol.util.Node
- getMass() - Method in interface org.jmol.util.SimpleNode
- getMatch() - Method in class jspecview.common.PeakInfo
- getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the matching atom or null.
- getMatchingAtomIndex() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the number of a matching atom in a molecule.
- getMatchingBond() - Method in class org.jmol.smiles.SmilesBond
- getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
- getMathExt() - Method in class org.jmol.script.ScriptEval
- getMatrix() - Method in class javajs.util.Quat
- getMatrix4f(M3, T3) - Static method in class org.jmol.script.ScriptMathProcessor
- getMatrixAndUnitCell(SimpleUnitCell, Object, M4) - Static method in class org.jmol.symmetry.UnitCell
- getMatrixFromString(String, float[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
-
MMCifReader only
- getMatrixFromString(SymmetryOperation, String, float[], boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format
- getMatrixFromXYZ(String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getMatrixSelected(int[], int) - Method in class javajs.util.Matrix
-
Get a submatrix for a give number of columns and selected row set.
- getMaxDim() - Method in class org.jmol.util.BoxInfo
- getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
- getMaxX() - Method in class jspecview.source.JDXDataObject
-
Calculates and returns the maximum x value in the list of coordinates Fairly expensive operation
- getMaxX(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
-
Returns the maximum x value value from an array of arrays of
Coordinate
s. - getMaxX(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
-
Returns the minimum x value of an array of
Coordinate
s - getMaxY() - Method in class jspecview.source.JDXDataObject
-
Calculates and returns the maximum y value in the list of coordinates Fairly expensive operation
- getMaxY() - Method in class jspecview.source.JDXDecompressor
- getMaxY(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
-
Returns the maximum y value of an array of
Coordinate
s - getMaxYUser(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
-
Returns the maximum y value value from an array of arrays of
Coordinate
s. - getMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
- getMeasurementCount() - Method in class org.jmol.api.JmolViewer
- getMeasurementCount() - Method in class org.jmol.viewer.Viewer
- getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
- getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
- getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
- getMeasurementListArray(String) - Method in class jspecview.common.IntegralData
- getMeasurementListArray(String) - Method in class jspecview.common.MeasurementData
- getMeasurementListArray(String) - Method in class jspecview.common.PeakData
- getMeasurementListArrayReal(String) - Method in class jspecview.common.IntegralData
- getMeasurementListArrayReal(String) - Method in class jspecview.common.PeakData
- getMeasurements(boolean, boolean) - Method in class org.jmol.modelset.MeasurementData
-
if this is the client, then this method can be called to get the result vector, either as a string or as an array.
- getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
-
Used by MouseManager and Picking Manager to build the script
- getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
- getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
- getMeasurementTable() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getMenu(String) - Method in class org.jmol.awt.AwtPopupHelper
- getMenu(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getMenu(String) - Method in interface org.jmol.popup.PopupHelper
- getMenu(String) - Method in class org.jmol.viewer.Viewer
- getMenuAsText(String) - Method in class jspecview.popup.JSVPopupResourceBundle
- getMenuAsText(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- getMenuAsText(String) - Method in class org.jmol.popup.MainPopupResourceBundle
- getMenuAsText(String) - Method in class org.jmol.popup.PopupResource
- getMenuHTML() - Method in class org.jmol.awtjs.swing.AbstractButton
- getMenuIcon() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getMenuIcon() - Method in interface org.openscience.jmol.app.JmolPlugin
- getMenuItem(String) - Method in class org.jmol.awt.AwtPopupHelper
- getMenuItem(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getMenuItem(String) - Method in interface org.jmol.popup.PopupHelper
- getMenuItem(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Fetch the menu item that was created for the given command.
- getMenuName() - Method in class jspecview.popup.JSVPopupResourceBundle
- getMenuName() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- getMenuName() - Method in class org.jmol.popup.MainPopupResourceBundle
- getMenuName() - Method in class org.jmol.popup.PopupResource
- getMenuPopup(String, char) - Method in class jspecview.java.AwtPlatform
- getMenuPopup(String, char) - Method in class jspecview.js2d.JsPlatform
- getMenuPopup(String, char) - Method in interface org.jmol.api.GenericPlatform
- getMenuPopup(String, char) - Method in class org.jmol.awt.Platform
- getMenuPopup(String, char) - Method in class org.jmol.awtjs2d.Platform
- getMenuScript(String) - Static method in class org.jmol.viewer.JC
- getMenuText() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getMenuText() - Method in interface org.openscience.jmol.app.JmolPlugin
- getMesh(String) - Method in class org.jmol.shape.MeshCollection
- getMeshList(String, boolean) - Method in class org.jmol.shape.MeshCollection
-
Get matching list of meshes, order reversed
- getMeshSlicer() - Method in class org.jmol.util.MeshSurface
- getMessage() - Method in exception class org.jmol.script.ScriptException
- getMessage() - Method in exception class org.jmol.smiles.InvalidSmilesException
- getMFArray(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
- getMinDistance2ForVertexGrouping() - Method in class org.jmol.shape.Mesh
- getMinDistance2ForVertexGrouping() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getMinDistances(MeasurementData) - Method in interface org.jmol.api.JmolNMRInterface
- getMinDistances(MeasurementData) - Method in class org.jmol.quantum.NMRCalculation
- getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
- getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
- getMinindex() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- getMinindex() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getMinMax() - Method in class jme.JMEmol
- getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
- getMinMax(Object, int, boolean) - Method in class org.jmol.scriptext.MathExt
- getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getMinX() - Method in class jspecview.source.JDXDataObject
-
Calculates and returns the minimum x value in the list of coordinates Fairly expensive operation
- getMinX(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
-
Returns the minimum x value value from an array of arrays of
Coordinate
s. - getMinX(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
-
Returns the minimum x value of an array of
Coordinate
s - getMinY() - Method in class jspecview.source.JDXDataObject
-
Calculates and returns the minimum y value in the list of coordinates Fairly expensive operation
- getMinY() - Method in class jspecview.source.JDXDecompressor
- getMinY(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
-
Returns the minimum y value of an array of
Coordinate
s - getMinYUser(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
-
Returns the minimum y value value from an array of arrays of
Coordinate
s. - getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
- getMissingHydrogenCount(Atom, boolean) - Method in class org.jmol.modelset.AtomCollection
- getMixingTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
get the mixing time
- getMixingTimeSec() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get the mixing time
- getMKState() - Method in class org.jmol.modelkit.ModelKit
- getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in interface org.jmol.api.SmilesMatcherInterface
- getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in class org.jmol.smiles.SmilesMatcher
-
called by ForceFieldMMFF.setAtomTypes only
- getMod(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.
- getMod(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getMode(String) - Static method in enum class jspecview.common.PanelData.LinkMode
- getMode(String) - Static method in enum class jspecview.common.Spectrum.IRMode
- getModel() - Method in class jspecview.common.PeakInfo
- getModel() - Method in class org.jmol.modelset.Group
-
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
- getModelAdapter() - Method in class org.jmol.api.JmolViewer
- getModelAdapter() - Method in class org.jmol.viewer.Viewer
- getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelSet
-
Note that this method returns all atoms, included deleted ones.
- getModelAtomBitSetIncludingDeletedBs(BS) - Method in class org.jmol.modelset.ModelSet
-
note -- this method returns ALL atoms, including deleted.
- getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelSet
- getModelBS(int, BS) - Method in class org.jmol.modelset.Trajectory
-
set bits for all trajectories associated with this model
- getModelBS(BS, boolean) - Method in class org.jmol.modelset.ModelSet
-
Get the set of models associated with a set of atoms.
- getModelCellRange(int) - Method in class org.jmol.modelset.ModelSet
- getModelCenter() - Method in class org.jmol.export.__CartesianExporter
- getModelCml(BS, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getModelCml(BS, int, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getModelCml(BS, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
- getModelCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getModelDataBaseName(BS) - Method in class org.jmol.modelset.ModelSet
- getModelDipole() - Method in class org.jmol.viewer.Viewer
- getModelDipole(int) - Method in class org.jmol.modelset.ModelSet
- getModelExtract(Object, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
-
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
- getModelExtract(BS, boolean, boolean, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getModelExtract(BS, boolean, boolean, String, boolean) - Method in class org.jmol.viewer.PropertyManager
-
V3000, SDF, MOL, JSON, CD (ChemDoodle), XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON, PWMAT, XSF MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)
- getModelFileData(String, String, boolean) - Method in class org.jmol.viewer.Viewer
- getModelFileInfo() - Method in class org.jmol.viewer.Viewer
- getModelFileInfo(BS) - Method in interface org.jmol.api.JmolPropertyManager
- getModelFileInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
- getModelFileName(int) - Method in class org.jmol.modelset.ModelSet
- getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
- getModelFileType(int) - Method in class org.jmol.modelset.ModelSet
- getModelForAtomIndex(int) - Method in class org.jmol.viewer.Viewer
- getModelIndex() - Method in class org.jmol.modelset.Atom
-
SMILES only
- getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
- getModelIndex() - Method in interface org.jmol.util.Node
- getModelIndexForAtom(int) - Method in class org.jmol.viewer.Viewer
- getModelIndexFromId(String) - Method in interface org.jmol.api.JmolAppletInterface
- getModelIndexFromId(String) - Method in class org.jmol.api.JmolViewer
- getModelIndexFromId(String) - Method in class org.jmol.modelset.ModelSet
- getModelIndexFromId(String) - Method in class org.jmol.util.GenericApplet
- getModelIndexFromId(String) - Method in class org.jmol.viewer.Viewer
- getModelIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
- getModelIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getModelInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
- getModelInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getModelInfo(String) - Method in class org.jmol.viewer.Viewer
-
get a value from the current model's Model.auxiliaryInfo
- getModelInfoAsString() - Method in class org.jmol.modelset.ModelSet
- getModelkit(boolean) - Method in class org.jmol.viewer.Viewer
- getModelkitPropertySafely(String) - Method in class org.jmol.viewer.Viewer
-
Get a ModelKit property.
- getModelName(int) - Method in class org.jmol.api.JmolViewer
- getModelName(int) - Method in class org.jmol.modelset.ModelSet
- getModelName(int) - Method in class org.jmol.viewer.Viewer
- getModelNumber() - Method in class org.jmol.modelset.Atom
- getModelNumber(int) - Method in class org.jmol.api.JmolViewer
- getModelNumber(int) - Method in class org.jmol.modelset.ModelSet
- getModelNumber(int) - Method in class org.jmol.viewer.Viewer
- getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
- getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelSet
- getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
- getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
- getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
- getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- getModelOrientation(int) - Method in class org.jmol.modelset.ModelSet
- getModelPeakInfoForAutoSelectOnLoad() - Method in class jspecview.common.Spectrum
- getModelProperties(int) - Method in class org.jmol.api.JmolViewer
- getModelProperties(int) - Method in class org.jmol.viewer.Viewer
- getModelProperty(int, String) - Method in class org.jmol.modelset.ModelSet
- getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
- getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
- getModelSetAuxiliaryInfo(BS) - Method in class org.jmol.modelset.ModelSet
-
Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.
- getModelSetAuxiliaryInfoForAtoms(Object) - Method in class org.jmol.viewer.Viewer
- getModelSetFileName() - Method in class org.jmol.api.JmolViewer
- getModelSetFileName() - Method in class org.jmol.viewer.Viewer
- getModelSetPathName() - Method in class org.jmol.api.JmolViewer
- getModelSetPathName() - Method in class org.jmol.viewer.Viewer
- getModelSetProperties() - Method in class org.jmol.api.JmolViewer
- getModelSetProperties() - Method in class org.jmol.viewer.Viewer
- getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
- getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelSet
- getModelTitle(int) - Method in class org.jmol.modelset.ModelSet
- getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
- getModelUndeletedAtomsBitSetBs(BS) - Method in class org.jmol.viewer.Viewer
- getModifiedTime() - Method in class com.jcraft.jzlib.GZIPHeader
- getModPoint(boolean) - Method in interface org.jmol.api.JmolModulationSet
- getModPoint(boolean) - Method in class org.jmol.util.ModulationSet
- getModType(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getModType(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getModulation() - Method in class org.jmol.modelset.Atom
- getModulation(char, T3, boolean) - Method in interface org.jmol.api.JmolModulationSet
- getModulation(char, T3, boolean) - Method in class org.jmol.util.ModulationSet
- getModulation(int) - Method in class org.jmol.modelset.AtomCollection
- getModulationList(BS, char, P3) - Method in class org.jmol.modelset.ModelSet
- getModulationMap() - Method in class org.jmol.adapter.readers.cif.MSRdr
- getModulationMap() - Method in interface org.jmol.adapter.smarter.MSInterface
- getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- getMoInfo(int) - Method in class org.jmol.shapesurface.MolecularOrbital
- getMolecularFormula(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
- getMolecularFormula(String, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
- getMolecularFormula(String, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
- getMolecularFormulaAtoms(Node[], BS, float[], boolean) - Static method in class org.jmol.util.JmolMolecule
- getMoleculeBitSet(BS) - Method in class org.jmol.modelset.ModelSet
-
return cumulative sum of all atoms in molecules containing these atoms
- getMoleculeBitSetForAtom(int) - Method in class org.jmol.modelset.ModelSet
- getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelSet
- getMoleculeInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
- getMoleculeNumber(boolean) - Method in class org.jmol.smiles.SmilesAtom
- getMoleculeNumber(boolean) - Method in interface org.jmol.util.Node
- getMolecules() - Method in class org.jmol.modelset.ModelSet
- getMolecules(Node[], BS[], Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
-
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
- getMonomerIndex() - Method in class org.jmol.modelset.Group
- getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMoreInfo() - Method in interface org.jmol.api.SymmetryInterface
- getMoreInfo() - Method in class org.jmol.symmetry.Symmetry
- getMOString(float[]) - Static method in class org.jmol.quantum.QS
- getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
- getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
- getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
- getMotionFixedAtoms(SymmetryInterface, BS) - Method in class org.jmol.viewer.Viewer
-
For the current SINGLE model only.
- getMouseAction(int, int, int) - Static method in class org.jmol.viewer.binding.Binding
- getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
- getMouseActionStr(String) - Static method in class org.jmol.viewer.binding.Binding
-
create an action code from a string such as "CTRL-LEFT-double click"
- getMouseEnabled() - Method in class org.jmol.viewer.Viewer
- getMouseManager(double, Object) - Method in class jspecview.java.AwtPlatform
- getMouseManager(double, Object) - Method in class jspecview.js2d.JsPlatform
- getMouseManager(double, Object) - Method in interface org.jmol.api.GenericPlatform
- getMouseManager(double, Object) - Method in class org.jmol.awt.Platform
- getMouseManager(double, Object) - Method in class org.jmol.awtjs2d.Platform
- getMoveToText(boolean) - Method in class org.jmol.modelset.Orientation
- getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
- getMSInfoB(String) - Method in class org.jmol.modelset.ModelSet
- getMyInfo(P3) - Method in class org.jmol.modelsetbio.Monomer
- getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getName() - Method in class com.jcraft.jzlib.GZIPHeader
- getName() - Method in interface com.sparshui.gestures.Gesture
-
Get the name of this gesture.
- getName() - Method in class javajs.util.OC
- getName() - Method in interface org.jmol.api.GenericFileInterface
- getName() - Method in interface org.jmol.api.JmolAbstractButton
- getName() - Method in interface org.jmol.api.JmolScriptFunction
- getName() - Method in interface org.jmol.api.SC
- getName() - Method in class org.jmol.awt.AwtSwingComponent
- getName() - Method in class org.jmol.awtjs.swing.Component
- getName() - Method in enum class org.jmol.c.STER
- getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
- getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- getName() - Method in class org.jmol.script.ScriptFunction
- getName() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getName() - Method in interface org.openscience.jmol.app.JmolPlugin
- getNameList() - Static method in enum class org.jmol.c.CBK
- getNameList(Lst<ScriptToken>) - Static method in enum class jspecview.common.ScriptToken
- getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
- getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
- getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
- getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
- getNavigationState() - Method in interface org.jmol.api.JmolNavigatorInterface
- getNavigationState() - Method in class org.jmol.navigate.Navigator
- getNavigationState() - Method in class org.jmol.viewer.TransformManager
- getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
- getNavPtHeight() - Method in class org.jmol.viewer.TransformManager
- getNBOAtomLabel(Atom) - Method in class org.jmol.adapter.readers.quantum.NBOParser
-
get the
- getNBOAtomLabel(Atom) - Method in class org.jmol.viewer.Viewer
- getNBOTypeFromName(String) - Static method in class org.jmol.viewer.JC
- getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
- getNearestIndexForX(Coordinate[], double) - Static method in class jspecview.common.Coordinate
- getNearestXWithYAbove(Coordinate[], double, double, boolean, boolean) - Static method in class jspecview.common.Coordinate
-
discovers nearest peak left or right of x that is above threshold y
- getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
- getNetByID(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find or create a net with this netID, giving it a default name "Net"+id
- getNetFor(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find or create a TNet for this id and label.
- getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
- getNewDfCoefMap() - Static method in class org.jmol.quantum.QS
- getNewScales(int, boolean, double, double) - Method in class jspecview.common.ViewData
- getNext(Object, int) - Method in class javajs.util.MessagePackReader
- getNextDataToken() - Method in interface javajs.api.GenericCifDataParser
- getNextDataToken() - Method in class javajs.util.CifDataParser
-
first checks to see if the next token is an unquoted control code, and if so, returns null
- getNextStatement() - Method in interface org.jmol.api.JmolScriptEvaluator
- getNextStatement() - Method in class org.jmol.script.ScriptEval
-
when paused, indicates what statement will be next
- getNextToken() - Method in interface javajs.api.GenericCifDataParser
- getNextToken() - Method in class javajs.util.CifDataParser
-
Get a token as a String value (for the reader)
- getNextTokenObject() - Method in class javajs.util.CifDataParser
-
Get the token as a Java Object
- getNextTokenProtected() - Method in class javajs.util.CifDataParser
-
Just makes sure
- getNextVoxelValue() - Method in class org.jmol.jvxl.readers.JvxlReader
- getNextVoxelValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getNextVoxelValue() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getNHPoint(P3, V3, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
- getNitrogenAtom() - Method in class org.jmol.modelset.Group
- getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getNMRCalculation() - Method in class org.jmol.viewer.Viewer
- getNmrDataJSON() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- getNMRfreq() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
gets the NMR frequency
- getNMRfreqMHz() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
gets the NMR frequency
- getNMRPredict(String) - Method in class org.jmol.viewer.Viewer
- getNoeExprefValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getnoeNPrefIndices() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getNOEorJHH(Atom[], int) - Method in interface org.jmol.api.JmolNMRInterface
- getNOEorJHH(Atom[], int) - Method in class org.jmol.quantum.NMRCalculation
- getNoesy() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get if NOESY or ROESY was used for simulation
- getNoesy() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getNoeWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- getNominalMass() - Method in class org.jmol.modelset.Atom
- getNominalSpecFreq(String, double) - Static method in class jspecview.source.JDXDataObject
- getNormal() - Method in class javajs.util.Quat
- getNormalDirected(V3) - Method in class javajs.util.Quat
- getNormalFromCenter(P3, P3, P3, P3, boolean, V3, V3) - Static method in class javajs.util.Measure
- getNormalMap(T3[], int, BS, Lst<String>) - Method in class org.jmol.export.__CartesianExporter
- getNormals(T3[], P4) - Method in class org.jmol.shape.Mesh
- getNormalsTemp() - Method in class org.jmol.shape.Mesh
- getNormalThroughPoints(T3, T3, T3, T3, T3) - Static method in class javajs.util.Measure
- getNormalToLine(P3, P3, V3) - Static method in class javajs.util.Measure
- getNormixCount() - Static method in class org.jmol.util.Normix
- getNormixes() - Method in class org.jmol.shapespecial.Polyhedron
- getNormixV(V3, BS) - Static method in class org.jmol.util.Normix
- getNoValue() - Method in class org.jmol.quantum.NciCalculation
- getNoValue() - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
- getNPoints() - Method in class com.sparshui.common.messages.events.DragEvent
- getNPointsFound() - Method in class jspecview.source.JDXDecompressor
-
Report out the number of points found (for error reporting)
- getNumberOfGraphSets() - Method in class jspecview.common.PanelData
-
Returns the Number of Graph sets
- getNumberOfSpectra() - Method in class jspecview.source.JDXSource
-
Returns the number of Spectra in this Source
- getNumberOfSpectraInCurrentSet() - Method in class jspecview.common.PanelData
- getNumDim() - Method in class jspecview.source.JDXDataObject
- getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEval
- getObjectColix(int) - Method in class org.jmol.viewer.Viewer
- getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
- getObjectMad10(int) - Method in class org.jmol.viewer.Viewer
- getObjectMap(Map<String, ?>, char) - Method in class org.jmol.viewer.Viewer
-
used in autocompletion in console using TAB
- getObservedFreq() - Method in class jspecview.source.JDXDataObject
-
Returns the observed frequency (for NMR Spectra)
- getObservedNucleus() - Method in class jspecview.source.JDXDataObject
-
^1H, ^13C, for example
- getOccupancy() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getOccupancy100() - Method in class org.jmol.modelset.Atom
- getOccupancy100(boolean) - Method in class org.jmol.util.ModulationSet
- getOccupancy100(boolean) - Method in class org.jmol.util.Vibration
- getOccupancyFloat(int) - Method in class org.jmol.modelset.AtomCollection
- getOffset(int, int, boolean) - Static method in class org.jmol.viewer.JC
-
Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered".
- getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
- getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
- getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.Node
- getOffsetVertices(P4) - Method in class org.jmol.shape.Mesh
- geTokens() - Method in interface org.jmol.api.JmolScriptFunction
- geTokens() - Method in class org.jmol.script.ScriptFunction
- getOpacity255() - Method in interface javajs.api.GenericColor
- getOpacity255() - Method in class jspecview.java.AwtColor
- getOpacity255() - Method in class org.jmol.awt.AwtColor
- getOpacity255() - Method in class org.jmol.awtjs.swing.Color
- getOpAxis() - Method in class org.jmol.symmetry.SymmetryOperation
- getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
- getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in class org.jmol.dialog.Dialog
- getOpenSmiles(BS) - Method in class org.jmol.api.JmolViewer
- getOpenSmiles(BS) - Method in class org.jmol.viewer.Viewer
- getOperationRsVs(int) - Method in interface org.jmol.api.SymmetryInterface
- getOperationRsVs(int) - Method in class org.jmol.symmetry.Symmetry
- getOperativeSymmetry() - Method in class org.jmol.viewer.Viewer
-
Only return symmetry that has operators.
- getOpIsCCW() - Method in class org.jmol.symmetry.SymmetryOperation
- getOpOrder() - Method in class org.jmol.symmetry.SymmetryOperation
- getOpPoint() - Method in class org.jmol.symmetry.SymmetryOperation
- getOpPoint2() - Method in class org.jmol.symmetry.SymmetryOperation
- getOption(String[], String, String) - Method in interface jspecview.api.js.JSVAppletObject
- getOption(String, Viewer, String) - Static method in class org.jmol.api.Interface
-
Note! Do not use this method with "viewer." or "util." because when the JavaScript is built, "org.jmol.util" and "org.jmol.viewer" are condensed to "JU" and "JV" (javajs.util is also JU)
- getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.dialog.DialogManager
- getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.java.AwtDialogManager
- getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.js2d.JsDialogManager
- getOptionFromDialog(String[], String, String) - Method in class jspecview.common.JSViewer
- getOpTrans() - Method in class org.jmol.symmetry.SymmetryOperation
- getOpType() - Method in class org.jmol.symmetry.SymmetryOperation
- getOrAddBond(Atom, Atom, int, short, BS, float, boolean) - Method in class org.jmol.modelset.BondCollection
- getOrCalcPartialCharges(BS, BS) - Method in class org.jmol.viewer.Viewer
- getOrientation(int, String, BS, P3[]) - Method in class org.jmol.viewer.Viewer
- getOrigin() - Method in class jspecview.source.JDXHeader
-
Getter for property origin.
- getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
- getOriginVaVbVc() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- getOS() - Method in class com.jcraft.jzlib.GZIPHeader
- getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
- getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
- getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
- getOtherNode(SimpleNode) - Method in class org.jmol.modelset.Bond
- getOtherNode(SimpleNode) - Method in class org.jmol.smiles.SmilesBond
- getOtherNode(SimpleNode) - Method in interface org.jmol.util.SimpleEdge
- getOutputChannel(String, boolean) - Method in class jspecview.common.JSViewer
- getOutputChannel(String, String[]) - Method in class org.jmol.viewer.Viewer
- getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- getOverallSpan() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- getOverlayLegendData() - Method in class jspecview.common.PanelData
- getOwner() - Method in class jspecview.source.JDXHeader
-
Getter for property owner.
- getP(String) - Method in class org.jmol.viewer.Viewer
- getPackingRangeValue(float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getPalette(String) - Static method in enum class org.jmol.c.PAL
- getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
- getPaletteID(String) - Static method in enum class org.jmol.c.PAL
- getPaletteName(byte) - Static method in enum class org.jmol.c.PAL
- getPane() - Method in class org.jmol.console.JmolConsole
- getPanelData() - Method in interface jspecview.api.JSVPanel
- getPanelData() - Method in class jspecview.java.AwtPanel
- getPanelData() - Method in class jspecview.js2d.JsPanel
- getPanelMany(JSViewer, Lst<Spectrum>) - Static method in class jspecview.java.AwtPanel
-
Constructs a
JSVPanel
with List of spectra and corresponding start and end indices of data points that should be displayed - getPanelMany(JSViewer, Lst<Spectrum>) - Static method in class jspecview.js2d.JsPanel
-
Constructs a
JSVPanel
with List of spectra and corresponding start and end indices of data points that should be displayed - getPanelNode() - Method in interface jspecview.api.JSVTreeNode
- getPanelNode() - Method in class jspecview.application.AwtTreeNode
- getPanelNode() - Method in class jspecview.tree.SimpleTreeNode
- getPanelOne(JSViewer, Spectrum) - Static method in class jspecview.java.AwtPanel
-
Constructs a new JSVPanel
- getParameter(String) - Method in interface jspecview.api.AppletFrame
- getParameter(String) - Method in class jspecview.appletjs.JSVApplet
- getParameter(String) - Method in class org.jmol.api.JmolViewer
- getParameter(String) - Method in class org.jmol.viewer.Viewer
- getParameter(String, int, boolean) - Method in class org.jmol.script.ScriptParam
- getParameter(String, String) - Method in class jspecview.appletjs.JSVApplet
- getParameters() - Method in interface jspecview.api.AnnotationData
- getParameters() - Method in class jspecview.common.MeasurementData
- getParameters() - Method in class jspecview.dialog.JSVDialog
- getParameters(boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getParams() - Method in class org.jmol.quantum.NMRNoeMatrix
- getParamType(int) - Static method in class org.jmol.script.T
- getParent() - Method in interface org.jmol.api.SC
- getParent() - Method in class org.jmol.awt.AwtSwingComponent
- getParent() - Method in class org.jmol.awtjs.swing.Component
- getParentAsFile() - Method in interface org.jmol.api.GenericFileInterface
- getPartialBondDotted(int) - Static method in class org.jmol.util.Edge
- getPartialBondOrder(int) - Static method in class org.jmol.util.Edge
- getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.util.Edge
-
reads standard n.m double-as-integer (n*1000000 + m) and returns partial bond order as (n % 7) invalid input: '<'invalid input: '<' 5 + (m % 0x1F)
- getPartialCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getPartialCharge() - Method in class org.jmol.modelset.Atom
- getPartialCharges() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
- getPartialCharges(BS) - Method in class org.jmol.script.ScriptEval
- getPartnerAtom(NucleicMonomer) - Method in class org.jmol.modelsetbio.BasePair
- getPath() - Method in interface jspecview.api.JSVTreeNode
- getPath() - Method in class jspecview.tree.SimpleTreeNode
- getPathForAllFiles() - Method in class org.jmol.viewer.FileManager
- getPatternIndex() - Method in class org.jmol.smiles.SmilesAtom
- getPdbAtomData(BS, OC, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
-
PDB or PQR only
- getPdbData(int, String, BS, Object[], OC, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.PropertyManager
- getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.Viewer
- getPdbData(String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioModel
- getPDBHeader(int) - Method in class org.jmol.modelset.ModelSet
- getPdbID() - Method in class org.jmol.viewer.Viewer
- getPeakData() - Method in class jspecview.dialog.JSVDialog
- getPeakInfo() - Method in class jspecview.common.PeakPickEvent
- getPeakList() - Method in class jspecview.common.Spectrum
- getPeakListArray(Measurement, double[], double) - Method in class jspecview.source.JDXDataObject
- getPeakListing(Parameters, Boolean) - Method in class jspecview.common.PanelData
- getPeakTitle() - Method in class jspecview.common.Spectrum
- getPeakWidth() - Method in class jspecview.common.Spectrum
- getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
- getPercentMinimumY() - Method in class jspecview.common.IntegralData
- getPercentOffset() - Method in class jspecview.common.IntegralData
- getPercentYValueAt(double) - Method in class jspecview.common.IntegralData
- getPercentYValueAt(double) - Method in class jspecview.common.Spectrum
- getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
- getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
-
calculate the perspective factor based on z
- getPhiPsiForHelixType(String) - Method in class org.jmol.modelsetbio.BioExt
- getPhongExponent() - Method in class org.jmol.util.GData
- getPickedCoordinates(Coordinate, Coordinate) - Method in class jspecview.common.PanelData
-
click event processing
- getPickedPoint(T3, int) - Method in class org.jmol.shape.MeshCollection
- getPickingMode() - Method in class org.jmol.viewer.Viewer
- getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
- getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
- getPickingState() - Method in class org.jmol.viewer.ActionManager
- getPickingStyleIndex(String) - Static method in class org.jmol.viewer.ActionManager
- getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
- getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
- getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.JvxlReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
- getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
- getPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
- getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptEval
- getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.JvxlReader
-
Retrieve raw file planes and pass them to the calculation object for processing into new data.
- getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
Retrieve raw file planes and pass them to the calculation object for processing into new data.
- getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
-
Retrieve raw file planes and pass them to the calculation object for processing into new data.
- getPlaneProjection(T3, P4, T3, V3) - Static method in class javajs.util.Measure
-
Project a point onto a plane, also returning the normal vector and the directed distance to the plane.
- getPlaneSR(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getPlaneThroughPoint(T3, V3, P4) - Static method in class javajs.util.Measure
- getPlaneThroughPoints(T3, T3, T3, V3, V3, P4) - Static method in class javajs.util.Measure
- getPlatformInterface(String) - Method in class jspecview.common.JSViewer
- getPlotColors(String) - Method in class jspecview.common.ColorParameters
- getPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getPmeshData(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getPngZipStream(BufferedInputStream, boolean) - Static method in class javajs.util.Rdr
-
Either advance a PNGJ stream to its zip file data or pull out the ZIP data bytes and create a new stream for them from which a ZIP utility can start extracting files.
- getPoint(int, P3) - Method in class org.jmol.jvxl.data.VolumeData
- getPoint(int, T3) - Method in class org.jmol.shapecgo.CGOMesh
- getPoint3f(int, boolean) - Method in class org.jmol.scriptext.ScriptExt
- getPoint3f(int, boolean, boolean) - Method in class org.jmol.script.ScriptParam
-
Get an {x,y,z} value, possibly fractional, with option to throw an error.
- getPoint4f(int) - Method in class org.jmol.script.ScriptParam
- getPointArray(int, int, boolean) - Method in class org.jmol.script.ScriptParam
-
may return null values in some cases
- getPointer(int) - Static method in class org.jmol.viewer.JC
- getPointerName(int) - Static method in class org.jmol.viewer.JC
- getPointGroupAsString(BS, String, int, float, P3[], P3, String) - Method in class org.jmol.modelset.ModelSet
- getPointGroupInfo(int, String, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
- getPointGroupInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
- getPointGroupInfo(BS) - Method in class org.jmol.modelset.ModelSet
- getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
- getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
- getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- getPointOrCenterVector(T) - Method in class org.jmol.script.ScriptParam
- getPointOrPlane(int, int) - Method in class org.jmol.script.ScriptParam
-
Get the point or plane at an index
- getPoints() - Method in interface org.jmol.api.JmolEnvCalc
- getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getPointsOnPlane(P3[], P4) - Static method in class javajs.util.Measure
-
Based on a set of centering points, returns the list of points on a given plane.
- getPointTransf(int, Atom, Quat, P3) - Method in class org.jmol.modelset.ModelSet
-
pick up the appropriate value for this atom
- getPointVector(T, int) - Method in class org.jmol.script.ScriptParam
- getPolygonColorData(int, short[], int[][], BS) - Static method in class org.jmol.shapesurface.Isosurface
- getPolymerPointsAndVectors(int, BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
- getPolymerPointsAndVectors(BS, Lst<P3[]>) - Method in class org.jmol.viewer.Viewer
- getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelset.ModelSet
- getPolymerSequenceAtoms(int, int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- getPopulation() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- getPopupMenu() - Method in interface org.jmol.api.SC
- getPopupMenu() - Method in class org.jmol.awt.AwtSwingComponent
- getPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
- getPopupMenu() - Method in class org.jmol.awtjs.swing.JMenu
- getPOrNull(String) - Method in class org.jmol.viewer.Viewer
- getPort() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- getPort() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getPosition() - Method in interface javajs.api.GenericBinaryDocument
- getPosition() - Method in class javajs.util.BinaryDocument
- getPosition() - Method in interface org.jmol.api.AtomIndexIterator
- getPosition() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- getPosition() - Method in class org.jmol.symmetry.UnitCellIterator
- getPosXY() - Method in class jspecview.dialog.IntegrationDialog
- getPosXY() - Method in class jspecview.dialog.JSVDialog
- getPosXY() - Method in class jspecview.dialog.MeasurementsDialog
- getPosXY() - Method in class jspecview.dialog.OverlayLegendDialog
- getPosXY() - Method in class jspecview.dialog.PeakListDialog
- getPosXY() - Method in class jspecview.dialog.ViewsDialog
- getPrecision() - Method in interface org.jmol.api.SymmetryInterface
- getPrecision() - Method in class org.jmol.symmetry.Symmetry
- getPrecision() - Method in class org.jmol.util.SimpleUnitCell
- getPreference(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getPreferences() - Method in class jspecview.application.PreferencesDialog
-
Returns the preferences (
Properties
Object) - getPreserveState() - Method in class org.jmol.viewer.Viewer
-
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
- getPreviousMolecule() - Method in class jme.JME
- getPrintJobTitle(boolean) - Method in class jspecview.common.PanelData
- getPrintLayout() - Method in interface jspecview.api.JSVPrintDialog
- getPrintLayout() - Method in class jspecview.java.AwtPrintDialog
-
Returns the PrintLayout object
- getPrivateKey() - Method in class org.jmol.export.Export3D
- getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
- getProjectedLineSegment(P3[], int, P3, V3, V3) - Static method in class javajs.util.Measure
- getPropC(String, int) - Method in class org.jmol.shapesurface.Contact
- getPropDataMC(String, Object[]) - Method in class org.jmol.shape.MeshCollection
- getProperties() - Method in class org.openscience.jmol.app.HistoryFile
- getproperty - Static variable in class org.jmol.script.T
- getProperty(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
- getProperty(String) - Method in class org.jmol.modelkit.ModelKit
-
Get a property of the modelkit.
- getProperty(String) - Method in class org.jmol.util.GenericApplet
- getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
only called from org.openscience.jvxl.Jvxl.main
- getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
- getProperty(String, int) - Method in class org.jmol.shape.Axes
- getProperty(String, int) - Method in class org.jmol.shape.Labels
- getProperty(String, int) - Method in class org.jmol.shape.Measures
- getProperty(String, int) - Method in class org.jmol.shape.Shape
- getProperty(String, int) - Method in class org.jmol.shape.Sticks
- getProperty(String, int) - Method in class org.jmol.shapecgo.CGO
- getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
- getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
- getProperty(String, int) - Method in class org.jmol.shapespecial.Polyhedra
- getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
- getProperty(String, int) - Method in class org.jmol.shapesurface.Contact
- getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
- getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
- getProperty(String, int) - Method in class org.jmol.shapesurface.Pmesh
- getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- getProperty(String, String) - Method in class org.jmol.util.GenericApplet
-
@XXXj2sOverride
- getProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
-
Get the value of a property
- getProperty(String, String, Object) - Method in interface org.jmol.api.JmolPropertyManager
- getProperty(String, String, Object) - Method in class org.jmol.api.JmolViewer
- getProperty(String, String, Object) - Method in class org.jmol.viewer.PropertyManager
- getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
- GETPROPERTY - Enum constant in enum class jspecview.common.ScriptToken
- getPropertyAsJavaObject(String) - Method in interface jspecview.api.JSVAppletInterface
- getPropertyAsJavaObject(String) - Method in class jspecview.app.JSVApp
- getPropertyAsJavaObject(String) - Method in class jspecview.appletjs.JSVApplet
- getPropertyAsJavaObject(String) - Method in class jspecview.application.MainFrame
- getPropertyAsJavaObject(String) - Method in class jspecview.common.JSViewer
- getPropertyAsJSON(String) - Method in interface jspecview.api.JSVAppletInterface
- getPropertyAsJSON(String) - Method in class jspecview.app.JSVApp
- getPropertyAsJSON(String) - Method in class jspecview.appletjs.JSVApplet
- getPropertyAsJSON(String) - Method in class jspecview.application.MainFrame
- getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsJSON(String) - Method in class org.jmol.util.GenericApplet
- getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsJSON(String, String) - Method in class org.jmol.util.GenericApplet
-
@XXXj2sOverride
- getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsString(String) - Method in class org.jmol.util.GenericApplet
- getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsString(String, String) - Method in class org.jmol.util.GenericApplet
-
@XXXj2sOverride
- getPropertyData(String, Object[]) - Method in class org.jmol.shape.Echo
- getPropertyData(String, Object[]) - Method in class org.jmol.shape.Shape
- getPropertyData(String, Object[]) - Method in class org.jmol.shapecgo.CGO
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Draw
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
- getPropertyData(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
- getPropertyNumber(String) - Method in interface org.jmol.api.JmolPropertyManager
- getPropertyNumber(String) - Method in class org.jmol.viewer.PropertyManager
- getPropertyNumber(String) - Method in class org.jmol.viewer.Viewer
- getPropI(String, int) - Method in class org.jmol.shapesurface.Isosurface
- getPropMC(String, int) - Method in class org.jmol.shape.MeshCollection
- getPropMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
- getPropShape(String, Object[]) - Method in class org.jmol.shape.Shape
- getProteinStructure(int) - Method in class org.jmol.modelsetbio.AlphaPolymer
- getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
- getProteinStructureState(BS, int) - Method in class org.jmol.modelset.ModelSet
- getProteinStructureSubType() - Method in class org.jmol.modelset.Group
- getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getProteinStructureTag() - Method in class org.jmol.modelset.Group
- getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
- getProteinStructureType() - Method in class org.jmol.modelset.Group
- getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getProteinStructureType(String) - Static method in enum class org.jmol.c.STR
-
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
- getPymolScreenOffset(P3, P3i, int, P3, double) - Method in class org.jmol.modelset.Text
-
PyMOL will use 1 here for pymolOffset[0] for relative, 0 or absolute.
- getQCoefs(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getQCoefs(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getQuadrupolarConstant(Tensor) - Method in interface org.jmol.api.JmolNMRInterface
-
Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
- getQuadrupolarConstant(Tensor) - Method in class org.jmol.quantum.NMRCalculation
- getQualifiedDataType() - Method in class jspecview.source.JDXHeader
- getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
- getQuality(String) - Method in class org.jmol.dialog.Dialog
- getQuantumShellTag(int) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getQuantumShellTag(int) - Static method in class org.jmol.quantum.QS
- getQuantumShellTagID(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getQuantumShellTagID(String) - Static method in class org.jmol.quantum.QS
- getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.quantum.QS
- getQuaternion(char) - Method in class org.jmol.modelset.Group
- getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
- getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
- getQuaternionAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternionArray(Object, int) - Method in class org.jmol.script.ScriptEval
- getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
- getQuaternionFrame(P3, T3, T3) - Static method in class javajs.util.Quat
-
returns a quaternion frame based on three points (center, x, and any point in xy plane) or two vectors (vA, vB).
- getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
- getQuaternionFrameCenterAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternionFrameV(V3, V3, V3, boolean) - Static method in class javajs.util.Quat
-
Create a quaternion based on a frame
- getQuaternionP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getQuaternionParameter(int, BS, boolean) - Method in class org.jmol.script.ScriptParam
- getQuaternionRotation(String) - Method in interface org.jmol.api.SymmetryInterface
- getQuaternionRotation(String) - Method in class org.jmol.symmetry.Symmetry
- getQuotedAttribute(String, String) - Static method in class javajs.util.PT
- getQuotedOrUnquotedAttribute(String, String) - Static method in class javajs.util.PT
-
single- or double-quoted string or up to the first space -- like HTML5 not case-sensitive
- getQuotedStringAt(String, int) - Static method in class javajs.util.PT
- getQuotedStringNext() - Method in class org.jmol.jvxl.readers.JvxlReader
- getQuotedStringNext() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getQuotedStringNext() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getQuotedStringNext(String, int[]) - Static method in class javajs.util.PT
- getQuotedStringOrObject(char) - Method in class javajs.util.CifDataParser
-
CIF 1.0 only.
- getQuotedStringOrObject(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
final get for quoted object
- getRadio(String) - Method in class org.jmol.awt.AwtPopupHelper
- getRadio(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getRadio(String) - Method in interface org.jmol.popup.PopupHelper
- getRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getRadius() - Method in class org.jmol.api.JmolAdapterBondIterator
- getRadius() - Method in class org.jmol.modelset.Atom
- getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
- getRange(BS, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
- getRangeGroups(int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- getRasMolRadius() - Method in class org.jmol.modelset.Atom
- getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
- getReader(String, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
-
Get a reader based on its name.
- getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
- getRealCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
- getRealEigenvalues() - Method in class javajs.util.Eigen
-
Return the real parts of the eigenvalues
- getReciprocal(T3[], T3[], float) - Static method in class org.jmol.util.SimpleUnitCell
-
Generate the reciprocal unit cell, scaled as desired
- getRecord(String) - Method in interface org.jmol.api.JmolJDXMOLParser
- getRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
- getRedField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- getRedField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- getRedValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getRedValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getRefreshing() - Method in class org.jmol.viewer.Viewer
- getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
- getRegistryInfo() - Method in class org.jmol.util.GenericApplet
- getRegistryInfo() - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
- getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
- getRemainingScript() - Method in class jspecview.common.ScriptTokenizer
- getRendering() - Method in class org.jmol.shape.Mesh
- getResno() - Method in class org.jmol.modelset.Atom
- getResno() - Method in class org.jmol.modelset.Group
- getResno() - Method in class org.jmol.smiles.SmilesAtom
- getResno() - Method in interface org.jmol.util.Node
- getResolution() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getResolution() - Method in class org.jmol.util.MeshSurface
- getResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getResourceString(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getResourceString(Object, String, String[]) - Static method in class jspecview.common.JSVFileManager
- getRGB() - Method in interface javajs.api.GenericColor
- getRGB() - Method in class org.jmol.awtjs.swing.Color
- getRhoStar() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getRhoStarField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getRiboseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
- getRmsd(P3[][], Quat) - Static method in class javajs.util.Measure
- getRootNode() - Method in interface jspecview.api.JSVTree
- getRootNode() - Method in class jspecview.application.AwtTree
- getRootNode() - Method in class jspecview.tree.SimpleTree
- getRotateBondIndex() - Method in class org.jmol.modelkit.ModelKit
- getRotation() - Method in class com.sparshui.common.messages.events.RotateEvent
- getRotation() - Method in class javajs.util.Matrix
-
similarly to M3/M4 standard rotation/translation matrix we set a rotationTranslation matrix to be: [ nxn rot nx1 trans 1xn 0 1x1 1 ]
- getRotation(int) - Method in class javajs.export.PDFCreator
- getRotation(M3) - Method in class org.jmol.viewer.TransformManager
- getRotationMatrix(P3, P3, float) - Method in class org.jmol.export.___Exporter
- getRotationMatrix(P3, P3, float, P3, P3) - Method in class org.jmol.export.___Exporter
- getRotationQ() - Method in class org.jmol.viewer.TransformManager
- getRotationScale(M3) - Method in class javajs.util.M4
-
Gets the upper 3x3 values of this matrix and places them into the matrix m1.
- getRotationX() - Method in class com.sparshui.common.messages.events.SpinEvent
- getRotationY() - Method in class com.sparshui.common.messages.events.SpinEvent
- getRotationZ() - Method in class com.sparshui.common.messages.events.SpinEvent
- getRow(int, float[]) - Method in class javajs.util.M3
-
Copies the matrix values in the specified row into the array parameter.
- getRow(int, float[]) - Method in class javajs.util.M34
- getRow(int, float[]) - Method in class javajs.util.M4
-
Copies the matrix values in the specified row into the array parameter.
- getRow33(int, float[]) - Method in class javajs.util.M34
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getRowDimension() - Method in class javajs.util.Matrix
-
Get row dimension.
- getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
- getRuleName(int) - Method in class org.jmol.symmetry.CIPChirality
- getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
- getSavedState(String) - Method in class org.jmol.viewer.StateManager
- getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
- getSavedUnitCell(String) - Method in class org.jmol.viewer.StateManager
- getSaveFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
- getSaveFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
- getScale() - Method in class com.sparshui.common.messages.events.ZoomEvent
- getScale() - Method in class jspecview.common.ViewData
- getScale() - Method in interface org.jmol.api.JmolModulationSet
- getScale() - Method in class org.jmol.util.ModulationSet
- getScaleData() - Method in class jspecview.common.ViewData
- getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
- getScaleText(String, boolean, float, float[]) - Method in class org.jmol.viewer.Viewer
-
Depending upon the measure text, we need to indicate |-------| 1 A or 0.1 A for example.
- getScreenDim() - Method in class org.jmol.viewer.Viewer
- getScreenDimensions(Dimension) - Method in interface org.jmol.awtjs.swing.SwingController
-
Return the width and height of the window in d.
- getScreenHeight() - Method in class org.jmol.api.JmolViewer
- getScreenHeight() - Method in class org.jmol.viewer.Viewer
- getScreenImage() - Method in class org.jmol.viewer.Viewer
- getScreenImage() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getScreenImage(boolean) - Method in class org.jmol.g3d.Graphics3D
- getScreenImage(boolean) - Method in class org.jmol.util.GData
- getScreenImageBuffer(Object, boolean) - Method in class org.jmol.api.JmolViewer
- getScreenImageBuffer(Object, boolean) - Method in class org.jmol.viewer.Viewer
-
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
- getScreenNormal(T3, T3, float) - Method in class org.jmol.export._PovrayExporter
- getScreenNormal(T3, T3, float) - Method in class org.jmol.export._TachyonExporter
- getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager
- getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager4D
- getScreenWidth() - Method in class org.jmol.api.JmolViewer
- getScreenWidth() - Method in class org.jmol.viewer.Viewer
- getScript() - Method in interface org.jmol.api.JmolScriptEvaluator
- getScript() - Method in class org.jmol.script.ScriptEval
- getScriptContext(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- getScriptContext(String) - Method in class org.jmol.script.ScriptEval
- getScriptContext(String) - Method in class org.jmol.viewer.Viewer
- getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
- getScriptEditor() - Method in class org.jmol.console.GenericConsole
- getScriptEditor() - Method in class org.jmol.console.JmolConsole
- getScriptEditor() - Method in class org.jmol.consolejs.AppletConsole
- getScriptForCallback(SC, String, String) - Method in class jspecview.popup.JSVGenericPopup
- getScriptForCallback(SC, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
-
Secondary processing of menu item click
- getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.GenericPopup
- getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.JmolPopup
- getScriptItem(boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
- getScriptItem(boolean, boolean) - Method in class org.jmol.script.ScriptManager
- getScriptQueue() - Method in interface jspecview.api.JSVAppInterface
- getScriptQueue() - Method in class jspecview.app.JSVApp
- getScriptQueue() - Method in class jspecview.application.MainFrame
- getScriptQueue() - Method in interface org.jmol.api.JmolScriptManager
- getScriptQueue() - Method in class org.jmol.script.ScriptManager
- getScriptQueueInfo() - Method in class org.jmol.viewer.Viewer
- getScriptToken(String) - Static method in enum class jspecview.common.ScriptToken
- getScriptTokenList(String, boolean) - Static method in enum class jspecview.common.ScriptToken
- getSDFDateLine(String) - Static method in class jme.JMEUtil
-
See CTFile -- this line is NOT optional.
- getSDFDateLine(String, boolean) - Static method in class org.jmol.viewer.PropertyManager
- getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
- getSelected() - Method in class org.jmol.shape.Measures
- getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
- getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getSelectedAtomIterator(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- getSelectedDisplayScheme() - Method in class jspecview.application.PreferencesDialog
-
Retruns the current Display Scheme
- getSelectedIndex() - Method in class org.jmol.awtjs.swing.JComboBox
- getSelectedIndex(Object) - Method in interface jspecview.api.PlatformDialog
- getSelectedIndex(Object) - Method in class jspecview.java.AwtDialog
- getSelectedIndex(Object) - Method in class jspecview.js2d.JsDialog
- getSelectedIntegral() - Method in class jspecview.common.PanelData
- getSelectedItem() - Method in class org.jmol.awtjs.swing.JComboBox
- getSelectedItem(Object) - Method in interface jspecview.api.PlatformDialog
- getSelectedItem(Object) - Method in class jspecview.java.AwtDialog
- getSelectedItem(Object) - Method in class jspecview.js2d.JsDialog
- getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
- getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
- getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
- getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
- getSelectedPeak() - Method in class jspecview.common.Spectrum
- getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
- getSelectionHalosEnabled() - Method in class org.jmol.viewer.Viewer
- getSelectionModel() - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
- getSelectionModel() - Method in class org.jmol.awtjs.swing.JTable
- getSelectorName(Object) - Method in class jspecview.dialog.DialogManager
- getSeqCode(T) - Static method in class org.jmol.script.ScriptEval
- getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
- getSeqcodeFor(int, char) - Static method in class org.jmol.modelset.Group
- getSeqcodeString() - Method in class org.jmol.modelset.Group
- getSeqcodeStringFor(int) - Static method in class org.jmol.modelset.Group
- getSeqID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSeqID() - Method in class org.jmol.modelset.Atom
- getSeqNumberFor(int) - Static method in class org.jmol.modelset.Group
- getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
- getSequenceBits(String, BS, BS) - Method in class org.jmol.modelset.ModelSet
- getSequenceNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSequenceNumber(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getSequenceNumber(int) - Method in interface org.jmol.api.PymolAtomReader
- getSerial() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getServiceCommand(String) - Static method in class org.jmol.viewer.JC
- getSetAxesTypeMad10(int) - Method in class org.jmol.script.ScriptEval
- getSetHistory(int) - Method in class org.jmol.api.JmolViewer
- getSetHistory(int) - Method in class org.jmol.util.CommandHistory
-
Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n invalid input: '<'= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
- getSetHistory(int) - Method in class org.jmol.viewer.Viewer
-
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n invalid input: '<'= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
- getSettableTokFromString(String) - Static method in class org.jmol.script.T
- getShadeB(float, float, float) - Method in class org.jmol.util.Shader
- getShadeFp8(float, float, float) - Method in class org.jmol.util.Shader
- getShadeIndex(float, float, float) - Method in class org.jmol.util.Shader
- getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
- getShadeN(float, float, float, float) - Method in class org.jmol.util.Shader
- getShades(short) - Method in class org.jmol.util.GData
- getShape(int) - Method in class org.jmol.viewer.ShapeManager
- getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JC
- getShapeDetail() - Method in class org.jmol.shape.Echo
- getShapeDetail() - Method in class org.jmol.shape.Shape
- getShapeDetail() - Method in class org.jmol.shapecgo.CGO
- getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
- getShapeDetail() - Method in class org.jmol.shapespecial.Draw
- getShapeDetail() - Method in class org.jmol.shapespecial.Polyhedra
- getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
- getShapeErrorState() - Method in class org.jmol.viewer.Viewer
- getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
-
Returns the shape type index for a shape object given the object name.
- getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEval
- getShapeProperty(int, String) - Method in class org.jmol.scriptext.ScriptExt
- getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
- getShapePropertyData(int, String, Object[]) - Method in class org.jmol.script.ScriptEval
- getShapePropertyData(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
- getShapePropertyIndex(int, String, int) - Method in class org.jmol.viewer.ShapeManager
- getShapeState() - Method in class org.jmol.shape.AtomShape
- getShapeState() - Method in class org.jmol.shape.FontLineShape
- getShapeState() - Method in class org.jmol.shape.Frank
- getShapeState() - Method in class org.jmol.shape.Shape
- getShapeState() - Method in class org.jmol.shape.Sticks
- getShapeState() - Method in class org.jmol.shape.TextShape
- getShapeState() - Method in class org.jmol.shapebio.BioShape
- getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
- getShapeState() - Method in class org.jmol.shapecgo.CGO
- getShapeState() - Method in class org.jmol.shapespecial.Dipole
- getShapeState() - Method in class org.jmol.shapespecial.Dipoles
- getShapeState() - Method in class org.jmol.shapespecial.Dots
- getShapeState() - Method in class org.jmol.shapespecial.Draw
- getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
- getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
- getShapeState() - Method in class org.jmol.shapesurface.Isosurface
- getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
- getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
- getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JC
- getShowAnnotation(Annotation.AType) - Method in class jspecview.common.PanelData
- getShowAxes() - Method in class org.jmol.viewer.Viewer
- getShowBbcage() - Method in class org.jmol.viewer.Viewer
- getShowFrank() - Method in class org.jmol.viewer.Viewer
- getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
- getShowSelectedOnce() - Method in class org.jmol.viewer.Viewer
- getShowUnitCell() - Method in class org.jmol.viewer.Viewer
- getSignature() - Method in interface org.jmol.api.JmolScriptFunction
- getSignature() - Method in class org.jmol.script.ScriptFunction
- getSimpleXmlReader(BufferedReader) - Method in class jspecview.source.AnIMLReader
- getSimulationFileData(String, String) - Static method in class jspecview.common.JSVFileManager
- getSimulationType(String) - Static method in class jspecview.common.JSVFileManager
- getSiteMultiplicity(P3) - Method in interface org.jmol.api.SymmetryInterface
- getSiteMultiplicity(P3) - Method in class org.jmol.symmetry.Symmetry
- getSize(int) - Method in class org.jmol.shape.AtomShape
- getSize(int) - Method in class org.jmol.shape.Shape
-
overridden in Dots, CGOMesh, and AtomShape
- getSize(int) - Method in class org.jmol.shapespecial.Dots
- getSize(int, boolean) - Static method in class org.jmol.shapecgo.CGOMesh
- getSizeG(Group) - Method in class org.jmol.shape.Shape
- getSizeG(Group) - Method in class org.jmol.shapebio.BioShapeCollection
- getSlabColor() - Method in class org.jmol.util.MeshSurface
- getSlabObjectType(int, Object, boolean, Object) - Static method in class org.jmol.util.TempArray
- getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
- getSlabType() - Method in class org.jmol.util.MeshSurface
- getSlabWithinRange(float, float) - Static method in class org.jmol.util.TempArray
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.AdfReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.AmsReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.DgridReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.AmsReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.DgridReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- getSmartsMap(String, BS, int) - Method in class org.jmol.viewer.Viewer
- getSmartsMatch(String, BS) - Method in class org.jmol.api.JmolViewer
- getSmartsMatch(String, BS) - Method in class org.jmol.viewer.Viewer
- getSmartsMatchForNodes(String, Node[]) - Method in class org.jmol.viewer.Viewer
- getSmiles(BS) - Method in class org.jmol.api.JmolViewer
- getSmiles(BS) - Method in class org.jmol.viewer.Viewer
-
NOT getting aromatic smiles
- getSmiles(Node[], int, BS, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSmiles(Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesMatcher
-
internal to Jmol -- called by org.jmol.Viewer.getSmiles
- getSmilesAtoms(String) - Method in class org.jmol.viewer.Viewer
- getSmilesChiralityArray() - Method in class org.jmol.symmetry.CIPDataSmiles
- getSmilesCorrelation(BS, BS, String, Lst<P3>, Lst<P3>, M4, Lst<BS>, boolean, int[][], P3, boolean, int) - Method in class org.jmol.scriptext.SmilesExt
-
The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
- getSmilesExt() - Method in class org.jmol.script.ScriptEval
- getSmilesFromJME(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSmilesFromJME(String) - Method in class org.jmol.smiles.SmilesMatcher
- getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
- getSmilesMatches(String, Object, BS, BS, int, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
- getSmilesOpt(BS, int, int, int, String) - Method in class org.jmol.viewer.Viewer
-
returns the SMILES string for a sequence or atom set does not include attached protons on groups
- getSolnColour() - Method in interface jspecview.api.JSVAppletInterface
-
Returns the calculated colour of a visible spectrum (Transmittance)
- getSolnColour() - Method in class jspecview.app.JSVApp
-
Returns the calculated colour of a visible spectrum (Transmittance)
- getSolnColour() - Method in class jspecview.appletjs.JSVApplet
- getSolnColour() - Method in class jspecview.application.MainFrame
- getSolutionColor(boolean) - Method in class jspecview.common.JSViewer
- GETSOLUTIONCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- getSolutionColorStr(boolean) - Method in class jspecview.common.JSViewer
- getSortingStatus(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getSource(String, BufferedReader) - Method in interface jspecview.api.SourceReader
- getSource(String, BufferedReader) - Method in class jspecview.source.AnIMLReader
- getSourceID() - Method in class jspecview.common.PanelData
- getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupInfoObj(String, Object, boolean, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupInfoObj(String, Object, boolean, boolean) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupJSON(Viewer, String, Object, int) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupJSON(Viewer, String, Object, int) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupNameType(String) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupNameType(String) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupOperationCode(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupTitle() - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
- getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
- getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
- getSpecialLabel(String, String) - Method in class org.jmol.popup.JmolPopup
-
menus or menu items with SPECIAL in their name are sent here for on-the-fly labeling
- getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
- getSpectra() - Method in class jspecview.source.JDXSource
-
Returns the Vector of Spectra
- getSpectraAsArray() - Method in class jspecview.source.JDXSource
-
Used in Android
- getSpectrum() - Method in interface jspecview.api.AnnotationData
- getSpectrum() - Method in class jspecview.common.Measurement
- getSpectrum() - Method in class jspecview.common.MeasurementData
- getSpectrum() - Method in class jspecview.common.PanelData
- getSpectrum() - Method in class jspecview.common.PanelNode
- getSpectrum() - Method in class jspecview.dialog.JSVDialog
- getSpectrumAt(int) - Method in class jspecview.common.PanelData
- getSpectrumListAsString(Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
- getSpecular() - Method in class org.jmol.util.GData
- getSpecularExponent() - Method in class org.jmol.util.GData
- getSpecularPercent() - Method in class org.jmol.util.GData
- getSpecularPower() - Method in class org.jmol.util.GData
- getSpeedLevel() - Method in class com.sparshui.common.messages.events.FlickEvent
- getSPF(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlReader
- getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getSphereData(int) - Static method in class org.jmol.util.MeshSurface
-
Calculates the data (faces, vertices, normals) for a sphere.
- getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
- getSpinOp(int) - Method in interface org.jmol.api.SymmetryInterface
- getSpinOp(int) - Method in class org.jmol.symmetry.Symmetry
- getSpinState() - Method in class org.jmol.viewer.Viewer
- getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
- getStartChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStartChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStartingPointIndex(int) - Method in class jspecview.common.PanelData
- getStartingPointIndex(int) - Method in class jspecview.common.ViewData
-
in some cases, there is only one scaleData, but there are more than that number of spectra this is no problem -- we just use mod to set this to 0
- getStartInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStartInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getState() - Method in class com.sparshui.common.messages.events.TouchEvent
- getState() - Method in class com.sparshui.server.GestureServer
- getState() - Method in class com.sparshui.server.TouchPoint
-
Get the touch point state.
- getState() - Method in interface jspecview.api.AnnotationData
- getState() - Method in class jspecview.common.MeasurementData
- getState() - Method in class jspecview.dialog.JSVDialog
- getState() - Method in interface org.jmol.api.JmolGestureServerInterface
- getState() - Method in interface org.jmol.api.JmolModulationSet
- getState() - Method in class org.jmol.modelset.Trajectory
- getState() - Method in class org.jmol.util.ModulationSet
- getState(String) - Method in class org.jmol.shape.Mesh
- getState(SB) - Method in interface org.jmol.api.JmolNMRInterface
- getState(SB) - Method in class org.jmol.quantum.NMRCalculation
- getState(ModelSet, int, SB) - Method in interface org.jmol.api.SymmetryInterface
- getState(ModelSet, int, SB) - Method in class org.jmol.symmetry.Symmetry
- getStateCreator() - Method in class org.jmol.viewer.Viewer
- getStateInfo() - Method in class org.jmol.api.JmolViewer
- getStateInfo() - Method in class org.jmol.viewer.Viewer
- getStateInfo3(String, int, int) - Method in class org.jmol.viewer.Viewer
- getStateText() - Method in class org.jmol.modelset.Text
- getStaticGraphics(Object, boolean) - Method in class jspecview.java.AwtPlatform
- getStaticGraphics(Object, boolean) - Method in class jspecview.js2d.JsPlatform
- getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.GenericPlatform
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs.Platform
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs2d.Platform
- getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
- getStereo() - Method in class org.jmol.smiles.SmilesAtom
- getStereoAtAt(SimpleNode[]) - Method in class org.jmol.smiles.SmilesAtom
- getStereoMode(String) - Static method in enum class org.jmol.c.STER
- getStrandCount() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStrandCount() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStrandCount(int) - Method in class org.jmol.viewer.Viewer
- getStrandID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStrandID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStream() - Method in class javajs.util.Rdr.StreamReader
- getStream(InputStream) - Method in class org.apache.tools.bzip2.CBZip2InputStreamFactory
-
jsjava addition for reflection
- getStreamAsBytes(BufferedInputStream, OC) - Static method in class javajs.util.Rdr
-
Read a an entire BufferedInputStream for its bytes, and either return them or leave them in the designated output channel.
- getStreamAsBytes(BufferedInputStream, OC) - Static method in class jspecview.common.JSVFileManager
- getStreamAsString(InputStream) - Static method in class javajs.util.ZipTools
- getString() - Method in class org.jmol.modelset.Measurement
- getString(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getStringArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
-
Retrieve a String array, possibly unpacking it if it is run-length encoded.
- getStringDetail() - Method in class org.jmol.modelset.Measurement
- getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getStringX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getStringX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getStringX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getStrucNo() - Method in class org.jmol.modelset.Group
- getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getStructure() - Method in class org.jmol.modelset.Group
- getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getStructuredModels() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStructuredModels() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStructureId() - Method in class org.jmol.modelset.Group
- getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
- getStructureId() - Method in class org.jmol.modelsetbio.Monomer
- getStructureID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStructureID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get a StructureIterator.
- getStructureList() - Method in class org.jmol.modelset.ModelSet
- getStructureList() - Method in class org.jmol.viewer.GlobalSettings
- getStructureList() - Method in class org.jmol.viewer.Viewer
- getStructureMap(Lst<Object>, String, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
-
Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
- getStructures(String, String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
-
Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
- getStructures46(String[], String, Lst<Object>, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
-
Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
- getStructureState() - Method in class org.jmol.viewer.Viewer
- getStructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStuctureAsText(String, String[][], String[][]) - Method in class org.jmol.popup.PopupResource
- getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Component
- getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Container
- getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.JSplitPane
- getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Component
- getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Container
- getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.JSplitPane
- getSubgroupJSON(Viewer, int, int, int, int) - Method in interface org.jmol.api.SymmetryInterface
- getSubgroupJSON(Viewer, int, int, int, int) - Method in class org.jmol.symmetry.Symmetry
-
Retrieve subgroup information for a space group.
- getSubIndex() - Method in class jspecview.common.Spectrum
- getSubIndex() - Method in class jspecview.common.SubSpecChangeEvent
- getSubmatrix(int, int, int, int) - Method in class javajs.util.Matrix
-
Get a submatrix.
- getSubSpectra() - Method in class jspecview.common.Spectrum
- getSubstructureSet(Object, Object, int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSubstructureSet(Object, Object, int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Returns a bitset matching the pattern within a set of Jmol atoms.
- getSubstructureSetArray(String, BS, int) - Method in class org.jmol.viewer.Viewer
- getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Returns a vector of bitsets indicating which atoms match the pattern.
- getSubstructureSetArrayForNodes(String, Node[], int) - Method in class org.jmol.viewer.Viewer
- getSubstructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
- getSubstructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getSubSystemUnitCell() - Method in interface org.jmol.api.JmolModulationSet
- getSubSystemUnitCell() - Method in class org.jmol.util.ModulationSet
- getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
- getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
- getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
- getSwingComponent(Object) - Method in class org.jmol.awt.AwtPopupHelper
- getSwingComponent(Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getSwingComponent(Object) - Method in interface org.jmol.popup.PopupHelper
- getSym(int) - Method in class org.jmol.modelkit.ModelKit
- getSymEditState() - Method in class org.jmol.modelkit.ModelKit
- getSymMatrices(int) - Method in class org.jmol.modelset.ModelSet
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- getSymmetry() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSymmetry(Viewer, String) - Static method in class org.jmol.api.Interface
- getSymmetryEquivAtoms(BS, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
-
Return a bitset of equivalent atoms
- getSymmetryEquivAtomsForAtom(int, BS, BS, BS) - Method in class org.jmol.modelset.ModelSet
-
Set a bitset of the equivalent atoms of an atom.
- getSymmetryEquivPointList(Lst<P3>, String) - Method in class org.jmol.viewer.Viewer
- getSymmetryEquivPoints(P3, String) - Method in class org.jmol.viewer.Viewer
- getSymmetryFromCode(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getSymmetryFromCode(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getSymmetryInfo(int, String, int, P3, P3, P3, int, String, float, int, int, int[]) - Method in class org.jmol.viewer.Viewer
-
A general method for retrieving symmetry information with full capability of the symop() scripting function.
- getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelSet
- getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int, int[]) - Method in interface org.jmol.api.SymmetryInterface
- getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int, int[]) - Method in class org.jmol.symmetry.Symmetry
- getSymmetryInfoStr() - Method in interface org.jmol.api.SymmetryInterface
- getSymmetryInfoStr() - Method in class org.jmol.symmetry.Symmetry
-
When information is desired about the space group, we use SymmetryInfo.
- getSymmetryInvariant(int) - Method in class org.jmol.modelset.ModelSet
- getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
- getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
- getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
-
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
- getSymopText() - Method in class org.jmol.modelkit.ModelKit
- getSymStatic() - Method in class org.jmol.viewer.Viewer
-
Retrieve the static Symmetry object, which should be used only statically
- getSymTemp() - Method in class org.jmol.viewer.Viewer
-
Retrieve a new Symmetry object.
- getSymViewState() - Method in class org.jmol.modelkit.ModelKit
- getSyncFlush() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- getSyncMode() - Method in class org.jmol.viewer.StatusManager
- getTableHeader() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getTableModel() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
- getTagName() - Method in class jspecview.source.XMLParser
- getTagName(String) - Static method in class jspecview.common.JSVFileManager
-
Returns a name that can be used as a tag, possibly abbreviated.
- getTagType() - Method in class jspecview.source.XMLParser
- getTaintedAtoms(int) - Method in class org.jmol.modelset.AtomCollection
- getTauField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getTensor(Viewer, float[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.UnitCell
- getTensorInfo(String, String, BS) - Method in interface org.jmol.api.JmolNMRInterface
- getTensorInfo(String, String, BS) - Method in class org.jmol.quantum.NMRCalculation
- getTensors() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getTensors() - Method in class org.jmol.modelset.Atom
- getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
- getText() - Method in interface org.jmol.api.js.GenericConsoleTextArea
- getText() - Method in interface org.jmol.api.SC
- getText() - Method in class org.jmol.awt.AwtSwingComponent
- getText() - Method in class org.jmol.awtjs.swing.Component
- getText() - Method in class org.jmol.console.GenericConsole
- getText() - Method in interface org.jmol.console.GenericTextArea
- getText() - Method in class org.jmol.console.ScriptEditor
- getText() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- getText(Object) - Method in interface jspecview.api.PlatformDialog
- getText(Object) - Method in class jspecview.java.AwtDialog
- getText(Object) - Method in class jspecview.js2d.JsDialog
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class jspecview.java.AwtPlatform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class jspecview.js2d.JsPlatform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
- getTextPosition() - Method in class org.jmol.util.GData
- getTFToggle(String) - Static method in class jspecview.common.Parameters
- getThermalRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoid
- getTheta() - Method in class javajs.util.Quat
- getThetaDirected(P4) - Method in class javajs.util.Quat
- getThetaDirectedV(V3) - Method in class javajs.util.Quat
- getThetaRadians() - Method in class javajs.util.Quat
- getThisContext() - Method in interface org.jmol.api.JmolScriptEvaluator
- getThisContext() - Method in class org.jmol.script.ScriptEval
- getThisModelAtoms() - Method in class org.jmol.viewer.Viewer
- getThread() - Method in class org.jmol.minimize.Minimizer
- getThresh() - Method in class jspecview.common.PeakData
- getTime() - Method in class com.sparshui.common.messages.events.DragEvent
- getTime() - Method in class com.sparshui.common.messages.events.RotateEvent
- getTime() - Method in class com.sparshui.common.messages.events.TouchEvent
- getTime() - Method in class com.sparshui.common.messages.events.ZoomEvent
- getTime() - Method in class com.sparshui.server.TouchPoint
- getTime() - Method in class jspecview.source.JDXHeader
-
Getter for property time.
- getTimerMsg(String, int) - Static method in class org.jmol.util.Logger
- getTip() - Method in enum class jspecview.common.ScriptToken
- getTitle() - Method in interface jspecview.api.JSVViewPanel
- getTitle() - Method in class jspecview.common.PanelData
-
Returns the title displayed on the graph
- getTitle() - Method in class jspecview.common.PeakInfo
- getTitle() - Method in class jspecview.java.AwtMainPanel
- getTitle() - Method in class jspecview.java.AwtPanel
- getTitle() - Method in class jspecview.js2d.JsMainPanel
- getTitle() - Method in class jspecview.js2d.JsPanel
- getTitle() - Method in class jspecview.source.JDXHeader
-
Getter for property title.
- getTitleLabel() - Method in class jspecview.common.Spectrum
- gettMixField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getTok() - Method in interface org.jmol.api.JmolScriptFunction
- getTok() - Method in class org.jmol.script.ScriptFunction
- getToken(int) - Method in class org.jmol.script.ScriptContext
- getToken(int) - Method in class org.jmol.script.ScriptParam
- getToken(int) - Method in class org.jmol.scriptext.ScriptExt
- getTokenCount() - Method in class org.jmol.script.ScriptContext
- getTokenFromName(String) - Static method in class org.jmol.script.T
- getTokenPeeked() - Method in interface javajs.api.GenericCifDataParser
- getTokenPeeked() - Method in class javajs.util.CifDataParser
- getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getTokens() - Method in class org.jmol.jvxl.readers.JvxlReader
- getTokens() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getTokens() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getTokens(String) - Static method in class javajs.util.PT
- getTokens(String) - Static method in enum class jspecview.common.ScriptToken
-
read a string for possibly quoted tokens separated by space until // or # is reached.
- getTokensAt(String, int) - Static method in class javajs.util.PT
- getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getTokensLike(String) - Static method in class org.jmol.script.T
- getTokensType(Map<String, Object>, int) - Static method in class org.jmol.script.T
- getTokFromName(String) - Static method in class org.jmol.script.T
- getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
- getTopPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
- getTorsionAngleRadians(double[], double[], double[], double[], V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- getTorsions(boolean) - Method in class org.jmol.minimize.Minimizer
- getTotalHydrogenCount() - Method in class org.jmol.modelset.Atom
- getTotalHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getTotalHydrogenCount() - Method in interface org.jmol.util.Node
- getTotalIn() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- getTotalIn() - Method in class com.jcraft.jzlib.InflaterInputStream
- getTotalIn() - Method in class com.jcraft.jzlib.ZStream
- getTotalOut() - Method in class com.jcraft.jzlib.DeflaterOutputStream
- getTotalOut() - Method in class com.jcraft.jzlib.InflaterInputStream
- getTotalOut() - Method in class com.jcraft.jzlib.ZStream
- getTotalValence() - Method in class org.jmol.modelset.Atom
- getTotalValence() - Method in class org.jmol.smiles.SmilesAtom
- getTotalValence() - Method in interface org.jmol.util.Node
- getTouchID() - Method in class com.sparshui.common.messages.events.TouchEvent
- getTrajectoryState() - Method in class org.jmol.viewer.Viewer
- getTransferData(DataFlavor) - Method in class jspecview.java.AwtClipboard
- getTransferData(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
- getTransferDataFlavors() - Method in class jspecview.java.AwtClipboard
- getTransferDataFlavors() - Method in class org.jmol.awt.AwtClipboard
- getTransform(P3, P3, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getTransform(P3, P3, boolean) - Method in class org.jmol.symmetry.Symmetry
- getTransform(UnitCell, SymmetryOperation[], P3, P3, boolean) - Method in class org.jmol.symmetry.SymmetryDesc
- getTransformABC(Object, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getTransformedVertexVectors() - Method in class org.jmol.util.GData
- getTransformMatrix4(Lst<P3>, Lst<P3>, M4, P3) - Static method in class javajs.util.Measure
-
Fills a 4x4 matrix with rotation-translation of mapped points A to B.
- getTranslation() - Method in class javajs.util.Matrix
- getTranslation(int) - Method in class org.jmol.modelset.ModelSet
- getTranslation(T3) - Method in class javajs.util.M4
-
Retrieves the translational components of this matrix.
- getTranslationScript() - Method in class org.jmol.viewer.TransformManager
- getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
- getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
- getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
- getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEval
- getTreeNode() - Method in class jspecview.common.PanelNode
- getTriad(T3) - Method in class org.jmol.export.___Exporter
- getTriad(T3) - Method in class org.jmol.export._PovrayExporter
- getTriadC(T3) - Method in class org.jmol.export.___Exporter
- getTriangulator() - Method in class org.jmol.viewer.Viewer
- getTrueAtomCount() - Method in class org.jmol.modelset.Model
-
not actually accessed -- just pointing out what it is
- getType() - Method in class javajs.util.OC
- getType() - Method in class jspecview.common.PeakInfo
- getType() - Method in interface org.jmol.api.JmolDialogInterface
- getType() - Method in class org.jmol.dialog.Dialog
- getType() - Method in class org.jmol.modelsetbio.BioPolymer
- getType(int) - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
- getType(String) - Static method in enum class jspecview.common.ExportType
- getType(Atom) - Static method in enum class org.jmol.c.HB
- getTypeLabel() - Method in class jspecview.source.JDXDataObject
- getUndoInfo() - Method in class org.jmol.viewer.StateManager
- getUndoMax() - Method in class org.jmol.viewer.StateManager
- getUndoRedoState(int) - Method in class org.jmol.viewer.StateManager
- getUnGzippedInputStream(byte[]) - Method in interface javajs.api.GenericZipTools
- getUnGzippedInputStream(byte[]) - Method in class javajs.util.ZipTools
- getUniqueID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
- getUniqueID(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getUniqueID(int) - Method in interface org.jmol.api.PymolAtomReader
- getUniqueTensorSet(BS) - Method in interface org.jmol.api.JmolNMRInterface
-
An attempt to find unique atoms using tensors.
- getUniqueTensorSet(BS) - Method in class org.jmol.quantum.NMRCalculation
- getUnitCell() - Method in class org.jmol.shape.Mesh
- getUnitCell() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getUnitCell(int) - Method in class org.jmol.modelset.ModelSet
- getUnitCell(T3[], boolean, String) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCell(T3[], boolean, String) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
- getUnitCellAtomIndex() - Method in class org.jmol.viewer.AnimationManager
- getUnitCellCenter() - Method in class org.jmol.script.ScriptParam
- getUnitCellDisplayName() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellDisplayName() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellForAtom(int) - Method in class org.jmol.modelset.ModelSet
- getUnitCellInfo(boolean) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellInfo(boolean) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
- getUnitCellInfoMap() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellInfoMap() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
- getUnitCellInfoType(int) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellInfoType(int) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellMultiplied() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellMultiplied() - Method in class org.jmol.symmetry.Symmetry
-
Note, this has no origin shift.
- getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellParams() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellParams() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellParams() - Method in class org.jmol.util.SimpleUnitCell
- getUnitCellPointsWithin(float, BS, P3, boolean) - Method in class org.jmol.modelset.ModelSet
- getUnitCellState() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellState() - Method in class org.jmol.modelkit.ModelKit
- getUnitCellState() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellVectors() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellVectors() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellVerticesNoOffset() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellVerticesNoOffset() - Method in class org.jmol.symmetry.Symmetry
- getUnitConversion(String, String) - Static method in class org.qcschema.QCSchemaUnits
-
Calculate the unit conversion between two units, using a static unit-to-unit cache for efficiency.
- getUnitID(int) - Method in class org.jmol.modelset.Atom
- getUnitID(Atom, int) - Method in class org.jmol.modelsetbio.BioModel
-
Get a unitID.
- getUnitIDFlags(String) - Static method in class org.jmol.viewer.JC
-
Get a unitID type
- getUnitsJSON(String, boolean) - Static method in class org.qcschema.QCSchemaUnits
-
Get the [name, toAU] JSON code or just a new String[] {name, toAU}.
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class jspecview.java.AwtPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- getUnlikely() - Static method in class javajs.util.P3
- getUnzippedInputStream(GenericZipTools, BufferedInputStream) - Static method in class javajs.util.Rdr
-
Drill down into a GZIP stack until no more layers.
- getUnzippedInputStreamBZip2(GenericZipTools, BufferedInputStream) - Static method in class javajs.util.Rdr
- getUnzippedReaderOrStreamFromName(String, Object, boolean, boolean, boolean, boolean, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
- getURLContents(URL, byte[], String, boolean) - Method in class jspecview.java.AwtPlatform
- getURLContents(URL, byte[], String, boolean) - Method in class jspecview.js2d.JsPlatform
- getURLContents(URL, byte[], String, boolean) - Method in interface org.jmol.api.GenericPlatform
- getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awt.Platform
- getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awtjs2d.Platform
- getURLContentsStatic(URL, byte[], String, boolean) - Static method in class org.jmol.awtjs2d.Platform
-
In case this needs to be performed directly, without interface
- getUrlFromDialog(String, String) - Method in interface jspecview.api.JSVFileHelper
- getUrlFromDialog(String, String) - Method in class jspecview.java.AwtFileHelper
- getUrlFromDialog(String, String) - Method in class jspecview.js2d.JsFileHelper
- getUserDirectory() - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
-
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
- getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
- getUserFunctionResult(String, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
- getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
- getUserYFactor() - Method in class jspecview.common.Spectrum
- getUtil(String, Viewer, String) - Static method in class org.jmol.api.Interface
- getV0abc(int, Object) - Method in class org.jmol.viewer.Viewer
-
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c.
- getV0abc(Object, M4) - Method in interface org.jmol.api.SymmetryInterface
- getV0abc(Object, M4) - Method in class org.jmol.symmetry.Symmetry
- getV3() - Method in interface org.jmol.api.JmolModulationSet
- getV3() - Method in class org.jmol.util.ModulationSet
- getValence() - Method in class org.jmol.modelset.Atom
-
return the total bond order for this atom
- getValence() - Method in class org.jmol.modelset.Bond
- getValence() - Method in class org.jmol.smiles.SmilesAtom
- getValence() - Method in class org.jmol.smiles.SmilesBond
- getValence() - Method in interface org.jmol.util.Node
- getValence() - Method in interface org.jmol.util.SimpleNode
- getValidValues(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getValidVertices(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getValue() - Method in class com.jcraft.jzlib.Adler32
- getValue() - Method in interface com.jcraft.jzlib.Checksum
- getValue() - Method in class com.jcraft.jzlib.CRC32
- getValue() - Method in class jspecview.common.Measurement
- getValue() - Method in class jspecview.source.JDXSourceStreamTokenizer
- getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
- getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
for readers only
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
- getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- getValue(String, String) - Method in class org.jmol.util.GenericApplet
- getValue(ScriptToken, ScriptTokenizer, String) - Static method in enum class jspecview.common.ScriptToken
-
tweak command options depending upon special cases
- getValue2(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getValueArray(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
- getValueAt(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getValueAtPoint(P3) - Method in class org.jmol.quantum.MepCalculation
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getValues(Mesh) - Method in class org.jmol.shape.MeshCollection
- getValues(Mesh) - Method in class org.jmol.shapesurface.Isosurface
- getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
- getVanderwaalsMar(int, VDW) - Static method in class org.jmol.util.Elements
- getVanderwaalsMarType(int, VDW) - Method in class org.jmol.viewer.Viewer
- getVanderwaalsRadiusFloat(Viewer, VDW) - Method in class org.jmol.modelset.Atom
- getVariable(Object) - Static method in class org.jmol.script.SV
- getVariable(String) - Method in class org.jmol.script.ScriptContext
-
Context variables go up the stack until a function is found.
- getVariableAD(double[]) - Static method in class org.jmol.script.SV
- getVariableList() - Method in class org.jmol.viewer.GlobalSettings
- getVariableList(Map<String, SV>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
- getVariableList(Lst<?>) - Static method in class org.jmol.script.SV
- getVariableMap(Map<String, ?>) - Static method in class org.jmol.script.SV
- getVarList(String) - Static method in class jspecview.source.JDXReader
- getVarParameter(String, boolean) - Method in class org.jmol.script.ScriptParam
- getVDW(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getVDW(int) - Method in interface org.jmol.api.PymolAtomReader
- getVdwLabel() - Method in enum class org.jmol.c.VDW
- getVdwType(String) - Static method in enum class org.jmol.c.VDW
- getVdwType2(String) - Static method in enum class org.jmol.c.VDW
- getVector(int) - Method in class javajs.util.Quat
- getVector(Location) - Method in class com.sparshui.common.Location
- getVectorScaled(int, float) - Method in class javajs.util.Quat
- getVersion() - Method in class javajs.util.CifDataParser
- getVersion() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
- getVersion() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getVersion() - Method in interface org.openscience.jmol.app.JmolPlugin
- getVertexCount(int) - Static method in class org.jmol.util.Geodesic
- getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
- getVertexVector(int) - Static method in class org.jmol.util.Geodesic
- getVertexVectors() - Static method in class org.jmol.util.Geodesic
- getVertexVectors() - Static method in class org.jmol.util.Normix
- getVertices() - Method in class org.jmol.util.MeshSurface
- getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
- getVertices(Mesh) - Method in class org.jmol.shapesurface.Isosurface
- getVerticesFromOABC(T3[]) - Static method in class org.jmol.util.BoxInfo
- getVib() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getVib(char) - Method in class org.jmol.modelset.Atom
- getVibCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
-
also handles modulation info
- getVibration(boolean) - Method in interface org.jmol.api.JmolModulationSet
- getVibration(boolean) - Method in class org.jmol.util.ModulationSet
- getVibration(int, boolean) - Method in class org.jmol.modelset.AtomCollection
- getVibrationPoint(Vibration, T3, float) - Method in class org.jmol.viewer.TransformManager
-
return
- getVibrationVector() - Method in class org.jmol.modelset.Atom
- getView() - Method in class jspecview.common.PanelData
- getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getViewpoint() - Method in class org.jmol.export._VrmlExporter
- getViewTitle() - Method in class jspecview.common.PanelData
- getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
- getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
- getVisibleSet(boolean) - Method in class org.jmol.modelset.AtomCollection
- getVisibleVBS() - Method in class org.jmol.shape.Mesh
- getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
- getVisibleVertexBitSet() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelDataAt(int) - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- getWebSite() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getWebSite() - Method in interface org.openscience.jmol.app.JmolPlugin
- getWidth() - Method in interface jspecview.api.JSVViewPanel
- getWidth() - Method in class jspecview.common.JSViewer
- getWidth() - Method in class jspecview.js2d.JsMainPanel
- getWidth() - Method in class jspecview.js2d.JsPanel
- getWidth() - Method in class org.jmol.awtjs.swing.Component
- getWindow(Container) - Static method in class jspecview.java.AwtPlatform
- getWindow(Container) - Static method in class org.jmol.awt.Platform
- getWindowBorder(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowInnerDimension(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowName() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getWindowName() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getWindowPosition(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowSize(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
- getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
- getWordContents() - Method in class jspecview.popup.JSVPopupResourceBundle
- getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
- getWordContents() - Method in class org.jmol.popup.PopupResource
- getWrappedStateScript() - Method in class org.jmol.viewer.Viewer
- getWyckoffPosition(boolean) - Method in class org.jmol.modelset.Atom
- getWyckoffPosition(Viewer, P3, String) - Method in interface org.jmol.api.SymmetryInterface
- getWyckoffPosition(Viewer, P3, String) - Method in class org.jmol.symmetry.Symmetry
- getX() - Method in class com.sparshui.common.Location
- getX() - Method in class com.sparshui.common.messages.events.RotateEvent
- getX() - Method in class com.sparshui.common.messages.events.TouchEvent
- getX() - Method in class com.sparshui.common.messages.events.ZoomEvent
- getX() - Method in class jspecview.common.PeakInfo
- getX() - Method in class org.jmol.script.ScriptMathProcessor
- getX(int) - Method in class jme.JMEmol
- getXdirection() - Method in class com.sparshui.common.messages.events.FlickEvent
- getXFactor() - Method in class jspecview.source.JDXDataObject
-
Returns the original x factor
- getXMax() - Method in class jspecview.common.PeakInfo
- getXMin() - Method in class jspecview.common.PeakInfo
- getXML(BufferedReader) - Method in class jspecview.source.AnIMLReader
- getXmlAttrib(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
- getXmlData(String, String, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
- getXmlDataLF(String, String, boolean, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
- getXmlPoint(String, String) - Method in class org.jmol.jvxl.readers.XmlReader
- getXOffset(int) - Static method in class org.jmol.viewer.JC
-
X offset in pixels.
- getXPixel() - Method in class jspecview.common.PeakInfo
- getXSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getXTok() - Method in class org.jmol.script.ScriptMathProcessor
- getXUnits() - Method in class jspecview.source.JDXDataObject
-
Returns the units for x-axis when spectrum is displayed
- getXVal() - Method in class jspecview.common.Coordinate
-
Returns the x value of the coordinate
- getXVal2() - Method in class jspecview.common.Measurement
- getXYCoords() - Method in class jspecview.common.IntegralData
- getXYCoords() - Method in class jspecview.common.Spectrum
-
Returns the array of coordinates
- getXYZ() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getXYZ() - Method in class org.jmol.modelset.Atom
- getXYZ() - Method in class org.jmol.smiles.SmilesAtom
- getXYZ() - Method in interface org.jmol.util.Node
- getXYZ() - Method in interface org.jmol.util.SimpleNode
- getXYZFromMatrix(M4, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getXYZFromMatrixFrac(M4, boolean, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getXYZFromRsVs(Matrix, Matrix, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getxyzTrans(T3) - Method in class org.jmol.symmetry.SymmetryOperation
- getY() - Method in class com.sparshui.common.Location
- getY() - Method in class com.sparshui.common.messages.events.RotateEvent
- getY() - Method in class com.sparshui.common.messages.events.TouchEvent
- getY() - Method in class com.sparshui.common.messages.events.ZoomEvent
- getY(int) - Method in class jme.JMEmol
- getY2D() - Method in class jspecview.source.JDXDataObject
- getY2DPPM() - Method in class jspecview.source.JDXDataObject
- getYdirection() - Method in class com.sparshui.common.messages.events.FlickEvent
- getYellowField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- getYellowField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- getYellowValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getYellowValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getYFactor() - Method in class jspecview.source.JDXDataObject
-
Returns the original y factor
- getYMax() - Method in class jspecview.common.PeakInfo
- getYMin() - Method in class jspecview.common.PeakInfo
- getYOffset(int) - Static method in class org.jmol.viewer.JC
-
Y offset in pixels; negative of this is the actual screen offset
- getYRef() - Method in class jspecview.source.JDXDataObject
- getYUnits() - Method in class jspecview.source.JDXDataObject
-
Returns the units for y-axis when spectrum is displayed
- getYVal() - Method in class jspecview.common.Coordinate
-
Returns the y value of the coordinate
- getYVal2() - Method in class jspecview.common.Measurement
- getYValueAt(double) - Method in class jspecview.common.Spectrum
- getYValueAt(Coordinate[], double) - Static method in class jspecview.common.Coordinate
- getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
- getZapName() - Method in class org.jmol.viewer.Viewer
- getZCurrent(float, float, int) - Method in class org.jmol.g3d.PrecisionRenderer
- getZipDirectory(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getZipDirectoryAndClose(BufferedInputStream, String) - Method in interface javajs.api.GenericZipTools
- getZipDirectoryAndClose(BufferedInputStream, String) - Method in class javajs.util.ZipTools
- getZipDirectoryAsString(String) - Method in class org.jmol.viewer.Viewer
- getZipDirectoryAsStringAndClose(BufferedInputStream) - Method in interface javajs.api.GenericZipTools
- getZipDirectoryAsStringAndClose(BufferedInputStream) - Method in class javajs.util.ZipTools
- getZipFileContentsAsBytes(BufferedInputStream, String[], int) - Method in interface javajs.api.GenericZipTools
- getZipFileContentsAsBytes(BufferedInputStream, String[], int) - Method in class javajs.util.ZipTools
- getZipFileDirectory(BufferedInputStream, String[], int, boolean) - Method in interface javajs.api.GenericZipTools
- getZipFileDirectory(BufferedInputStream, String[], int, boolean) - Method in class javajs.util.ZipTools
-
iteratively drills into zip files of zip files to extract file content or zip file directory.
- getZipOutputStream(Object) - Method in interface javajs.api.GenericZipTools
- getZipOutputStream(Object) - Method in class javajs.util.ZipTools
- getZipRoot(String) - Static method in class javajs.util.Rdr
-
We define a request for zip file extraction by vertical bar: zipName|interiorFileName.
- getZoomSetting() - Method in class org.jmol.viewer.TransformManager
- GhemicalMMReader - Class in org.jmol.adapter.readers.simple
-
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
- GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
- GifEncoder - Class in javajs.img
-
GifEncoder extensively adapted for Jmol by Bob Hanson Color quantization roughly follows the GIMP method "dither Floyd-Steinberg (normal)" but with some twists.
- GifEncoder() - Constructor for class javajs.img.GifEncoder
- GL_LINE_LOOP - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_LINE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_LINES - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_POINTS - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_TRIANGLE_FAN - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_TRIANGLE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_TRIANGLES - Static variable in class org.jmol.shapecgo.CGOMesh
- GLOBAL_AROMATICBONDS - Static variable in class org.jmol.viewer.JC
- GLOBAL_CONECT - Static variable in class org.jmol.viewer.JC
- GLOBAL_DOMAINS - Static variable in class org.jmol.viewer.JC
- GLOBAL_FRACTCOORD - Static variable in class org.jmol.viewer.JC
- GLOBAL_ISPDB - Static variable in class org.jmol.viewer.JC
- GLOBAL_MODULATED - Static variable in class org.jmol.viewer.JC
- GLOBAL_SUPERCELL - Static variable in class org.jmol.viewer.JC
- GLOBAL_SYMMETRY - Static variable in class org.jmol.viewer.JC
- GLOBAL_UNITCELLS - Static variable in class org.jmol.viewer.JC
- GLOBAL_VALIDATIONS - Static variable in class org.jmol.viewer.JC
- globalBooleans - Static variable in class org.jmol.viewer.JC
- GlobalSettings - Class in org.jmol.viewer
- goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- GOLD - Static variable in class org.jmol.util.C
- gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- gotocmd - Static variable in class org.jmol.script.T
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- gotoTop() - Method in class org.jmol.console.ScriptEditor
- grabPixels(Object, int, int, int[]) - Method in class jspecview.java.AwtPlatform
- grabPixels(Object, int, int, int[]) - Method in class jspecview.js2d.JsPlatform
- grabPixels(Object, int, int, int[]) - Method in interface org.jmol.api.GenericPlatform
- grabPixels(Object, int, int, int[]) - Method in class org.jmol.awt.Platform
- grabPixels(Object, int, int, int[]) - Method in class org.jmol.awtjs2d.Platform
- Graphics3D - Class in org.jmol.g3d
-
Provides high-level graphics primitives for 3D visualization for the software renderers.
- Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
- graphicsForMetrics - Variable in class org.jmol.util.GData
- graphSets - Variable in class jspecview.common.PanelData
- GRAY - Static variable in class org.jmol.util.C
- GREEN - Static variable in class org.jmol.util.C
- greyscalerendering - Static variable in class org.jmol.script.T
- Grid - Class in org.jmol.awtjs.swing
- GridBagConstraints - Class in org.jmol.awtjs.swing
- GridBagConstraints(int, int, int, int, double, double, int, int, Insets, int, int) - Constructor for class org.jmol.awtjs.swing.GridBagConstraints
- GridBagLayout - Class in org.jmol.awtjs.swing
- GridBagLayout() - Constructor for class org.jmol.awtjs.swing.GridBagLayout
- gridColor - Variable in class jspecview.common.PanelData
- GRIDCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- gridheight - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gridOn - Variable in class jspecview.common.PanelData
- GRIDON - Enum constant in enum class jspecview.common.ScriptToken
- gridpoints - Static variable in class org.jmol.script.T
- gridwidth - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gridx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gridy - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gRight - Variable in class org.jmol.util.GenericApplet
- GromacsReader - Class in org.jmol.adapter.readers.more
- GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
- gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- group - Variable in class org.jmol.modelset.Atom
- group - Static variable in class org.jmol.script.T
- group() - Method in class org.jmol.util.PatternMatcher.JSPattern
- Group - Class in com.sparshui.server
-
Represents a group of touch points for the gesture server.
- Group - Class in org.jmol.modelset
-
The essential container for every atom.
- Group() - Constructor for class org.jmol.modelset.Group
- Group(int, Lst<GestureType>, ServerToClientProtocol) - Constructor for class com.sparshui.server.Group
-
Construct a new group with the given gesture IDs and the given connection to the client.
- GROUP - Enum constant in enum class org.jmol.c.PAL
- group1 - Variable in class org.jmol.modelset.Group
- group1 - Static variable in class org.jmol.script.T
- group3 - Variable in class org.jmol.adapter.smarter.Atom
- group3Counts - Variable in class org.jmol.modelset.ModelLoader
- group3Lists - Variable in class org.jmol.modelset.ModelLoader
- group3NameCount - Static variable in class org.jmol.modelsetbio.BioResolver
- group3Names - Static variable in class org.jmol.modelset.Group
- groupCount - Variable in class org.jmol.modelset.Chain
- groupCount - Variable in class org.jmol.modelset.Model
- groupid - Static variable in class org.jmol.script.T
- groupID - Variable in class org.jmol.modelset.Group
- GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JC
- GROUPID_ARGININE - Static variable in class org.jmol.viewer.JC
- GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JC
- GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JC
- GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JC
- GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JC
- GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JC
- GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JC
- GROUPID_LYSINE - Static variable in class org.jmol.viewer.JC
- GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JC
- GROUPID_PROLINE - Static variable in class org.jmol.viewer.JC
- GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JC
- GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JC
- GROUPID_WATER - Static variable in class org.jmol.viewer.JC
- groupindex - Static variable in class org.jmol.script.T
- groupIndex - Variable in class org.jmol.modelset.Group
- groups - Variable in class org.jmol.modelset.Chain
-
Groups form the essence of what a Chain is.
- groups - Variable in class org.jmol.modelset.ModelLoader
- growArray(double[], int) - Static method in class jme.JMEUtil
- growArray(int[][], int) - Static method in class jme.JMEUtil
- growArray(int[], int) - Static method in class jme.JMEUtil
- growArray(String[], int) - Static method in class jme.JMEUtil
- growArray(T[], int) - Static method in class jme.JMEUtil
- growAtomArrays(int) - Method in class org.jmol.modelset.ModelSet
- GS - Static variable in class org.jmol.quantum.QS
- GT - Class in org.jmol.i18n
-
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
- GT() - Constructor for class org.jmol.i18n.GT
- GT(Viewer, String) - Constructor for class org.jmol.i18n.GT
- guessMimeTypeForBytes(byte[]) - Static method in class javajs.util.Rdr
- guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- GuiMap - Class in org.openscience.jmol.app.jmolpanel
- GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
- GulpReader - Class in org.jmol.adapter.readers.xtal
-
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
- GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
- GWT() - Constructor for class jme.JMEUtil.GWT
- GZIPException - Exception Class in com.jcraft.jzlib
- GZIPException() - Constructor for exception class com.jcraft.jzlib.GZIPException
- GZIPException(String) - Constructor for exception class com.jcraft.jzlib.GZIPException
- GZIPHeader - Class in com.jcraft.jzlib
- GZIPHeader() - Constructor for class com.jcraft.jzlib.GZIPHeader
- GZIPInputStream - Class in com.jcraft.jzlib
- GZIPInputStream() - Constructor for class com.jcraft.jzlib.GZIPInputStream
- GZIPOutputStream - Class in com.jcraft.jzlib
- GZIPOutputStream() - Constructor for class com.jcraft.jzlib.GZIPOutputStream
H
- halo - Static variable in class org.jmol.script.T
- Halos - Class in org.jmol.shape
- Halos() - Constructor for class org.jmol.shape.Halos
- HalosRenderer - Class in org.jmol.render
- HalosRenderer() - Constructor for class org.jmol.render.HalosRenderer
- halt - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- haltExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
- haltExecution() - Method in class org.jmol.script.ScriptEval
- haltScriptExecution() - Method in class org.jmol.api.JmolViewer
- haltScriptExecution() - Method in class org.jmol.viewer.Viewer
- handleAssignNew(MouseState, MouseState, MeasurementPending, int, int) - Method in class org.jmol.modelkit.ModelKit
-
handle a mouse-generated assignNew event
- handleError(Throwable, boolean) - Method in class org.jmol.viewer.Viewer
- handleEvent(Event) - Method in interface org.jmol.api.JmolAppletInterface
- handleEvent(Event) - Method in class org.jmol.util.GenericApplet
- handleEvent(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManagerAwt
-
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
- handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManagerJS
-
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
- HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
- HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
- hasConstraint(int, boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
- hasContent() - Method in class org.jmol.g3d.Graphics3D
- hasCurrentMeasurements(Annotation.AType) - Method in class jspecview.common.PanelData
- hasDatabasePrefix(String) - Static method in class org.jmol.viewer.Viewer
- hasFileLoaded(String) - Method in class jspecview.common.PanelData
- hasFocus() - Method in interface jspecview.api.JSVPanel
- hasFocus() - Method in class jspecview.common.PanelData
- hasFocus() - Method in class jspecview.js2d.JsPanel
- hasFocus() - Method in class org.jmol.viewer.Viewer
- hasFocus(Object) - Method in class jspecview.java.AwtPlatform
- hasFocus(Object) - Method in class jspecview.js2d.JsPlatform
- hasFocus(Object) - Method in interface org.jmol.api.GenericPlatform
- hasFocus(Object) - Method in class org.jmol.awt.Platform
- hasFocus(Object) - Method in class org.jmol.awtjs2d.Platform
- hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- hash - Static variable in class org.jmol.script.T
- hashCode() - Method in class javajs.util.A4
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class javajs.util.BArray
- hashCode() - Method in class javajs.util.BS
-
Returns a hash code value for this bit set.
- hashCode() - Method in class javajs.util.M3
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class javajs.util.M4
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class javajs.util.T3
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class javajs.util.T3d
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class javajs.util.T3i
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class javajs.util.T4
-
Returns a hash number based on the data values in this object.
- hashCode() - Method in class org.jmol.modelset.Atom
- hashCode() - Method in class org.jmol.script.T
- hasMeasure(int[]) - Method in class org.jmol.modelset.Trajectory
- hasMoreElements() - Method in class jspecview.tree.SimpleTreeEnumeration
- hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
-
normal iterator predicate
- hasMoreTokens() - Method in class jspecview.common.ScriptTokenizer
- hasNext() - Method in class jspecview.source.JDXDecompressor
- hasNext() - Method in class jspecview.source.XMLParser
- hasNext() - Method in class org.jmol.adapter.smarter.StructureIterator
- hasNext() - Method in interface org.jmol.api.AtomIndexIterator
- hasNext() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- hasNext() - Method in class org.jmol.api.JmolAdapterBondIterator
- hasNext() - Method in class org.jmol.api.JmolAdapterStructureIterator
- hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
- hasNext() - Method in interface org.jmol.modelset.BondIterator
- hasNext() - Method in class org.jmol.symmetry.UnitCellIterator
- hasNext2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- hasOuputSocket() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- hasOuputSocket() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
- hasPrevious() - Method in class jme.JME
- hasRasmolHBonds - Variable in class org.jmol.modelset.Model
- hasRingData(int) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
- hasSelected - Variable in class org.jmol.viewer.Viewer
- hasStructure - Variable in class org.jmol.modelsetbio.BioPolymer
- hasStructure(String, String[], int) - Method in interface org.jmol.api.SmilesMatcherInterface
- hasStructure(String, String[], int) - Method in class org.jmol.smiles.SmilesMatcher
-
Look for pattern in each smilesSet string.
- hasStructure(String, String, boolean) - Method in class org.jmol.viewer.Viewer
- hasValues() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- hasVibration() - Method in class org.jmol.modelset.Atom
- hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
- hAtomRadius - Variable in class org.jmol.atomdata.AtomData
- hAtoms - Variable in class org.jmol.atomdata.AtomData
- have(byte[], byte) - Static method in class org.jmol.modelsetbio.Monomer
- haveAccess(Viewer.ACCESS) - Method in class org.jmol.viewer.Viewer
- haveAnisou - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- haveAtropicBonds - Variable in class org.jmol.modelset.BondCollection
- haveBioModels - Variable in class org.jmol.modelset.ModelSet
- haveBorder - Variable in class org.openscience.jmol.app.JmolApp
- haveBsDisplay - Variable in class org.jmol.render.MeshRenderer
- haveChirality - Variable in class org.jmol.modelset.AtomCollection
- haveCommon(BS, BS) - Static method in class org.jmol.util.BSUtil
- haveConsole - Variable in class org.openscience.jmol.app.JmolApp
- haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- haveData - Variable in class javajs.util.CifDataParser
- haveDisplay - Variable in class org.jmol.viewer.Viewer
- haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
- haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- haveDocumentAccess - Variable in class org.jmol.util.GenericApplet
- haveEnergy - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- haveFileSet() - Method in class org.jmol.viewer.Viewer
- haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
- haveMacro - Variable in class org.jmol.script.ScriptCompiler
- haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- haveModified - Variable in class org.jmol.modelset.MeasurementPending
- haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
- haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
- haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
- haveNotifiedError - Variable in class org.jmol.util.GenericApplet
- haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
- haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
- havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- havePlanarContours - Variable in class org.jmol.shape.Mesh
- havePoints - Variable in class org.jmol.quantum.MOCalculation
- haveQuads - Variable in class org.jmol.util.MeshSurface
- haveReference - Variable in class org.jmol.thread.JmolThread
- haveSelectedSpectrum() - Method in class jspecview.common.PanelData
- haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
- haveStraightness - Variable in class org.jmol.modelset.AtomCollection
- haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
- haveTarget - Variable in class org.jmol.modelset.MeasurementPending
- haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
- haveTranslucentObjects() - Method in class org.jmol.export.Export3D
- haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
- haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- haveUnitCell - Variable in class org.jmol.adapter.writers.XtlWriter
- haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
- haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
- haveUnitCells - Variable in class org.jmol.modelset.ModelSet
- haveXyPoints - Variable in class org.jmol.shape.Mesh
- HB - Enum Class in org.jmol.c
-
Enum for hydrogen bonding donor/acceptor type
- hBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- hbond - Static variable in class org.jmol.script.T
- HBond - Class in org.jmol.modelset
- HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
- hbondhxdistancemaximum - Static variable in class org.jmol.script.T
- hbondnodistancemaximum - Static variable in class org.jmol.script.T
- hbondsangleminimum - Static variable in class org.jmol.script.T
- hbondsbackbone - Static variable in class org.jmol.script.T
- hbondsrasmol - Static variable in class org.jmol.script.T
- hbondssolid - Static variable in class org.jmol.script.T
- HC - Static variable in class org.jmol.quantum.QS
- hDashes - Static variable in class org.jmol.render.FontLineShapeRenderer
- HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
- HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
- HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
- HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
- headerTable - Variable in class jspecview.source.JDXHeader
- headless - Variable in class org.jmol.viewer.Viewer
-
determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN
, ANIMATION ON turns SPIN into just ROTATE - height - Variable in class javajs.img.ImageEncoder
- height - Variable in class org.jmol.awtjs.swing.Component
- height - Variable in class org.jmol.awtjs.swing.Dimension
- height - Variable in class org.jmol.util.GData
- height - Variable in class org.jmol.util.Rectangle
- height - Variable in class org.jmol.viewer.TransformManager
- helix - Static variable in class org.jmol.script.T
- Helix - Class in org.jmol.modelsetbio
- HELIX - Enum constant in enum class org.jmol.c.STR
- helix310 - Static variable in class org.jmol.script.T
- HELIX310 - Enum constant in enum class org.jmol.c.STR
- helixalpha - Static variable in class org.jmol.script.T
- HELIXALPHA - Enum constant in enum class org.jmol.c.STR
- helixpi - Static variable in class org.jmol.script.T
- HELIXPI - Enum constant in enum class org.jmol.c.STR
- helixRockets - Variable in class org.jmol.renderbio.RocketsRenderer
- helixstep - Static variable in class org.jmol.script.T
- help - Static variable in class org.jmol.script.T
- HELP - Enum constant in enum class jspecview.common.ScriptToken
- HelpDialog - Class in org.openscience.jmol.app.jmolpanel
- HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
- HelpDialog(JFrame, String, boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
- HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
-
If url is null, then the default help url is taken.
- helper - Variable in class org.jmol.popup.GenericPopup
- helppath - Static variable in class org.jmol.script.T
- hermitelevel - Static variable in class org.jmol.script.T
- HermiteRenderer - Class in org.jmol.g3d
-
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
- HermiteRenderer() - Constructor for class org.jmol.g3d.HermiteRenderer
- hetero - Static variable in class org.jmol.script.T
- HEX_TO_RHOMB - Static variable in class org.jmol.util.SimpleUnitCell
- hi - Variable in class org.jmol.util.ColorEncoder
- hidden - Variable in class org.jmol.modelset.Text
- hidden - Static variable in class org.jmol.script.T
- HIDDEN - Enum constant in enum class jspecview.common.ScriptToken
- hiddenlinesdashed - Static variable in class org.jmol.script.T
- hide - Static variable in class org.jmol.script.T
- hidenameinpopup - Static variable in class org.jmol.script.T
- hidenavigationpoint - Static variable in class org.jmol.script.T
- hidenotselected - Static variable in class org.jmol.script.T
- HIGH - Static variable in class org.jmol.util.ColorEncoder
- highlight - Static variable in class org.jmol.script.T
- highlight(BS) - Method in class org.jmol.viewer.Viewer
- HIGHLIGHT - Enum constant in enum class jspecview.common.ScriptToken
- highlightBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
-
from Sticks
- highlightColor - Variable in class jspecview.common.PanelData
- HIGHLIGHTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- highresolution - Static variable in class org.jmol.script.T
- history - Static variable in class org.jmol.script.T
- historyButton - Variable in class org.jmol.console.GenericConsole
- historyDisabled - Variable in class org.jmol.script.ScriptEval
- historyFile - Variable in class org.openscience.jmol.app.JmolApp
- historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- HistoryFile - Class in org.openscience.jmol.app
-
The history file contains data from previous uses of Jmol.
- HistoryFile(File, String) - Constructor for class org.openscience.jmol.app.HistoryFile
-
Creates a history file.
- historyFind(String, int) - Method in class org.jmol.viewer.Viewer
- historylevel - Static variable in class org.jmol.script.T
- hkl - Static variable in class org.jmol.script.T
- hklParameter(int, Lst<P3>, boolean) - Method in class org.jmol.script.ScriptParam
- holdRepaint - Variable in class org.jmol.render.RepaintManager
- homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- homePosition() - Method in class org.jmol.api.JmolViewer
- homePosition() - Method in class org.jmol.viewer.Viewer
- homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
- homo - Static variable in class org.jmol.script.T
- HORIZONTAL_SPLIT - Static variable in class org.jmol.awtjs.swing.JSplitPane
- HOTPINK - Static variable in class org.jmol.util.C
- hover - Static variable in class org.jmol.script.T
- Hover - Class in org.jmol.shape
- Hover() - Constructor for class org.jmol.shape.Hover
- HOVER - Enum constant in enum class org.jmol.c.CBK
- hoverdelay - Static variable in class org.jmol.script.T
- hoverEnabled - Variable in class org.jmol.thread.JmolThread
- hoverlabel - Static variable in class org.jmol.script.T
- hoverLabel - Variable in class org.jmol.shape.Mesh
- hoverOnPt(int, int, String, String, T3) - Method in class org.jmol.viewer.Viewer
-
Hover over an arbitrary point.
- HoverRenderer - Class in org.jmol.render
- HoverRenderer() - Constructor for class org.jmol.render.HoverRenderer
- hoverText - Variable in class org.jmol.shape.Hover
- hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
- HoverWatcherThread - Class in org.jmol.thread
- HoverWatcherThread(ActionManager, MouseState, MouseState, Viewer) - Constructor for class org.jmol.thread.HoverWatcherThread
- HS - Static variable in class org.jmol.quantum.QS
- hslToRGB(P3) - Static method in class javajs.util.CU
-
Convert HSL (hue/saturation/luninance) values to RGB
- ht3 - Variable in class org.jmol.util.GData
- htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
- htBooleans - Variable in class jspecview.common.Parameters
- htCheckbox - Variable in class org.jmol.popup.GenericPopup
- htDialogs - Variable in class jspecview.dialog.DialogManager
- htElementMap - Static variable in class org.jmol.util.Elements
- htFields - Static variable in class javajs.util.CifDataParser
-
A global, static map that contains field information.
- htGroup - Static variable in class org.jmol.modelsetbio.BioResolver
- htGroup1 - Variable in class org.jmol.adapter.readers.cif.CifReader
- htGroup1 - Static variable in class org.jmol.modelsetbio.NucleicPolymer
- htHetero - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- htMenus - Variable in class org.jmol.popup.GenericPopup
- htMessageCallbacks - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- htMin - Variable in class org.jmol.modelset.MeasurementData
- html5Applet - Variable in class jspecview.common.JSViewer
- html5Applet - Variable in class org.jmol.viewer.Viewer
- HTMLElement - Interface in org.jmol.awtjs.swing
- htmlMenuOpener(String) - Method in class org.jmol.awtjs.swing.AbstractButton
- htmlName - Variable in class org.jmol.util.GenericApplet
- htmlName - Variable in class org.jmol.viewer.Viewer
- HTMLWindowEvent - Interface in org.jmol.awtjs.swing
-
The window.Event in HTML5 See SwingController.
- htModelAtomMap - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- htObjects - Variable in class org.jmol.shape.MeshCollection
- htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- htParams - Variable in class org.jmol.util.GenericApplet
- htPeaks - Variable in class org.jmol.modelset.ModelSet
- htRegistry - Static variable in class org.jmol.util.GenericApplet
- htSites - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- htTracker - Variable in class org.jmol.symmetry.CIPDataTracker
-
a table to track decision making when only one atom is selected for calculation
- htUij - Variable in class org.jmol.util.ModulationSet
-
current value of anisotropic parameter modulation
- htUserFunctions - Variable in class org.jmol.script.ScriptCompiler
- HUGE - Static variable in class org.jmol.util.GData
- HYDRO - Enum constant in enum class org.jmol.c.VDW
- hydrogen - Static variable in class org.jmol.script.T
- hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
- hydrogenCount - Variable in class org.jmol.modelset.Model
- hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- hydrophobicity - Static variable in class org.jmol.script.T
- HyperChemReader - Class in org.jmol.adapter.readers.simple
-
Support for .hin, HyperChem's native file format.
- HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
- hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
- hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
I
- i - Variable in class org.jmol.util.Point3fi
-
index in full collection
- i(int) - Static method in class org.jmol.script.T
- i(String, int) - Static method in class org.jmol.i18n.GT
- iA - Variable in class org.jmol.util.MeshSurface
- iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
- iB - Variable in class org.jmol.util.MeshSurface
- iC - Variable in class org.jmol.util.MeshSurface
- IC - Static variable in class org.jmol.quantum.QS
- ich - Variable in class javajs.util.CifDataParser
-
pointer to current character on str
- ichComment - Variable in class org.jmol.script.ScriptCompiler
- ichCurrentCommand - Variable in class org.jmol.script.ScriptCompiler
- ichEnd - Variable in class org.jmol.script.ScriptCompiler
- ichToken - Variable in class org.jmol.script.ScriptCompiler
- iCommand - Variable in class org.jmol.script.ScriptCompiler
- iCommandError - Variable in class org.jmol.script.ScriptContext
- iCommandError - Variable in class org.jmol.script.ScriptError
- id - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- id - Variable in class jspecview.common.PanelNode
- id - Variable in class jspecview.common.Spectrum
- id - Variable in class org.jmol.awtjs.swing.Component
- id - Variable in enum class org.jmol.c.PAL
- id - Variable in class org.jmol.minimize.Minimizer
- id - Variable in class org.jmol.modelset.TickInfo
- id - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- id - Variable in class org.jmol.script.ScriptContext
- id - Static variable in class org.jmol.script.T
- id - Variable in class org.jmol.shapespecial.Polyhedron
- id - Variable in class org.jmol.util.BZone
- id - Variable in class org.jmol.util.Tensor
- ID_ALL - Static variable in class org.jmol.modelset.Atom
- ID_ATOMS - Static variable in class org.jmol.modelset.Atom
- ID_CHIME - Static variable in class org.jmol.modelset.Atom
- ID_U - Static variable in class org.jmol.modelset.Atom
- ID_XTAL - Static variable in class org.jmol.modelset.Atom
- ident - Variable in class jspecview.export.AMLExporter
- ident - Variable in class jspecview.export.CMLExporter
- identifier - Variable in class jspecview.source.AnIMLReader
- identifier - Static variable in class org.jmol.script.T
- identify - Static variable in class org.jmol.script.T
- identity(int, int) - Static method in class javajs.util.Matrix
-
Generate identity matrix
- idFontFace - Variable in class org.jmol.util.Font
- idFontStyle - Variable in class org.jmol.util.Font
- idSpherical - Static variable in class org.jmol.quantum.QS
- ifcmd - Static variable in class org.jmol.script.T
- iformat(int, int) - Static method in class jme.JMEUtil
-
right-justify using spaces
- ignore - Static variable in class org.jmol.script.T
- ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
- ignoreError - Variable in class org.jmol.script.ScriptError
- ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- ignoreStructure - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
- iHaveCoefMaps - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cif.CifReader
- iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHideBackground - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- ijkToPoint3f(int, P3, int, int) - Static method in class org.jmol.util.SimpleUnitCell
-
Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499 for example, a 3x3x3 block of 27 cells: {444 666 1} or {1494949 1515151 1} or {1499499499 1501501501 1}
- image - Variable in class org.jmol.console.ImageDialog
- image - Variable in class org.jmol.modelset.Text
- image - Static variable in class org.jmol.script.T
- IMAGE - Enum constant in enum class org.jmol.c.CBK
- IMAGE_OR_SCENE - Static variable in class org.jmol.viewer.JC
- IMAGE_TYPES - Static variable in class org.jmol.viewer.JC
- imageableHeight - Variable in class jspecview.common.PrintLayout
- imageableWidth - Variable in class jspecview.common.PrintLayout
- imageableX - Variable in class jspecview.common.PrintLayout
- imageableY - Variable in class jspecview.common.PrintLayout
- imageChoices - Variable in class org.jmol.dialog.Dialog
- ImageDialog - Class in org.jmol.console
- ImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Constructor for class org.jmol.console.ImageDialog
- ImageEncoder - Class in javajs.img
-
Generic abstract image creator: (1) set parameters (2) encode the image bytes, if necessary (3) generate the image
- ImageEncoder() - Constructor for class javajs.img.ImageEncoder
- imageExtensions - Variable in class org.jmol.dialog.Dialog
- imageFontScaling - Variable in class org.jmol.render.FontLineShapeRenderer
- imageFontScaling - Variable in class org.jmol.render.MeshRenderer
- imageFontScaling - Variable in class org.jmol.viewer.Viewer
- imageScale - Variable in class org.jmol.modelset.Text
- imagestate - Static variable in class org.jmol.script.T
- imageType - Variable in class org.jmol.dialog.Dialog
- imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- imesh - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- implicitStringCommand - Static variable in class org.jmol.script.T
- in - Static variable in class org.jmol.script.T
- inchi - Static variable in class org.jmol.script.T
- inchi() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- InChIJNI - Class in org.jmol.inchi
- InChIJNI() - Constructor for class org.jmol.inchi.InChIJNI
- InChIJS - Class in org.jmol.inchi
-
This class adapts Richard Apodaca's 2020 molfile-to-inchi LLVM-derived Web Assembly implementation of IUPAC InChI v.
- InChIJS() - Constructor for class org.jmol.inchi.InChIJS
- inchikey - Static variable in class org.jmol.script.T
- increasing - Variable in class jspecview.source.AnIMLReader
- increment - Static variable in class org.jmol.script.T
- incrementID() - Method in class org.jmol.modelsetbio.ProteinStructure
- incrementModel(int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- inDefinedStateBlock - Variable in class org.jmol.modelset.StateScript
- indent - Variable in class org.jmol.util.JSONWriter
- INDENT - Static variable in class org.jmol.shapecgo.CGOMesh
- index - Variable in class jspecview.application.AwtTreeNode
- index - Variable in class jspecview.tree.SimpleTreeNode
- index - Variable in class org.jmol.adapter.smarter.Atom
- index - Variable in class org.jmol.minimize.MinBond
- index - Variable in class org.jmol.modelset.Measurement
- index - Variable in class org.jmol.quantum.SlaterData
- index - Variable in class org.jmol.script.SV
- index - Variable in class org.jmol.shape.Mesh
- index - Variable in class org.jmol.util.BZone
- index - Variable in class org.jmol.util.Edge
- indexes - Variable in class org.jmol.minimize.MMConstraint
- indexInFrame(Atom) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- indexInModel - Variable in class org.jmol.util.JmolMolecule
- indexOf(String) - Method in class javajs.util.SB
- indexOf2(String, int) - Method in class javajs.util.SB
- inflate(int) - Method in class com.jcraft.jzlib.Inflater
- inflater - Variable in class com.jcraft.jzlib.InflaterInputStream
- Inflater - Class in com.jcraft.jzlib
- Inflater() - Constructor for class com.jcraft.jzlib.Inflater
- InflaterInputStream - Class in com.jcraft.jzlib
- InflaterInputStream(InputStream, Inflater, int, boolean) - Constructor for class com.jcraft.jzlib.InflaterInputStream
- info - Variable in class org.jmol.atomdata.RadiusData
- info - Static variable in class org.jmol.script.T
- info - Variable in class org.jmol.shapespecial.Ellipsoid
- info - Variable in class org.openscience.jmol.app.JmolApp
- info(String) - Method in class org.jmol.util.DefaultLogger
- info(String) - Static method in class org.jmol.util.Logger
-
og* Writes a log at INFO level.
- info(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at INFO level.
- INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_IS_HEXAGONAL - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_IS_RHOMBOHEDRAL - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_SPACE_GROUP - Static variable in class org.jmol.viewer.JC
- INFO_SPACE_GROUP_ASSIGNED - Static variable in class org.jmol.viewer.JC
- INFO_SPACE_GROUP_INDEX - Static variable in class org.jmol.viewer.JC
- INFO_SPACE_GROUP_INFO - Static variable in class org.jmol.viewer.JC
- INFO_SPACE_GROUP_NAME - Static variable in class org.jmol.viewer.JC
- INFO_SPACE_GROUP_NOTE - Static variable in class org.jmol.viewer.JC
- INFO_SPACE_GROUP_TITLE - Static variable in class org.jmol.viewer.JC
- INFO_UNIT_CELL - Static variable in class org.jmol.viewer.JC
- INFO_UNIT_CELL_CONVENTIONAL - Static variable in class org.jmol.viewer.JC
- INFO_UNIT_CELL_OFFSET - Static variable in class org.jmol.viewer.JC
- INFO_UNIT_CELL_PARAMS - Static variable in class org.jmol.viewer.JC
- INFO_UNIT_CELL_RANGE - Static variable in class org.jmol.viewer.JC
-
used to set atom symmetry 555 556 etc.
- INFO_UNIT_CELLS - Static variable in class org.jmol.viewer.JC
- infofontsize - Static variable in class org.jmol.script.T
- INFORMATION_MESSAGE - Static variable in class jspecview.dialog.DialogManager
- infoText - Variable in class jme.JME
- inFront - Variable in class org.jmol.modelset.Measurement
- inGreyscaleMode - Variable in class org.jmol.util.GData
- INHERIT - Static variable in class org.jmol.util.ColorEncoder
- INHERIT_ALL - Static variable in class org.jmol.util.C
- INHERIT_COLOR - Static variable in class org.jmol.util.C
- init() - Method in class jspecview.appletjs.JSVApplet
-
Initializes applet with parameters and load the
JDXSource
called by the browser - init() - Method in class jspecview.appletjs.JSVAppletPro
- init() - Method in class org.jmol.symmetry.CIPData
-
initializer -- called also by CIPDataSmiles
- init(float[]) - Method in class org.jmol.util.SimpleUnitCell
- init(int, boolean) - Method in class com.jcraft.jzlib.Inflater
- init(int, int, boolean) - Method in class com.jcraft.jzlib.Deflater
- init(Object) - Method in class org.jmol.scriptext.MathExt
- init(Object) - Method in class org.jmol.scriptext.ScriptExt
- init(Object) - Method in class org.jmol.scriptext.SmilesExt
- init(Object) - Method in class org.jmol.util.GenericApplet
- init(String, Object, String, SC) - Method in interface org.jmol.api.SC
- init(String, Object, String, SC) - Method in class org.jmol.awt.AwtSwingComponent
- init(String, Object, String, SC) - Method in class org.jmol.awtjs.swing.AbstractButton
- init(String, Viewer, Lst<Object>) - Method in class org.jmol.modelset.MeasurementData
- init(URL, String) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
- INIT - Static variable in class org.jmol.thread.JmolThread
- initArrays(int) - Method in class org.jmol.quantum.NMRNoeMatrix
-
create an empty atom list for subsequent population with atoms
- initBS() - Method in class org.jmol.renderbio.BioMeshRenderer
- initForm(JSViewer, OC) - Method in class jspecview.export.AMLExporter
- initForm(JSViewer, OC) - Method in class jspecview.export.CMLExporter
- initForm(JSViewer, OC) - Method in class jspecview.export.SVGExporter
- initialEndIndex - Variable in class jspecview.common.JSViewer
- initialize - Static variable in class org.jmol.script.T
- initialize() - Method in class jme.JME
- initialize(boolean, boolean) - Method in class org.jmol.viewer.Viewer
- initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.MOCalculation
- initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- initialize(int, P3[], BS) - Method in class org.jmol.bspt.Bspf
- initialize(int, T3[], P4) - Method in class org.jmol.shape.Mesh
- initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- initialize(T3, float, boolean) - Method in class org.jmol.bspt.CubeIterator
-
initialize to return all points within the sphere defined by center and radius
- initialize(JSViewer, PopupResource, String) - Method in class jspecview.popup.JSVGenericPopup
- initialize(AtomSetCollectionReader, int) - Method in class org.jmol.adapter.readers.cif.MSRdr
- initialize(AtomSetCollectionReader, int) - Method in interface org.jmol.adapter.smarter.MSInterface
- initialize(ShapeRenderer, BioShape, int) - Method in class org.jmol.renderbio.BioMeshRenderer
- initialize(Viewer, GenericPlatform) - Method in class org.jmol.g3d.Graphics3D
- initialize(Viewer, GenericPlatform) - Method in class org.jmol.util.GData
- initialize(Viewer, PopupResource, String) - Method in class org.jmol.popup.JmolGenericPopup
- initialize0(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- initializeAnnotation(SV, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
- initializeAnnotation(SV, int, int) - Method in class org.jmol.dssx.AnnotationParser
-
We create a main list of mappings, where each mapping has _atoms and _path
- initializeBspf() - Method in class org.jmol.modelset.ModelSet
- initializeBspt(int) - Method in class org.jmol.modelset.ModelSet
- initializeExporter(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
- initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.Export3D
- initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
- initializeForModel() - Method in class org.jmol.modelkit.ModelKit
-
Not clear this is a good idea.
- initializeHydrogenAddition() - Method in class org.jmol.modelsetbio.BioResolver
- initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
- initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
- initializeOnePointQC() - Method in class org.jmol.quantum.QuantumCalculation
- initializeOrientation(M3) - Method in interface org.jmol.api.SymmetryInterface
- initializeOrientation(M3) - Method in class org.jmol.symmetry.Symmetry
- initializeOutput(Viewer, double, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
- initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.export.Export3D
- initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
- initializeReader() - Method in class org.jmol.adapter.readers.cif.CifReader
- initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
- initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
- initializeReader() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- initializeReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- initializeReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.AmsReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.JSONReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- initializeReader() - Method in class org.jmol.adapter.readers.spartan.OdysseyReader
- initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
- initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CmdfReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
not sure how to work with symmetry here...
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeShape(Viewer, ModelSet, int) - Method in class org.jmol.shape.Shape
- initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeSymmetryOptions() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeTrajectoryFile() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initialStartIndex - Variable in class jspecview.common.JSViewer
- initMany(Lst<Spectrum>, int, int) - Method in class jspecview.common.PanelData
- initModelSet() - Method in class org.jmol.shape.AtomShape
- initModelSet() - Method in class org.jmol.shape.Measures
- initModelSet() - Method in class org.jmol.shape.Shape
- initModelSet() - Method in class org.jmol.shape.TextShape
- initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
- initModelSet() - Method in class org.jmol.shapespecial.Vectors
- initOne(Spectrum) - Method in class jspecview.common.PanelData
- initOptions() - Method in class org.jmol.util.GenericApplet
- initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
- initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._PovrayExporter
- initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._TachyonExporter
- initParams(String) - Method in class jspecview.app.JSVApp
-
starts or restarts applet display from scratch or from a JSVApplet.script() JavaScript command Involves a two-pass sequence through parsing the parameters, because order is not important in this sort of call.
- initRenderer() - Method in class org.jmol.render.AxesRenderer
- initRenderer() - Method in class org.jmol.render.BbcageRenderer
- initRenderer() - Method in class org.jmol.render.MeasuresRenderer
- initRenderer() - Method in class org.jmol.render.ShapeRenderer
- initRenderer() - Method in class org.jmol.render.UccageRenderer
- initRenderer() - Method in class org.jmol.renderspecial.DotsRenderer
- initShape() - Method in class org.jmol.shape.AtomShape
- initShape() - Method in class org.jmol.shape.Axes
- initShape() - Method in class org.jmol.shape.Bbcage
- initShape() - Method in class org.jmol.shape.Echo
- initShape() - Method in class org.jmol.shape.FontLineShape
- initShape() - Method in class org.jmol.shape.Frank
- initShape() - Method in class org.jmol.shape.Hover
- initShape() - Method in class org.jmol.shape.Labels
- initShape() - Method in class org.jmol.shape.Measures
- initShape() - Method in class org.jmol.shape.MeshCollection
- initShape() - Method in class org.jmol.shape.Shape
- initShape() - Method in class org.jmol.shape.Sticks
- initShape() - Method in class org.jmol.shape.Uccage
- initShape() - Method in class org.jmol.shapebio.Backbone
- initShape() - Method in class org.jmol.shapebio.BioShapeCollection
- initShape() - Method in class org.jmol.shapebio.Cartoon
- initShape() - Method in class org.jmol.shapebio.MeshRibbon
- initShape() - Method in class org.jmol.shapebio.Rockets
- initShape() - Method in class org.jmol.shapebio.Trace
- initShape() - Method in class org.jmol.shapespecial.Dipoles
- initShape() - Method in class org.jmol.shapespecial.Dots
- initShape() - Method in class org.jmol.shapespecial.Draw
- initShape() - Method in class org.jmol.shapespecial.Ellipsoids
- initShape() - Method in class org.jmol.shapespecial.GeoSurface
- initShape() - Method in class org.jmol.shapesurface.Contact
- initShape() - Method in class org.jmol.shapesurface.Isosurface
- initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
- initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
- initShape() - Method in class org.jmol.shapesurface.NBO
- initShape() - Method in class org.jmol.shapesurface.Plot3D
- initShape() - Method in class org.jmol.shapesurface.Pmesh
- initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- initSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
- initSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- initSwing(String, PopupResource, Object, boolean, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
- initVars() - Method in class org.jmol.export._PovrayExporter
- initVars() - Method in class org.jmol.export._TachyonExporter
- initViewer() - Method in class jspecview.appletjs.JSVApplet
- inline - Static variable in class org.jmol.script.T
- inp - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- input - Variable in class org.jmol.console.GenericConsole
- INPUT_DEVICE - Static variable in class com.sparshui.common.ConnectionType
- InputDeviceConnection - Class in com.sparshui.server
-
Represents a connection to the input device.
- InputDeviceConnection(GestureServer, Socket) - Constructor for class com.sparshui.server.InputDeviceConnection
-
Create a new input device connection with the given gesture server and socket.
- inputFileName - Variable in class org.jmol.dialog.Dialog
- InputReader - Class in org.jmol.adapter.readers.simple
- InputReader() - Constructor for class org.jmol.adapter.readers.simple.InputReader
- InputScannerThread - Class in org.openscience.jmol.app
- inRange(int, int, int) - Method in class org.jmol.viewer.MouseState
- inscode - Static variable in class org.jmol.script.T
- insert(int, String) - Method in class javajs.util.SB
- insert(SC, int) - Method in interface org.jmol.api.SC
- insert(SC, int) - Method in class org.jmol.awt.AwtSwingComponent
- insert(SC, int) - Method in class org.jmol.awtjs.swing.AbstractButton
- insertComponent(Component, int) - Method in class org.jmol.awtjs.swing.Container
- insertion - Static variable in class org.jmol.script.T
- INSERTION - Enum constant in enum class org.jmol.c.PAL
- insertionCode - Variable in class org.jmol.adapter.smarter.Atom
- insertNodeInto(JSVTreeNode, JSVTreeNode, int) - Method in class jspecview.tree.SimpleTreeModel
- insertString(int, String, Object) - Method in interface org.jmol.awtjs.swing.Document
- insertString(int, String, Object) - Method in class org.jmol.awtjs.swing.JTextPane
- Insets - Class in org.jmol.awtjs.swing
- Insets(int, int, int, int) - Constructor for class org.jmol.awtjs.swing.Insets
- insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- insideout - Static variable in class org.jmol.script.T
- insideOut - Variable in class org.jmol.jvxl.data.JvxlData
- insideOut - Variable in class org.jmol.shape.Mesh
- INSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- Int2IntHash - Class in org.jmol.util
- Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
- integer - Static variable in class org.jmol.script.T
- integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptError
- Integral - Class in jspecview.common
- Integral() - Constructor for class jspecview.common.Integral
- IntegralData - Class in jspecview.common
-
from IntegralGraph a data structure for integration settings
- IntegralData(double, double, double, Spectrum) - Constructor for class jspecview.common.IntegralData
- IntegralData(Spectrum, Parameters) - Constructor for class jspecview.common.IntegralData
- IntegralData.IntMode - Enum Class in jspecview.common
- integralDrawAll - Variable in class jspecview.common.Parameters
- integralMinY - Variable in class jspecview.common.Parameters
- integralOffset - Variable in class jspecview.common.Parameters
- INTEGRALOFFSET - Enum constant in enum class jspecview.common.ScriptToken
- integralPlotColor - Variable in class jspecview.common.PanelData
- INTEGRALPLOTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- integralRange - Variable in class jspecview.common.Parameters
- INTEGRALRANGE - Enum constant in enum class jspecview.common.ScriptToken
- integralShiftMode - Variable in class jspecview.common.PanelData
- INTEGRATE - Enum constant in enum class jspecview.common.ScriptToken
- integrateAll(ColorParameters) - Method in class jspecview.common.PanelData
- integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
- integration - Variable in class org.jmol.jvxl.data.JvxlData
- integration - Variable in class org.jmol.quantum.QuantumCalculation
- Integration - Enum constant in enum class jspecview.common.Annotation.AType
- INTEGRATION - Enum constant in enum class jspecview.common.ScriptToken
- IntegrationDialog - Class in jspecview.dialog
-
Dialog for managing the integral listing for a Spectrum within a GraphSet
- IntegrationDialog() - Constructor for class jspecview.dialog.IntegrationDialog
- INTEGRATIONRATIOS - Enum constant in enum class jspecview.common.ScriptToken
- Interface - Class in javajs.api
- Interface - Class in org.jmol.api
- Interface() - Constructor for class javajs.api.Interface
- Interface() - Constructor for class org.jmol.api.Interface
- INTERFACE - Enum constant in enum class jspecview.common.ScriptToken
- interfaceOverlaid - Variable in class jspecview.common.JSViewer
- interior - Static variable in class org.jmol.script.T
- intermolecular - Static variable in class org.jmol.script.T
- internal - Static variable in class org.jmol.script.T
- internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
- internalSlab - Variable in class org.jmol.viewer.TransformManager
- internalTranslation - Variable in class org.jmol.viewer.TransformManager
- interrupt() - Method in interface org.jmol.api.JmolNavigatorInterface
- interrupt() - Method in class org.jmol.thread.AnimationThread
- interrupt() - Method in class org.jmol.thread.JmolThread
- interrupt() - Method in class org.jmol.thread.MoveToThread
- intersection - Variable in class org.jmol.jvxl.readers.Parameters
- intersection - Static variable in class org.jmol.script.T
- intersection(int[], int[]) - Static method in class jme.JMEUtil
- intersectLine(P3[], int, P3, V3) - Method in class org.jmol.util.Triangulator
- intersectPlane(P4, T3[], int) - Method in class org.jmol.util.Triangulator
-
a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.
- intersects(BS) - Method in class javajs.util.BS
-
Returns true if the specified
BitSet
has any bits set totrue
that are also set totrue
in thisBitSet
. - intparam - Static variable in class org.jmol.script.T
- intParameter(int) - Method in class org.jmol.script.ScriptParam
- intParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- intParameterRange(int, int, int) - Method in class org.jmol.script.ScriptParam
- intproperty - Static variable in class org.jmol.script.T
- intramolecular - Variable in class org.jmol.modelset.MeasurementData
- intramolecular - Static variable in class org.jmol.script.T
- intToByteArray(byte[], int, int) - Static method in class com.sparshui.common.utils.Converter
- intToByteArray(int) - Static method in class com.sparshui.common.utils.Converter
-
Converts an integer intBits into a byte array.
- intToFloat(int) - Static method in class javajs.util.BC
- intToSignedInt(int) - Static method in class javajs.util.BC
- intValue - Variable in class org.jmol.script.T
- inv() - Method in class javajs.util.Quat
- INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- invalidatePolygons() - Method in class org.jmol.util.MeshSurface
- invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
- invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
- invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
- invalidateVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
- invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
- InvalidSmilesException - Exception Class in org.jmol.smiles
-
Exception thrown for invalid SMILES String
- InvalidSmilesException(String) - Constructor for exception class org.jmol.smiles.InvalidSmilesException
-
Constructs a
InvalidSmilesException
with a detail message. - invArg() - Method in class org.jmol.script.ScriptError
- invArg() - Method in class org.jmol.scriptext.ScriptExt
- invArgStr(String) - Method in class org.jmol.script.ScriptError
- inverse() - Method in class javajs.util.Matrix
-
Matrix inverse or pseudoinverse
- invert() - Method in class javajs.util.M3
-
Sets the value of this matrix to its inverse.
- invert() - Method in class javajs.util.M4
-
Sets the value of this matrix to its inverse.
- invertAtomCoord(P3, P4, BS, int, boolean) - Method in class org.jmol.viewer.Viewer
- invertInPlace(BS, int) - Static method in class org.jmol.util.BSUtil
-
inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
- invertM(M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to the matrix inverse of the passed matrix m1.
- invertSelected - Static variable in class org.jmol.script.T
- invertSelected(P3, P4, int, BS) - Method in class org.jmol.modelset.ModelSet
-
Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.
- invertSelected(P3, P4, int, BS) - Method in class org.jmol.viewer.Viewer
- INVERTY - Enum constant in enum class jspecview.common.ScriptToken
- invertYAxis() - Method in class jspecview.source.JDXDataObject
- invPO() - Method in class org.jmol.scriptext.ScriptExt
- ipadx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- ipady - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- IRMODE - Enum constant in enum class jspecview.common.ScriptToken
- iRowColSelected - Variable in class jspecview.dialog.JSVDialog
- is(int) - Method in class org.jmol.modelset.Bond
- is(MouseState) - Method in class org.jmol.viewer.MouseState
- IS - Static variable in class org.jmol.quantum.QS
- IS_APPEND - Static variable in interface org.jmol.api.JmolScriptManager
- IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
- is1D() - Method in class jspecview.source.JDXDataObject
- is2D - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- is2DPoint(T3) - Static method in class org.jmol.shapespecial.Draw
- isAB(Object) - Static method in class javajs.util.AU
- isAB(Object) - Static method in class jspecview.common.JSVFileManager
- isAbsorbance() - Method in class jspecview.source.JDXDataObject
- isActive - Variable in class org.jmol.shape.AtomShape
- isActive() - Method in class org.jmol.shapespecial.Ellipsoids
- isActiveLevel(int) - Static method in class org.jmol.util.Logger
-
Tells if a logging level is active.
- isAD(Object) - Static method in class javajs.util.AU
- isADD(Object) - Static method in class javajs.util.AU
- isADDD(Object) - Static method in class javajs.util.AU
- isAdded(int) - Method in class org.jmol.modelset.Group
- isADF - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- isAF(Object) - Static method in class javajs.util.AU
- isAFF(Object) - Static method in class javajs.util.AU
- isAFFF(Object) - Static method in class javajs.util.AU
- isAFloat(Object) - Static method in class javajs.util.AU
- isAI(Object) - Static method in class javajs.util.AU
- isAII(Object) - Static method in class javajs.util.AU
- isAll - Variable in class org.jmol.modelset.MeasurementData
- isAmide - Variable in class org.jmol.minimize.MinBond
- isAngstroms - Variable in class org.jmol.jvxl.readers.JvxlReader
- isAngstroms - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- isAngstroms - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isAntialiased() - Method in interface org.jmol.api.JmolGraphicsInterface
- isAntialiased() - Method in class org.jmol.export.Export3D
-
is full scene / oversampling antialiasing in effect
- isAntialiased() - Method in class org.jmol.util.GData
-
is full scene / oversampling antialiasing in effect
- isAP(Object) - Static method in class javajs.util.AU
- isAppendSelected() - Method in class org.jmol.dialog.FilePreview
- isApplet - Variable in class jspecview.common.JSViewer
- isApplet - Variable in class org.jmol.popup.GenericPopup
- isApplet - Variable in class org.jmol.viewer.Viewer
- isApplet() - Method in class jspecview.common.JSVFileManager
- isApprox(V3d, V3d, double) - Static method in class org.jmol.minimize.Util
- isaromatic - Static variable in class org.jmol.script.T
- isAromatic - Variable in class org.jmol.minimize.MinBond
- isArrayParameter(int) - Method in class org.jmol.script.ScriptParam
- isAS(Object) - Static method in class javajs.util.AU
- isASS(Object) - Static method in class javajs.util.AU
- isAtomExpression(int) - Method in class org.jmol.script.ScriptEval
- isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
- isAtomPDB(int) - Method in class org.jmol.modelset.ModelSet
- isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
- isAtropism(int) - Static method in class org.jmol.util.Edge
- isAutoOverlayFromJmolClick() - Method in class jspecview.source.JDXDataObject
- isAV(Object) - Static method in class org.jmol.util.Escape
- isBarb - Variable in class org.jmol.shapespecial.DrawMesh
- isBase64() - Method in class javajs.util.OC
- isBase64(SB) - Static method in class javajs.util.Rdr
- isBiColor() - Method in enum class org.jmol.c.STER
- isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
- isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
- isBicolorMap - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- isBigEndian - Variable in class javajs.util.BinaryDocument
- isBigEndian() - Method in interface javajs.api.GenericOutputChannel
- isBigEndian() - Method in class javajs.util.OC
- isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isBinary(BufferedInputStream, int) - Static method in class javajs.util.Rdr
-
Just looking for non-printable characters.
- isBinaryUrl(String) - Method in interface javajs.api.js.J2SObjectInterface
- isBio - Variable in class org.jmol.symmetry.Symmetry
- isBio() - Method in interface org.jmol.api.SymmetryInterface
- isBio() - Method in class org.jmol.symmetry.Symmetry
- isBioModel - Variable in class org.jmol.modelset.Model
- isBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- isBioShape - Variable in class org.jmol.shape.Shape
- isBondable(float, float, float, float, float) - Method in class org.jmol.modelset.ModelSet
- isBonded(Atom) - Method in class org.jmol.modelset.Atom
- isBondSet - Variable in class org.jmol.script.ScriptParam
- isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
- isBound(int, int) - Method in class org.jmol.viewer.Viewer
- isBZip2B(byte[]) - Static method in class javajs.util.Rdr
- isBZip2S(InputStream) - Static method in class javajs.util.Rdr
- isCA2(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isCarbohydrate - Variable in class org.jmol.renderbio.BackboneRenderer
- isCarbohydrate - Variable in class org.jmol.renderbio.CartoonRenderer
- isCarbohydrate - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- isCarbohydrate - Variable in class org.jmol.renderbio.RibbonsRenderer
- isCarbohydrate - Variable in class org.jmol.renderbio.RocketsRenderer
- isCarbohydrate - Variable in class org.jmol.renderbio.StrandsRenderer
- isCarbohydrate - Variable in class org.jmol.renderbio.TraceRenderer
- isCarbohydrate() - Method in class org.jmol.modelset.Group
- isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
- isCartoonsSelected() - Method in class org.jmol.dialog.FilePreview
- isCDX - Variable in class org.jmol.adapter.readers.xml.XmlCdxReader
-
true when this reader is being used after CDX conversion
- isCellEditable(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- isCenterParameter(int) - Method in class org.jmol.script.ScriptParam
- isChain - Variable in class org.jmol.smiles.SmilesBond
- isChanged() - Method in class com.sparshui.server.TouchPoint
-
Get the value of the changed flag.
- isClaimed() - Method in class com.sparshui.server.TouchPoint
-
The GestureServer needs to know whether an incoming touchPoint is bound to a client or not so that it can tell the input device whether or not to consume the event.
- isClearAll() - Method in class jspecview.common.PeakInfo
- isClickable() - Method in class org.jmol.modelset.Atom
- isClipped(int, int) - Method in class org.jmol.export.Export3D
- isClipped(int, int) - Method in class org.jmol.util.GData
- isClipped(int, int, int) - Method in class org.jmol.export.Export3D
- isClipped3(int, int, int) - Method in class org.jmol.util.GData
- isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
- isClippedXY(int, int, int) - Method in class org.jmol.util.GData
- isClippedZ(int) - Method in class org.jmol.util.GData
- isColixColorInherited(short) - Static method in class org.jmol.util.C
- isColixLastAvailable(short) - Static method in class org.jmol.util.C
- isColixTranslucent(short) - Static method in class org.jmol.util.C
- isColorParam(int) - Method in class org.jmol.script.ScriptParam
- isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
- isColorSolid - Variable in class org.jmol.util.MeshSurface
- isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptCompiler
- isCommensurate - Variable in class org.jmol.adapter.readers.cif.MSRdr
- isComplete - Variable in class org.jmol.script.ScriptContext
- isCompoundDocumentB(byte[]) - Static method in class javajs.util.Rdr
- isCompoundDocumentS(InputStream) - Static method in class javajs.util.Rdr
- isCompoundSource - Variable in class jspecview.source.JDXSource
- isConcatenated - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isConnect() - Method in class org.jmol.modelset.StateScript
- isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
- isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
- isContainedIn(BS) - Method in class org.jmol.modelset.Model
- isContinuous() - Method in class jspecview.source.JDXDataObject
-
Returns true if spectrum is continuous
- isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isContoured - Variable in class org.jmol.jvxl.data.JvxlData
- isContoured - Variable in class org.jmol.jvxl.readers.Parameters
- isCore - Variable in class org.jmol.quantum.SlaterData
- isCourseGrained - Variable in class org.jmol.adapter.readers.cif.CifReader
- isCovalent() - Method in class org.jmol.modelset.Bond
- isCovalent() - Method in class org.jmol.smiles.SmilesBond
- isCovalent() - Method in class org.jmol.util.Edge
- isCovalent() - Method in interface org.jmol.util.SimpleEdge
- isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
- isCovalentNotPartial0() - Method in class org.jmol.modelset.Bond
- iscroll - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- isCrossLinked(Group) - Method in class org.jmol.modelset.Group
- isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
- isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
- isCrossLinked(Node) - Method in class org.jmol.modelset.Atom
- isCrossLinked(Node) - Method in class org.jmol.smiles.SmilesAtom
- isCrossLinked(Node) - Method in interface org.jmol.util.Node
- iScrPt - Variable in class org.jmol.viewer.TransformManager
- isCurrentGraphSet(GraphSet) - Method in class jspecview.common.PanelData
- isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
- isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
- isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
- isCyclic() - Method in class org.jmol.modelsetbio.BioPolymer
- isDatabaseCode(char) - Static method in class org.jmol.viewer.Viewer
- isDataFlavorSupported(DataFlavor) - Method in class jspecview.java.AwtClipboard
- isDataFlavorSupported(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
- isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
- isDefault - Variable in class jspecview.common.ColorParameters
- isDefined() - Method in class org.jmol.smiles.SmilesAtom
- isDeleted() - Method in class org.jmol.modelset.Atom
- isDeleted() - Method in class org.jmol.smiles.SmilesAtom
- isDeleted() - Method in interface org.jmol.util.Node
- isDeleted(Atom) - Static method in class org.jmol.modelset.AtomCollection
- isDialog() - Method in interface jspecview.api.AnnotationData
- isDialog() - Method in class jspecview.common.MeasurementData
- isDialog() - Method in class jspecview.dialog.JSVDialog
- isDigit(char) - Static method in class javajs.util.PT
- isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
- isDirectory() - Method in interface org.jmol.api.GenericFileInterface
- isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
- isDna() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isDnaByID() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isDoublePrecision - Static variable in class org.jmol.viewer.Viewer
- isDrawPolygon - Variable in class org.jmol.util.MeshSurface
- isDSSP1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isDssrSet - Variable in class org.jmol.modelsetbio.NucleicPolymer
- isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isEcho - Variable in class org.jmol.modelset.Text
- isEditor - Variable in class org.jmol.script.ScriptContext
- isEditorScript - Variable in class org.jmol.script.ScriptContext
- iSelected - Variable in class jspecview.dialog.JSVDialog
- isElement(int, int) - Static method in class org.jmol.util.Elements
- isEmbeddable(String) - Static method in class org.jmol.viewer.FileManager
-
Check to see if it is possible that this file has been embedded by Jmol using JC.EMBEDDED_SCRIPT_TAG.
- isEmbeddedExpression - Variable in class org.jmol.script.ScriptCompiler
- isEmpty() - Method in class javajs.util.BS
-
Returns true if this
BitSet
contains no bits that are set totrue
. - isEmpty() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- isEnabled() - Method in interface jspecview.api.JSVViewPanel
- isEnabled() - Method in class jspecview.js2d.JsMainPanel
- isEnabled() - Method in class jspecview.js2d.JsPanel
- isEnabled() - Method in interface org.jmol.api.JmolModulationSet
- isEnabled() - Method in interface org.jmol.api.SC
- isEnabled() - Method in class org.jmol.awt.AwtSwingComponent
- isEnabled() - Method in class org.jmol.awtjs.swing.Component
- isEnabled() - Method in class org.jmol.util.ModulationSet
- isEquiv(Tensor) - Method in class org.jmol.util.Tensor
- iSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- isExecuting() - Method in interface org.jmol.api.JmolScriptEvaluator
- isExecuting() - Method in class org.jmol.script.ScriptEval
- isExport - Variable in class org.jmol.render.ShapeRenderer
- isExportMode(String) - Static method in enum class jspecview.common.ExportType
- isExportXAxisLeftToRight() - Method in class jspecview.common.Spectrum
- isFieldValid() - Method in class org.jmol.adapter.readers.cif.BCIFReader
- isFieldValid() - Method in class org.jmol.adapter.readers.cif.CifReader
- isFinalized - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isFinite(double) - Static method in class org.jmol.minimize.Util
- isFixed - Variable in class org.jmol.shape.MeshCollection
- isFloatInfo(String) - Static method in class org.jmol.util.Tensor
- isFloatParameter(int) - Method in class org.jmol.script.ScriptParam
- isFloatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- isFocusable() - Method in interface jspecview.api.JSVViewPanel
- isFocusable() - Method in class jspecview.js2d.JsMainPanel
- isFocusable() - Method in class jspecview.js2d.JsPanel
- isForcedSubset() - Method in class jspecview.common.Spectrum
- isFullyLit() - Method in class org.jmol.jvxl.readers.Parameters
- isFunction(String) - Method in class org.jmol.script.ScriptEval
- isFunction(String) - Method in class org.jmol.viewer.Viewer
- isGC() - Method in class jspecview.source.JDXDataObject
- isGhostPass - Variable in class org.jmol.render.MeshRenderer
- isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isGzipB(byte[]) - Static method in class javajs.util.Rdr
- isGzipS(InputStream) - Static method in class javajs.util.Rdr
- isHeadless() - Method in class jspecview.java.AwtPlatform
- isHeadless() - Method in class jspecview.js2d.JsPlatform
- isHeadless() - Method in interface org.jmol.api.GenericPlatform
- isHeadless() - Method in class org.jmol.awt.Platform
- isHeadless() - Method in class org.jmol.awtjs2d.Platform
- isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isHelix() - Method in class org.jmol.modelsetbio.Monomer
- isHetero - Variable in class org.jmol.adapter.smarter.Atom
- isHetero() - Method in class org.jmol.modelset.Atom
- isHetero(String) - Method in class org.jmol.modelsetbio.BioResolver
-
MMCif, Gromacs, MdTop, Mol2 readers only
- isHexagonal(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- isHexagonalSG(int, float[]) - Static method in class org.jmol.symmetry.UnitCell
- isHidden - Variable in class org.jmol.modelset.Measurement
- isHidden() - Method in class org.jmol.modelkit.ModelKit
- isHighDPI() - Static method in class jme.JMEUtil
-
Check if the applet is showing in highDPI or not.
- isHighPrecision - Variable in class org.jmol.adapter.writers.XtlWriter
-
in SwingJS this is always true
- isHighPrecision - Static variable in class org.jmol.viewer.Viewer
-
adjustable
- isHNMR() - Method in class jspecview.source.JDXDataObject
-
Determines if a spectrum is an HNMR spectrum
- isHoverable() - Method in class org.jmol.viewer.ActionManager
- iShowSolid - Variable in class org.jmol.renderspecial.DotsRenderer
- isHydrogen() - Method in class org.jmol.modelset.Bond
- isHydrogen() - Method in class org.jmol.smiles.SmilesBond
- isHydrogen() - Method in class org.jmol.util.Edge
- isHZtoPPM() - Method in class jspecview.source.JDXDataObject
-
Determines if the spectrum should be displayed with abscissa unit of Part Per Million (PPM) instead of Hertz (HZ)
- isIDcmd(int) - Static method in class org.jmol.script.T
-
commands that allow implicit ID as first parameter
- isImaginary() - Method in class jspecview.source.JDXDataObject
- isInchiOpposite(int, int, int, int) - Method in class org.jmol.inchi.InChIJNI
- isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
- isInDisplayRange(int, int) - Method in class org.jmol.util.GData
- isInitializedIndex(int) - Method in class org.jmol.bspt.Bspf
- isInPosition(V3, float) - Method in class org.jmol.viewer.TransformManager
- isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
- isInRange(Atom, Atom, float, float, boolean, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
-
Consider the min/max option for CONNECT
- isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
- isInsideOut() - Method in class org.jmol.jvxl.readers.Parameters
- isIntegralDrag - Variable in class jspecview.common.PanelData
- isInTetrahedron(P3, P3, P3, P3, P3, P4, V3, V3, boolean) - Static method in class javajs.util.Measure
- isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
- isInTriangle(P3, P3, P3, P3, V3, V3, V3) - Static method in class javajs.util.Measure
- isInverted() - Method in class jspecview.source.JDXDataObject
- isIsotropic - Variable in class org.jmol.util.Tensor
- isJmolDataFrame - Variable in class org.jmol.modelset.Model
- isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
- isJmolDataFrameForModel(int) - Method in class org.jmol.modelset.ModelSet
- isJmolType(String) - Static method in class org.jmol.viewer.FileManager
-
Check to see if this is a Jmol WRITE file type that might be or have attached a ZIP collection .
- isJNLP - Variable in class org.jmol.viewer.Viewer
- isJS - Static variable in class jspecview.common.JSViewer
- isJS - Variable in class org.jmol.popup.GenericPopup
- isJS - Variable in class org.jmol.script.ScriptEval
- isJS - Variable in class org.jmol.thread.JmolThread
- isJS - Static variable in class org.jmol.util.GenericApplet
- isJS - Static variable in class org.jmol.viewer.Viewer
- isJSNoAWT - Variable in class org.jmol.viewer.Viewer
- isJSThread - Variable in class org.jmol.script.ScriptContext
- isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
- iskiosk - Static variable in class org.jmol.script.T
- isKiosk - Variable in class org.openscience.jmol.app.JmolApp
- isKnownPDBGroup(String, int) - Method in class org.jmol.modelsetbio.BioResolver
- isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
after reading a model, Q: Is this the last model?
- isLeadAtom() - Method in class org.jmol.modelset.Atom
- isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
- isLeadAtom() - Method in interface org.jmol.util.Node
- isLeadAtom(int) - Method in class org.jmol.modelset.Group
- isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
- isLeaf() - Method in interface jspecview.api.JSVTreeNode
- isLeaf() - Method in class jspecview.tree.SimpleTreeNode
- isLetter(char) - Static method in class javajs.util.PT
- isLetterOrDigit(char) - Static method in class javajs.util.PT
- isLigand - Variable in class org.jmol.adapter.readers.cif.CifReader
- isLike(String, String) - Static method in class javajs.util.PT
-
a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
- isLike(SV, SV) - Static method in class org.jmol.script.SV
-
a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
- isLinked - Variable in class jspecview.common.PanelData
- isLocal(String) - Static method in class javajs.util.OC
- isLocal(String) - Static method in class jspecview.common.JSVFileManager
- isLoggable(int[], int) - Method in class org.jmol.minimize.Minimizer
- isLoop - Variable in class org.jmol.adapter.readers.cif.CifReader
- isLoopKey() - Method in class org.jmol.adapter.readers.cif.CifReader
- isLowerCase(char) - Static method in class javajs.util.PT
- isM3D - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
- isMagCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
- isMapped - Variable in class org.jmol.jvxl.readers.Parameters
- isMatch(String, String) - Static method in class jspecview.common.Parameters
- isMatch(String, String, boolean, boolean) - Static method in class javajs.util.PT
-
A general non-regex (for performance) text matcher that utilizes ? and *.
- isMathExpressionCommand - Variable in class org.jmol.script.ScriptCompiler
- isMeasure - Variable in class org.jmol.modelset.Text
- isMenuItem(Object) - Method in class org.jmol.console.GenericConsole
- isMenuItem(Object) - Method in class org.jmol.console.JmolConsole
- isMenuItem(Object) - Method in class org.jmol.consolejs.AppletConsole
- isMerged - Variable in class org.jmol.util.MeshSurface
- isMessagePackB(byte[]) - Static method in class javajs.util.Rdr
- isMessagePackS(InputStream) - Static method in class javajs.util.Rdr
- isMin(Map<String, Integer>) - Method in class org.jmol.modelset.Measurement
- isMMCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
- isModelConnected - Variable in class org.jmol.jvxl.data.JvxlData
- isModelConnected - Variable in class org.jmol.jvxl.readers.Parameters
- isModelConnected - Variable in class org.jmol.shape.Mesh
- isModelKit - Variable in class org.jmol.modelset.Model
- isModelKitOption(char, String) - Method in class org.jmol.viewer.Viewer
- isModelkitPickingRotateBond() - Method in class org.jmol.viewer.Viewer
- isModelPDB(int) - Method in class org.jmol.viewer.Viewer
- isModulated - Variable in class org.jmol.util.Tensor
- isModulated(int) - Method in class org.jmol.modelset.AtomCollection
- isMolecular - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isMonoclinicSG(int) - Static method in class org.jmol.symmetry.UnitCell
- isMouseDown - Variable in class jspecview.app.GenericMouse
- isMouseUp() - Method in class jspecview.common.PanelData
- isMovie - Variable in class org.jmol.viewer.AnimationManager
- isMS() - Method in class jspecview.source.JDXDataObject
- isMTClient() - Method in class org.jmol.viewer.ActionManager
- isMTServer() - Method in class org.jmol.viewer.ActionManager
- isMultiTouch - Variable in class org.jmol.viewer.ActionManager
- isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
- isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
- isNaN() - Method in class org.jmol.script.SV
- isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
- isNavigating() - Method in class org.jmol.viewer.TransformManager
- isNear(double, double) - Static method in class org.jmol.minimize.Util
- isNear(TouchPoint) - Method in class com.sparshui.server.TouchPoint
- isNear3(double, double, double) - Static method in class org.jmol.minimize.Util
- isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
- isNearZero(double) - Static method in class org.jmol.minimize.Util
- isNearZero2(double, double) - Static method in class org.jmol.minimize.Util
- isNegDisorder - Variable in class org.jmol.adapter.smarter.Atom
- isNegligible(double, double) - Static method in class org.jmol.minimize.Util
- isNegligible3(double, double, double) - Static method in class org.jmol.minimize.Util
- isNewSet - Variable in class org.jmol.script.ScriptCompiler
- isNext(String) - Method in class org.jmol.jvxl.readers.XmlReader
- isNMR() - Method in class jspecview.source.JDXDataObject
- isNonStringPrimitive(Object) - Static method in class javajs.util.PT
- isNonzero() - Method in class org.jmol.util.ModulationSet
- isNonzero() - Method in class org.jmol.util.Vibration
- isNucleic - Variable in class org.jmol.renderbio.BackboneRenderer
- isNucleic - Variable in class org.jmol.renderbio.CartoonRenderer
- isNucleic - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- isNucleic - Variable in class org.jmol.renderbio.RibbonsRenderer
- isNucleic - Variable in class org.jmol.renderbio.RocketsRenderer
- isNucleic - Variable in class org.jmol.renderbio.StrandsRenderer
- isNucleic - Variable in class org.jmol.renderbio.TraceRenderer
- isNucleic() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isNucleic() - Method in class org.jmol.modelsetbio.BioPolymer
- isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isNucleic() - Method in class org.jmol.smiles.SmilesAtom
- isNucleicMonomer() - Method in class org.jmol.modelset.Group
- isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isNull(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- isNumericAndNonZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- isOccupied() - Method in class org.jmol.modelset.Atom
- IsoExt - Class in org.jmol.scriptext
- IsoExt() - Constructor for class org.jmol.scriptext.IsoExt
- isOffsetAbsolute(int) - Static method in class org.jmol.viewer.JC
- isomeshes - Variable in class org.jmol.shapesurface.Isosurface
- isOneOf(String, String) - Static method in class javajs.util.PT
- isOpen(Lst<PanelNode>, String) - Static method in class jspecview.common.PanelNode
- isOpenShell() - Method in class org.jmol.adapter.readers.quantum.NBOParser
- isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isOrderH(int) - Static method in class org.jmol.util.Edge
- isOrderly - Variable in class org.jmol.modelset.Model
-
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] array
- isosurface - Static variable in class org.jmol.script.T
- Isosurface - Class in org.jmol.shapesurface
- Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
- isosurfacekey - Static variable in class org.jmol.script.T
- IsosurfaceMesh - Class in org.jmol.shapesurface
- isosurfacepropertysmoothing - Static variable in class org.jmol.script.T
- isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.T
- IsosurfaceRenderer - Class in org.jmol.rendersurface
- IsosurfaceRenderer() - Constructor for class org.jmol.rendersurface.IsosurfaceRenderer
- ISOTOPE_MASS_OFFSET - Static variable in class org.jmol.util.Elements
- ISOTOPE_NUMBER_MASK - Static variable in class org.jmol.util.Elements
- isotopeMass - Static variable in class org.jmol.util.Elements
- isotropy() - Method in class org.jmol.util.Tensor
-
isotropy = average of eigenvalues
- isPaletteVariable(byte) - Static method in enum class org.jmol.c.PAL
- isParallel() - Method in class org.jmol.viewer.Viewer
- isPartial() - Method in class org.jmol.modelset.Bond
- isPartial() - Method in class org.jmol.smiles.SmilesBond
- isPartial() - Method in class org.jmol.util.Edge
- isPass2 - Variable in class org.jmol.util.GData
- isPaused - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- isPaused() - Method in interface org.jmol.api.JmolScriptEvaluator
- isPaused() - Method in class org.jmol.script.ScriptEval
- isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
- isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
- isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
- isPeriodic - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isPhosphorusOnly - Variable in class org.jmol.renderbio.BackboneRenderer
- isPhosphorusOnly - Variable in class org.jmol.renderbio.CartoonRenderer
- isPhosphorusOnly - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- isPhosphorusOnly - Variable in class org.jmol.renderbio.RibbonsRenderer
- isPhosphorusOnly - Variable in class org.jmol.renderbio.RocketsRenderer
- isPhosphorusOnly - Variable in class org.jmol.renderbio.StrandsRenderer
- isPhosphorusOnly - Variable in class org.jmol.renderbio.TraceRenderer
- isPickAtomAssignCharge() - Method in class org.jmol.modelkit.ModelKit
- isPickleB(byte[]) - Static method in class javajs.util.Rdr
- isPickleS(InputStream) - Static method in class javajs.util.Rdr
- isPixels - Variable in class jspecview.common.Annotation
- isPlugin - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- isPlugin() - Method in class org.openscience.jmol.app.janocchio.Nmr
- isPngZipB(byte[]) - Static method in class javajs.util.Rdr
- isPngZipStream(InputStream) - Static method in class javajs.util.Rdr
- isPoint3f(int) - Method in class org.jmol.script.ScriptParam
- isPolarSG(int) - Static method in class org.jmol.symmetry.UnitCell
- isPolygonDisplayable(int) - Method in class org.jmol.render.MeshRenderer
- isPolygonDisplayable(int) - Method in class org.jmol.renderspecial.DrawRenderer
- isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
- isPolymer - Variable in class org.jmol.render.AxesRenderer
- isPolymer - Variable in class org.jmol.render.BbcageRenderer
- isPolymer - Variable in class org.jmol.render.UccageRenderer
- isPolymer() - Method in interface org.jmol.api.SymmetryInterface
- isPolymer() - Method in class org.jmol.symmetry.Symmetry
- isPolymer() - Method in class org.jmol.util.SimpleUnitCell
- isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
- isPossibleHBond(HB, HB) - Static method in enum class org.jmol.c.HB
- isPreviewOnly - Variable in class org.jmol.viewer.Viewer
- isPrimitive - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isPrinting - Variable in class jspecview.common.PanelData
- isPrintOnly - Variable in class org.jmol.viewer.Viewer
- isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
- isPro() - Method in interface jspecview.api.JSVAppletInterface
- isPro() - Method in class jspecview.app.JSVApp
- isPro() - Method in class jspecview.app.JSVAppPro
- isPro() - Method in class jspecview.appletjs.JSVApplet
- isPro() - Method in class jspecview.appletjs.JSVAppletPro
- isPro() - Method in class jspecview.application.MainFrame
- isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isProtein() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isPurine() - Method in class org.jmol.modelset.Atom
- isPurine() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isPurine() - Method in class org.jmol.smiles.SmilesAtom
- isPurine() - Method in interface org.jmol.util.Node
- isPurineByID() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isPyrimidine() - Method in class org.jmol.modelset.Atom
- isPyrimidine() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
- isPyrimidine() - Method in interface org.jmol.util.Node
- isPyrimidineByID() - Method in class org.jmol.modelset.Group
- isQuantumBasisSupported(char) - Static method in class org.jmol.quantum.QS
- isQueueProcessing() - Method in interface org.jmol.api.JmolScriptManager
- isQueueProcessing() - Method in class org.jmol.script.ScriptManager
- isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isQuote(char) - Method in class javajs.util.CifDataParser
-
CIF 1.0 only; we handle various quote types here
- isQuote(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Includes all possible operator tokens
- isRadio - Variable in class org.jmol.awtjs.swing.JRadioButtonMenuItem
- isRandom - Variable in class javajs.util.BinaryDocument
- isRemote(String) - Static method in class javajs.util.OC
- isRenderScalable() - Method in class org.jmol.shapespecial.DrawMesh
- isRepaintPending() - Method in interface org.jmol.api.JmolRepaintManager
- isRepaintPending() - Method in class org.jmol.render.RepaintManager
- isRepaintPending() - Method in class org.jmol.viewer.Viewer
- isReset - Variable in class org.jmol.thread.JmolThread
- isReversed - Variable in class org.jmol.util.ColorEncoder
- isRhombohedral(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- isRna() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isRnaByID() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isRotation() - Method in class javajs.util.M3
- isScalable() - Method in class jspecview.source.JDXDataObject
- isScalar(SV) - Static method in class org.jmol.script.SV
- isScaleSet - Variable in class org.jmol.shapespecial.DrawMesh
- isScript() - Static method in class jme.JMEUtil.GWT
- isScriptExecuting() - Method in class org.jmol.api.JmolViewer
- isScriptExecuting() - Method in class org.jmol.viewer.Viewer
- isScriptQueued() - Method in interface org.jmol.api.JmolScriptManager
- isScriptQueued() - Method in class org.jmol.script.ScriptManager
- isScriptType(String) - Static method in class org.jmol.viewer.FileManager
- isSelected - Variable in class jspecview.common.PanelNode
- isSelected() - Method in interface org.jmol.api.JmolAbstractButton
- isSelected() - Method in interface org.jmol.api.SC
- isSelected() - Method in class org.jmol.awt.AwtSwingComponent
- isSelected() - Method in class org.jmol.awtjs.swing.AbstractButton
- isSelected() - Method in class org.jmol.console.JmolLabel
- isSelected(int) - Method in class org.jmol.viewer.SelectionManager
- isSelected(Object) - Method in interface jspecview.api.PlatformDialog
- isSelected(Object) - Method in class jspecview.java.AwtDialog
- isSelected(Object) - Method in class jspecview.js2d.JsDialog
- isSelected(BS) - Method in class org.jmol.modelset.Group
- isSelected(BS, int) - Method in class org.jmol.util.Tensor
- isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- isServer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- isSet - Variable in class org.jmol.shape.AtomShape
- isSetBrace - Variable in class org.jmol.script.ScriptCompiler
- isSetOrDefine - Variable in class org.jmol.script.ScriptCompiler
- isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isSheet() - Method in class org.jmol.modelsetbio.Monomer
- isShell - Variable in class org.jmol.render.MeshRenderer
- isShell - Variable in class org.jmol.shape.Mesh
- isShowAllStacked() - Method in class jspecview.common.PanelData
- isSigned - Variable in class jspecview.common.JSViewer
- isSigned - Variable in class org.jmol.popup.GenericPopup
- isSigned - Variable in class org.jmol.util.GenericApplet
- isSigned() - Method in interface jspecview.api.JSVAppletInterface
- isSigned() - Method in interface jspecview.api.ScriptInterface
- isSigned() - Method in class jspecview.app.JSVApp
- isSigned() - Method in class jspecview.app.JSVAppPro
- isSigned() - Method in class jspecview.appletjs.JSVApplet
- isSigned() - Method in class jspecview.application.JSpecView
- isSigned() - Method in class jspecview.application.MainFrame
- isSignedApplet - Variable in class org.jmol.viewer.Viewer
- isSilent - Variable in class org.jmol.jvxl.readers.Parameters
- isSilent - Variable in class org.openscience.jmol.app.JmolApp
- isSimple() - Method in interface org.jmol.api.SymmetryInterface
- isSimple() - Method in class org.jmol.symmetry.Symmetry
- isSimulation - Variable in class jspecview.common.PanelNode
- isSimulation - Variable in class jspecview.source.JDXDataObject
- isSingleThreaded - Variable in class jspecview.common.JSViewer
- isSingleThreaded - Variable in class org.jmol.viewer.Viewer
- isSingleThreaded() - Method in class jspecview.java.AwtPlatform
- isSingleThreaded() - Method in class jspecview.js2d.JsPlatform
- isSingleThreaded() - Method in interface org.jmol.api.GenericPlatform
- isSingleThreaded() - Method in class org.jmol.awt.Platform
- isSingleThreaded() - Method in class org.jmol.awtjs2d.Platform
- isSlab - Variable in class org.jmol.render.AxesRenderer
- isSlab - Variable in class org.jmol.render.BbcageRenderer
- isSlab - Variable in class org.jmol.render.UccageRenderer
- isSlab() - Method in interface org.jmol.api.SymmetryInterface
- isSlab() - Method in class org.jmol.symmetry.Symmetry
- isSlab() - Method in class org.jmol.util.SimpleUnitCell
- isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
- isSlabEnabled - Variable in class org.jmol.export._PovrayExporter
- isSlabEnabled - Variable in class org.jmol.export._TachyonExporter
- isSmilesCanonical(String) - Static method in class org.jmol.viewer.JC
- isSorting() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- isSpaceGroupInfoKey(String) - Static method in class org.jmol.viewer.JC
-
When UNITCELL NONE is given, clear out all space group and unit cell keys from model info.
- isSpinFixed - Variable in class org.jmol.viewer.TransformManager
- isSpinInternal - Variable in class org.jmol.viewer.TransformManager
- isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isSquared - Variable in class org.jmol.jvxl.readers.Parameters
- isSquaredLinear - Variable in class org.jmol.jvxl.readers.Parameters
- isSSG - Variable in class org.jmol.symmetry.SpaceGroup
- isStackable() - Method in class jspecview.source.JDXDataObject
- isStarted() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- isStarted() - Method in interface org.openscience.jmol.app.JmolPlugin
- isStateScript - Variable in class org.jmol.script.ScriptEval
- isStateScript - Variable in class org.jmol.script.ScriptCompiler
- isStateScript() - Method in interface org.jmol.api.JmolScriptEvaluator
- isStateScript() - Method in class org.jmol.script.ScriptEval
- isStepping() - Method in interface org.jmol.api.JmolScriptEvaluator
- isStepping() - Method in class org.jmol.script.ScriptEval
- isStereoOpposite(int, int, int) - Method in class org.jmol.smiles.SmilesAtom
- isStereoSlave - Variable in class org.jmol.util.GenericApplet
- isStopped() - Method in interface org.jmol.api.JmolScriptEvaluator
- isStopped() - Method in class org.jmol.script.ScriptEval
- isStringArray(String) - Static method in class org.jmol.util.Escape
- isSubstructure(String, String) - Method in class org.jmol.viewer.Viewer
- isSupercell() - Method in interface org.jmol.api.SymmetryInterface
- isSupercell() - Method in class org.jmol.symmetry.Symmetry
- isSupercell() - Method in class org.jmol.util.SimpleUnitCell
- isSUPERCELL - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
actual SUPERCELL keyword, not just "cell="
- isSurface - Variable in class org.jmol.shapespecial.Dots
- isSwingJS - Static variable in class jspecview.common.JSViewer
- isSwingJS - Static variable in class org.jmol.viewer.Viewer
- isSymmetryCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
- isSymmetryCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
- isSyntaxAndFileCheck - Variable in class org.jmol.viewer.Viewer
- isSyntaxCheck - Variable in class org.jmol.viewer.Viewer
- isTainted - Variable in class org.jmol.popup.GenericPopup
- isTainted() - Method in class org.jmol.modelset.Measurement
- isTar(BufferedInputStream) - Static method in class javajs.util.Rdr
- isTerminator(char) - Method in class javajs.util.CifDataParser
-
The token terminator is space or tab in CIF 1.0, but it can be quoted strings in CIF 2.0.
- isTetragonalSG(int) - Static method in class org.jmol.symmetry.UnitCell
- isTracker() - Method in class org.jmol.symmetry.CIPData
-
Subclass identifier
- isTracker() - Method in class org.jmol.symmetry.CIPDataTracker
- isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isTrajectory - Variable in class org.jmol.modelset.Measurement
- isTrajectory - Variable in class org.jmol.modelset.ModelLoader
- isTrajectory(int) - Method in class org.jmol.modelset.ModelSet
-
could be the base model or one of the subframes
- isTrajectoryMeasurement(int[]) - Method in class org.jmol.modelset.ModelSet
- isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelSet
- isTranslucent - Variable in class org.jmol.render.MeshRenderer
- isTranslucent - Variable in class org.jmol.util.ColorEncoder
- isTranslucentInherit - Variable in class org.jmol.render.MeshRenderer
- isTransmittance() - Method in class jspecview.source.JDXDataObject
- isTrue(String) - Static method in class jspecview.common.Parameters
- isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
- isTwoSided - Variable in class org.jmol.shape.Mesh
- isUnits(String) - Static method in class org.jmol.modelset.Measurement
- isUnmodulated - Variable in class org.jmol.util.Tensor
- isUpperCase(char) - Static method in class javajs.util.PT
- isURL(String) - Static method in class jspecview.common.JSVFileManager
- isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
- isUserFunction(String) - Method in class org.jmol.script.ScriptCompiler
- isValid - Variable in class org.jmol.bspt.Bspf
- isValid - Variable in class org.jmol.jvxl.data.JvxlData
- isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- isValid - Variable in class org.jmol.modelset.Measurement
- isValid - Variable in class org.jmol.shape.Mesh
- isValid - Variable in class org.jmol.shapespecial.Ellipsoid
- isValid - Variable in class org.jmol.shapespecial.Polyhedron
- isValid() - Method in class jspecview.common.SubSpecChangeEvent
- isValid() - Method in class org.jmol.modelset.Measurement
- isValid() - Method in class org.jmol.modelset.StateScript
- isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.readers.xtal.ShelxReader
- isValidFontName(String) - Method in class jspecview.common.ColorParameters
- isValidFontName(String) - Method in class jspecview.java.AwtParameters
- isValidFontName(String) - Method in class jspecview.js2d.JsParameters
- isValidSym1(char) - Static method in class org.jmol.adapter.smarter.Atom
- isValidSym2(char, char) - Static method in class org.jmol.adapter.smarter.Atom
- isValidSymNoCase(char, char) - Static method in class org.jmol.adapter.smarter.Atom
- isVariableType(Object) - Static method in class org.jmol.script.SV
-
Must be updated if getVariable is updated!
- isVector - Variable in class org.jmol.shapespecial.DrawMesh
- isView - Variable in class jspecview.common.PanelNode
- isView - Variable in class jspecview.source.JDXSource
- isVisible - Variable in class org.jmol.modelset.Measurement
- isVisible - Variable in class org.jmol.shape.Bbcage
- isVisible() - Method in interface jspecview.api.AnnotationData
- isVisible() - Method in interface jspecview.api.JSVViewPanel
- isVisible() - Method in interface jspecview.api.PlatformDialog
- isVisible() - Method in class jspecview.common.MeasurementData
- isVisible() - Method in class jspecview.dialog.JSVDialog
- isVisible() - Method in class jspecview.js2d.JsMainPanel
- isVisible() - Method in class jspecview.js2d.JsPanel
- isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
- isVisible() - Method in class org.jmol.awtjs.swing.Component
- isVisible(int) - Method in class org.jmol.modelset.Atom
- isVisibleForMe(Atom) - Method in class org.jmol.render.ShapeRenderer
- isVisibleNormix(short) - Method in class org.jmol.render.MeshRenderer
- isWebGL - Variable in class org.jmol.popup.GenericPopup
- isWebGL - Variable in class org.jmol.viewer.Viewer
- isWebGL() - Method in interface org.jmol.api.JmolRendererInterface
- isWebGL() - Method in class org.jmol.export.Export3D
- isWebGL() - Method in class org.jmol.g3d.Graphics3D
- isWhitespace(char) - Static method in class javajs.util.PT
- isWhiteSpace(String, int) - Static method in class javajs.util.PT
- isWild(String) - Static method in class javajs.util.PT
- isWindowCentered() - Method in class org.jmol.viewer.TransformManager
- isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
- isWithin(P3) - Method in class org.jmol.util.BoxInfo
- isWithinCell(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- isWithinStructure(STR) - Method in class org.jmol.modelset.Group
- isWithinStructure(STR) - Method in class org.jmol.modelsetbio.AlphaMonomer
- isWithinUnitCell(P3, float, float, float) - Method in interface org.jmol.api.SymmetryInterface
- isWithinUnitCell(P3, float, float, float) - Method in class org.jmol.symmetry.Symmetry
- isXIncreasing() - Method in class jspecview.source.JDXDataObject
-
Returns true if the spectrum is increasing; used by SVGExporter only
- isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
- isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
- isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- isXtalState() - Method in class org.jmol.modelkit.ModelKit
- isXYZ - Variable in class org.jmol.modelset.ModelSet
- isYInRange(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
-
Determines if the y values of a spectrum are in a certain range
- isZipB(byte[]) - Static method in class javajs.util.Rdr
- isZipFile(InputStream) - Static method in class jspecview.common.JSVFileManager
- isZipS(InputStream) - Static method in class javajs.util.Rdr
-
Check for a ZIP input stream - starting with "PKinvalid input: '<'03>invalid input: '<'04>"
- isZipStream(Object) - Method in interface javajs.api.GenericZipTools
- isZipStream(Object) - Method in class javajs.util.ZipTools
- isZipStream(Object) - Method in class org.jmol.viewer.FileManager
- itemKeys - Variable in class org.jmol.console.KeyJMenu
- itemStateChanged(ItemEvent) - Method in class org.jmol.awt.AwtPopupHelper
- itemStateChanged(ItemEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- itemStateChanged(ItemEvent) - Method in class org.jmol.dialog.Dialog.ExportChoiceListener
- iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelsetbio.BioResolver
-
Pull in all spans of helix, etc.
- iToken - Variable in class org.jmol.script.ScriptParam
- itokenInfix - Variable in class org.jmol.script.ScriptCompiler
- iType - Variable in class com.sparshui.GestureType
- iType - Variable in class org.jmol.util.Tensor
- iValue(T) - Static method in class org.jmol.script.SV
- ivspoints - Variable in class jspecview.source.AnIMLReader
J
- J2SIgnoreImport - Annotation Interface in javajs
- J2SObjectInterface - Interface in javajs.api.js
-
methods in j2s JavaScript accessed in Jmol
- J2SRequireImport - Annotation Interface in javajs
- JaguarReader - Class in org.jmol.adapter.readers.quantum
-
Jaguar reader tested for the two samples files in CVS.
- JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
- JanaReader - Class in org.jmol.adapter.readers.xtal
-
A reader for Jana M50+M40 file pairs.
- JanaReader() - Constructor for class org.jmol.adapter.readers.xtal.JanaReader
- javajs - package javajs
- javajs.api - package javajs.api
- javajs.api.js - package javajs.api.js
- javajs.export - package javajs.export
- javajs.img - package javajs.img
- javajs.util - package javajs.util
- javascript - Static variable in class org.jmol.script.T
- JButton - Class in org.jmol.awtjs.swing
- JButton() - Constructor for class org.jmol.awtjs.swing.JButton
- jc - Variable in class org.jmol.awt.AwtSwingComponent
- JC - Class in org.jmol.viewer
- JC() - Constructor for class org.jmol.viewer.JC
- jcampdx - Variable in class jspecview.source.JDXHeader
- JcampdxReader - Class in org.jmol.adapter.readers.more
-
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS=
acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ... - JcampdxReader() - Constructor for class org.jmol.adapter.readers.more.JcampdxReader
- jcd - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- JCH3_AYDIN_GUETHER - Static variable in class org.jmol.quantum.NMRCalculation
- JCH3_NONE - Static variable in class org.jmol.quantum.NMRCalculation
- JCH3_TVAROSKA_TARAVEL - Static variable in class org.jmol.quantum.NMRCalculation
- JCH3_WASYLISHEN_SCHAEFER - Static variable in class org.jmol.quantum.NMRCalculation
- JCheckBox - Class in org.jmol.awtjs.swing
- JCheckBox() - Constructor for class org.jmol.awtjs.swing.JCheckBox
- JCheckBoxMenuItem - Class in org.jmol.awtjs.swing
- JCheckBoxMenuItem() - Constructor for class org.jmol.awtjs.swing.JCheckBoxMenuItem
- JComboBox<T> - Class in org.jmol.awtjs.swing
- JComboBox(String[]) - Constructor for class org.jmol.awtjs.swing.JComboBox
- JComponent - Class in org.jmol.awtjs.swing
- JComponent(String) - Constructor for class org.jmol.awtjs.swing.JComponent
- JContentPane - Class in org.jmol.awtjs.swing
- JContentPane() - Constructor for class org.jmol.awtjs.swing.JContentPane
- JDialog - Class in org.jmol.awtjs.swing
-
There is really no need here for awt.Dialog.
- JDialog() - Constructor for class org.jmol.awtjs.swing.JDialog
- JDXDataObject - Class in jspecview.source
-
spectrum data AS READ FROM FILE
- JDXDataObject() - Constructor for class jspecview.source.JDXDataObject
- JDXDecompressor - Class in jspecview.source
-
JDXDecompressor contains static methods to decompress the data part of JCAMP-DX spectra that have been compressed using DIF, FIX, SQZ or PAC formats.
- JDXDecompressor(String, int) - Constructor for class jspecview.source.JDXDecompressor
- JDXDecompressor(JDXSourceStreamTokenizer, double, double, double, double, int) - Constructor for class jspecview.source.JDXDecompressor
-
Initialises the
JDXDecompressor
from the compressed data, the x factor, the y factor and the deltaX value - JDXDecompressorTest - Class in jspecview.source
- JDXDecompressorTest() - Constructor for class jspecview.source.JDXDecompressorTest
- JDXExporter - Class in jspecview.export
-
class
JDXExporter
contains methods for exporting a JCAMP-DX Spectrum in one of the compression formats DIF, FIX, PAC, SQZ or as x, y values. - JDXExporter() - Constructor for class jspecview.export.JDXExporter
- JDXHeader - Class in jspecview.source
-
could be a spectrum or a source
- JDXHeader() - Constructor for class jspecview.source.JDXHeader
- JDXMOLParser - Class in org.jmol.jsv
-
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
- JDXMOLParser() - Constructor for class org.jmol.jsv.JDXMOLParser
- JDXReader - Class in jspecview.source
-
JDXFileReader
reads JDX data, including complex BLOCK files that contain NTUPLE blocks or nested BLOCK data. - JDXSource - Class in jspecview.source
-
JDXSource
is representation of all the data in the JCAMP-DX file or source. - JDXSource(int, String) - Constructor for class jspecview.source.JDXSource
- JDXSourceStreamTokenizer - Class in jspecview.source
- JEditorPane - Class in org.jmol.awtjs.swing
-
A simple implementation of a Swing JTextPane.
- JEditorPane() - Constructor for class org.jmol.awtjs.swing.JEditorPane
- JLabel - Class in org.jmol.awtjs.swing
- JLabel(String) - Constructor for class org.jmol.awtjs.swing.JLabel
- jme - package jme
- JME - Class in jme
- JME() - Constructor for class jme.JME
- JME(JFrame, boolean) - Constructor for class jme.JME
- jmeFile() - Method in class jme.JME
- jmeh - Variable in class jme.JME
- JMEmol - Class in jme
- JMEmol(JME, JmolAdapterAtomIterator, JmolAdapterBondIterator) - Constructor for class jme.JMEmol
- JMenu - Class in org.jmol.awtjs.swing
- JMenu() - Constructor for class org.jmol.awtjs.swing.JMenu
- JMenuItem - Class in org.jmol.awtjs.swing
- JMenuItem(String) - Constructor for class org.jmol.awtjs.swing.JMenuItem
- JMenuItem(String, int) - Constructor for class org.jmol.awtjs.swing.JMenuItem
- JmeReader - Class in org.jmol.adapter.readers.simple
- JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
- jmeToMolecule(String) - Static method in class org.jmol.smiles.SmilesMatcher
- JMEUtil - Class in jme
- JMEUtil() - Constructor for class jme.JMEUtil
- JMEUtil.GWT - Class in jme
-
Do nothing , support for JSME code splitting.
- JMEUtil.JSME_RunAsyncCallback - Class in jme
- JMEUtil.RunAsyncCallback - Interface in jme
-
A callback meant to be used by
- JMEUtil.RunWhenDataReadyCallback - Interface in jme
- jmol - Variable in class jspecview.application.JSpecView
- jmol - Static variable in class org.jmol.script.T
- Jmol - Class in org.jmol.appletjs
-
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
- Jmol - Class in org.openscience.jmol.app
- Jmol(Map<String, Object>) - Constructor for class org.jmol.appletjs.Jmol
- Jmol(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.Jmol
- Jmol() - Static method in class org.jmol.awtjs2d.Platform
- JMOL - Enum constant in enum class jspecview.common.ScriptToken
- JMOL - Enum constant in enum class org.jmol.c.PAL
- JMOL - Enum constant in enum class org.jmol.c.VDW
- JMOL - Static variable in class org.jmol.util.ColorEncoder
- JMOL_DIAMETER - Static variable in class org.jmol.shapecgo.CGOMesh
- JMOL_MODEL_KIT - Static variable in class org.jmol.viewer.JC
- JMOL_PS - Static variable in class org.jmol.shapecgo.CGOMesh
- JMOL_SCREEN - Static variable in class org.jmol.shapecgo.CGOMesh
- JMOL_UVMAP - Static variable in class org.jmol.shapecgo.CGOMesh
- JmolAbstractButton - Interface in org.jmol.api
- JmolAdapter - Class in org.jmol.api
-
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
- JmolAdapter() - Constructor for class org.jmol.api.JmolAdapter
- JmolAdapterAtomIterator - Interface in org.jmol.api
- JmolAdapterBondIterator - Class in org.jmol.api
- JmolAdapterBondIterator() - Constructor for class org.jmol.api.JmolAdapterBondIterator
- JmolAdapterStructureIterator - Class in org.jmol.api
- JmolAdapterStructureIterator() - Constructor for class org.jmol.api.JmolAdapterStructureIterator
- JmolAnnotationParser - Interface in org.jmol.api
- jmolApp - Variable in class org.openscience.jmol.app.JmolData
- jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- JmolApp - Class in org.openscience.jmol.app
- JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
- JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
-
standard Jmol application entry point
- JmolAppAPI - Interface in org.jmol.api
- JmolAppConsoleInterface - Interface in org.jmol.api
- JmolAppletInterface - Interface in org.jmol.api
-
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
- JmolAsyncException - Exception Class in org.jmol.viewer
- JmolAsyncException(String) - Constructor for exception class org.jmol.viewer.JmolAsyncException
- JmolAudio - Class in org.jmol.util
- JmolAudio() - Constructor for class org.jmol.util.JmolAudio
- JmolAudioPlayer - Interface in org.jmol.api
- JmolBinding - Class in org.jmol.viewer.binding
- JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
- JmolButton - Class in org.jmol.console
- JmolButton(String) - Constructor for class org.jmol.console.JmolButton
- JmolButton(ImageIcon) - Constructor for class org.jmol.console.JmolButton
- JmolCallbackListener - Interface in org.jmol.api
- JmolChimeMessenger - Interface in org.jmol.viewer
- JmolConsole - Class in org.jmol.console
- JmolConsole() - Constructor for class org.jmol.console.JmolConsole
- JmolData - Class in org.openscience.jmol.app
- JmolDataManager - Interface in org.jmol.api
- JmolDataReader - Class in org.jmol.adapter.readers.pdb
-
JmolData file reader, for a modified PDB format
- JmolDataReader() - Constructor for class org.jmol.adapter.readers.pdb.JmolDataReader
- JmolDialogInterface - Interface in org.jmol.api
- JmolDropEditor - Interface in org.jmol.api
- JmolEnvCalc - Interface in org.jmol.api
- JmolFilesReaderInterface - Interface in org.jmol.api
- JmolFrame - Interface in jspecview.java
- JmolFrame - Interface in org.jmol.awt
- JmolGenericPopup - Class in org.jmol.popup
-
An abstract popup class that is instantiated for a given platform and context as one of:
- JmolGenericPopup() - Constructor for class org.jmol.popup.JmolGenericPopup
- JmolGestureServerInterface - Interface in org.jmol.api
- JmolGraphicsInterface - Interface in org.jmol.api
- JmolInChI - Interface in org.jmol.api
- jmolinjspecview - Static variable in class org.jmol.script.T
- JmolJDXMOLParser - Interface in org.jmol.api
- JmolJDXMOLReader - Interface in org.jmol.api
- jmolJME - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- JmolJME - Class in org.openscience.jmol.app.jmolpanel
- JmolJME() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolJME
- JmolJniClientAdapter - Class in org.jmol.multitouch.jni
- JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
- JmolJSpecView - Interface in org.jmol.api
- JmolLabel - Class in org.jmol.console
- JmolLabel(String, int) - Constructor for class org.jmol.console.JmolLabel
- JmolMeasurementClient - Interface in org.jmol.api
- JmolModulationSet - Interface in org.jmol.api
- JmolMolecule - Class in org.jmol.util
-
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
- JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
- JmolMovieCreatorInterface - Interface in org.jmol.api
- JmolMultiTouchAdapter - Interface in org.jmol.multitouch
- JmolMultiTouchClient - Interface in org.jmol.multitouch
- JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
- JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
- JmolNavigatorInterface - Interface in org.jmol.api
- JmolNMRInterface - Interface in org.jmol.api
- jmolObject - Static variable in class jspecview.common.JSViewer
- jmolObject - Static variable in class org.jmol.viewer.Viewer
- jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- JmolPanel - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
- JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.AnimButton - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
-
To shutdown when run as an application.
- JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
-
An Action to copy the current image into the clipboard.
- JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.CreditsAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.TwoDEditorAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
- JmolParallelProcessor - Interface in org.jmol.api
- JmolPdfCreatorInterface - Interface in org.jmol.api
- JmolPlugin - Interface in org.openscience.jmol.app
- JmolPopup - Class in org.jmol.popup
-
An abstract popup class that is instantiated for a given platform and context as one of:
- JmolPopup() - Constructor for class org.jmol.popup.JmolPopup
- jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
- JmolPropertyManager - Interface in org.jmol.api
- JmolRendererInterface - Interface in org.jmol.api
- JmolRepaintManager - Interface in org.jmol.api
- JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
-
Provides access to resources (for example, strings and images).
- JmolSceneGenerator - Interface in org.jmol.api
- JmolScriptEditorInterface - Interface in org.jmol.api
- JmolScriptEvaluator - Interface in org.jmol.api
- JmolScriptFunction - Interface in org.jmol.api
- JmolScriptManager - Interface in org.jmol.api
- JmolSelectionListener - Interface in org.jmol.api
-
listen to atom selections in a Jmol Viewer
- Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS - Search tag in package org.jmol.smiles
- Section
- Jmol SMILES and Jmol SMARTS Definition of "aromatic" - Search tag in package org.jmol.smiles
- Section
- JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
- JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- JmolStateCreator - Class in org.jmol.viewer
- JmolStateCreator() - Constructor for class org.jmol.viewer.JmolStateCreator
- JmolStatusListener - Interface in org.jmol.api
- JmolSyncInterface - Interface in org.jmol.api
- JmolThread - Class in org.jmol.thread
- JmolThread() - Constructor for class org.jmol.thread.JmolThread
- JmolToggleButton - Class in org.jmol.console
- JmolToggleButton(ImageIcon) - Constructor for class org.jmol.console.JmolToggleButton
- JmolToJSmolInterface - Interface in org.jmol.api.js
-
methods in JSmol JavaScript accessed in Jmol
- JmolTouchSimulator - Class in com.sparshui.inputdevice
-
allows Jmol to implement multitouch testing using the mouse press CTRL-LEFT and drag twice for a two-stroke multitouch gesture that will be sent to the server in an interlaced fashion.
- JmolTouchSimulator() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator
- JmolTouchSimulator.TouchData - Class in com.sparshui.inputdevice
- JmolTouchSimulator.TouchDataComparator - Class in com.sparshui.inputdevice
- JmolTouchSimulatorInterface - Interface in org.jmol.api
- JmolUtil - Class in org.jmol.io
- JmolUtil() - Constructor for class org.jmol.io.JmolUtil
- JmolViewer - Class in org.jmol.api
-
JmolViewer is the main API for the Viewer class.
- JmolViewer() - Constructor for class org.jmol.api.JmolViewer
- JmolWriter - Interface in org.jmol.api
- JmolZipUtilities - Interface in org.jmol.api
- join - Static variable in class org.jmol.script.T
- join(String[], char, int) - Static method in class javajs.util.PT
- JPanel - Class in org.jmol.awtjs.swing
- JPanel(LayoutManager) - Constructor for class org.jmol.awtjs.swing.JPanel
- JPEG_CONTINUE_STRING - Static variable in class org.jmol.viewer.FileManager
- JPEG_EXTENSIONS - Static variable in class org.jmol.viewer.JC
- JPG - Enum constant in enum class jspecview.common.ExportType
- Jpg64Encoder - Class in javajs.img
- Jpg64Encoder() - Constructor for class javajs.img.Jpg64Encoder
- JpgEncoder - Class in javajs.img
-
JpegEncoder - The JPEG main program which performs a jpeg compression of an image.
- JpgEncoder() - Constructor for class javajs.img.JpgEncoder
- jpiDispose() - Method in class jspecview.popup.JSVGenericPopup
- jpiDispose() - Method in interface org.jmol.api.GenericMenuInterface
- jpiDispose() - Method in class org.jmol.popup.GenericPopup
- jpiDispose() - Method in class org.jmol.popup.JmolGenericPopup
- jpiDispose() - Method in class org.jmol.popup.JmolPopup
- jpiGetMenuAsObject() - Method in class jspecview.popup.JSVGenericPopup
- jpiGetMenuAsObject() - Method in interface org.jmol.api.GenericMenuInterface
- jpiGetMenuAsObject() - Method in class org.jmol.popup.JmolGenericPopup
- jpiGetMenuAsString(String) - Method in interface org.jmol.api.GenericMenuInterface
- jpiGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
- jpiInitialize(PlatformViewer, String) - Method in class jspecview.java.AwtPopup
- jpiInitialize(PlatformViewer, String) - Method in class jspecview.js2d.JsPopup
- jpiInitialize(PlatformViewer, String) - Method in interface org.jmol.api.GenericMenuInterface
- jpiInitialize(PlatformViewer, String) - Method in class org.jmol.popup.JmolGenericPopup
- jpiShow(int, int) - Method in class jspecview.popup.JSVGenericPopup
- jpiShow(int, int) - Method in interface org.jmol.api.GenericMenuInterface
- jpiShow(int, int) - Method in class org.jmol.modelkit.ModelKitPopup
- jpiShow(int, int) - Method in class org.jmol.popup.JmolGenericPopup
- jpiUpdateComputedMenus() - Method in class jspecview.popup.JSVGenericPopup
- jpiUpdateComputedMenus() - Method in interface org.jmol.api.GenericMenuInterface
- jpiUpdateComputedMenus() - Method in class org.jmol.modelkit.ModelKitPopup
- jpiUpdateComputedMenus() - Method in class org.jmol.popup.JmolPopup
- JPopupMenu - Class in org.jmol.awtjs.swing
- JPopupMenu(String) - Constructor for class org.jmol.awtjs.swing.JPopupMenu
- JRadioButtonMenuItem - Class in org.jmol.awtjs.swing
- JRadioButtonMenuItem() - Constructor for class org.jmol.awtjs.swing.JRadioButtonMenuItem
- JSAppletObject - Interface in javajs.api.js
- JSConsole - Interface in org.jmol.api.js
- JScrollPane - Class in org.jmol.awtjs.swing
- JScrollPane(JComponent) - Constructor for class org.jmol.awtjs.swing.JScrollPane
- JsDialog - Class in jspecview.js2d
-
just a class I made to separate the construction of the AnnotationDialogs from their use
- JsDialog(DialogManager, JSVDialog, String) - Constructor for class jspecview.js2d.JsDialog
- JsDialogManager - Class in jspecview.js2d
-
A DialogManager for JavaScript.
- JsDialogManager() - Constructor for class jspecview.js2d.JsDialogManager
- jsDocumentBase - Static variable in class jspecview.common.JSVFileManager
- jsDocumentBase - Static variable in class org.jmol.viewer.Viewer
- jsEval(String) - Method in class org.jmol.viewer.Viewer
- jsEvalSV(String) - Method in class org.jmol.viewer.Viewer
- JSExporter - Class in org.jmol.export
-
A class to output WebGL graphics.
- JSExporter() - Constructor for class org.jmol.export.JSExporter
- JsFileHelper - Class in jspecview.js2d
- JsFileHelper() - Constructor for class jspecview.js2d.JsFileHelper
- JSFunction - Interface in javajs.api
-
A flag that this object is really a JavaScript function that, for example, might be called from setTimeout().
- JsG2D - Class in jspecview.js2d
-
generic 2D drawing methods for JSpecView -- JavaScript version
- JsG2D - Class in org.jmol.awtjs2d
-
generic 2D drawing methods -- JavaScript version
- JsG2D() - Constructor for class jspecview.js2d.JsG2D
- JsG2D() - Constructor for class org.jmol.awtjs2d.JsG2D
- JSInterface - Interface in javajs.api
-
called by JSmol JavaScript methods using this._applet.xxxx()
- JSJmolPopup - Class in org.jmol.awtjs2d
- JSJmolPopup() - Constructor for class org.jmol.awtjs2d.JSJmolPopup
-
The main popup window for the applet -- as JavaScript
- JSJSONParser - Class in javajs.util
-
a very simple JSON parser for JSON objects that are compatible with JavaScript A gross simplification of https://github.com/douglascrockford/JSON-java A SUBSET of JSON with similarly to window.JSON.parse(): In JavaScript returns "null" for a null value, not null -- requires quoted strings for keys and values -- does not allow /xxx/ objects
- JSJSONParser() - Constructor for class javajs.util.JSJSONParser
- JsMainPanel - Class in jspecview.js2d
- JsMainPanel() - Constructor for class jspecview.js2d.JsMainPanel
- JSME_RunAsyncCallback() - Constructor for class jme.JMEUtil.JSME_RunAsyncCallback
- JSModelKitPopup - Class in org.jmol.awtjs2d
- JSModelKitPopup() - Constructor for class org.jmol.awtjs2d.JSModelKitPopup
- JSmolAppletObject - Interface in org.jmol.api.js
- json - Static variable in class org.jmol.script.T
- JSONEncodable - Interface in javajs.api
- JSONException - Exception Class in javajs.util
- JSONException(String) - Constructor for exception class javajs.util.JSONException
- JsonNioClient - Interface in org.openscience.jmol.app.jsonkiosk
-
a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
- JsonNioClient.TouchHandler - Class in org.openscience.jmol.app.jsonkiosk
- JsonNioClientThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
- JsonNioServer - Interface in org.openscience.jmol.app.jsonkiosk
- JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
- JsonNioService - Class in org.openscience.jmol.app.jsonkiosk
-
A class for interacting with Jmol over local sockets.
- JsonNioService() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService
- JsonNioService.JsonNioClientThread - Class in org.openscience.jmol.app.jsonkiosk
- JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jsonkiosk
- JSONReader - Class in org.jmol.adapter.readers.simple
- JSONReader() - Constructor for class org.jmol.adapter.readers.simple.JSONReader
- JSONWriter - Class in org.jmol.util
- JSONWriter() - Constructor for class org.jmol.util.JSONWriter
- JsPanel - Class in jspecview.js2d
-
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
- JsParameters - Class in jspecview.js2d
- JsParameters() - Constructor for class jspecview.js2d.JsParameters
- JSPattern(String, boolean) - Constructor for class org.jmol.util.PatternMatcher.JSPattern
- JSpecView - Class in jspecview.application
-
The Main Class or Entry point of the JSpecView Application.
- JSpecView - Class in org.jmol.jsv
- JSpecView() - Constructor for class org.jmol.jsv.JSpecView
- JSpecView(boolean, JSVInterface) - Constructor for class jspecview.application.JSpecView
- jspecview.api - package jspecview.api
- jspecview.api.js - package jspecview.api.js
- jspecview.app - package jspecview.app
- jspecview.appletjs - package jspecview.appletjs
- jspecview.application - package jspecview.application
- jspecview.common - package jspecview.common
- jspecview.dialog - package jspecview.dialog
- jspecview.exception - package jspecview.exception
- jspecview.export - package jspecview.export
- jspecview.java - package jspecview.java
- jspecview.js2d - package jspecview.js2d
- jspecview.popup - package jspecview.popup
- jspecview.source - package jspecview.source
- jspecview.tree - package jspecview.tree
- JsPlatform - Class in jspecview.js2d
-
JavaScript 2D canvas version requires Ajax-based URL stream processing.
- JsPlatform() - Constructor for class jspecview.js2d.JsPlatform
- JSplitPane - Class in org.jmol.awtjs.swing
- JSplitPane(int) - Constructor for class org.jmol.awtjs.swing.JSplitPane
- JsPopup - Class in jspecview.js2d
- JsPopup() - Constructor for class jspecview.js2d.JsPopup
- JSPopupHelper - Class in org.jmol.awtjs2d
-
For menus, popup-related awt/swing class references are in this file.
- JSPopupHelper(GenericPopup) - Constructor for class org.jmol.awtjs2d.JSPopupHelper
- jsSurface(Object, T3[], T3[], int[][], int, int, int, BS, int, int, int[], int[]) - Method in class org.jmol.export.JSExporter
- JSV - Enum constant in enum class jspecview.common.ScriptToken
- JSV_CLOSE - Static variable in class org.jmol.viewer.JC
- JSV_NOT - Static variable in class org.jmol.viewer.JC
- JSV_SELECT - Static variable in class org.jmol.viewer.JC
- JSV_SEND_C13SIMULATE - Static variable in class org.jmol.viewer.JC
- JSV_SEND_H1SIMULATE - Static variable in class org.jmol.viewer.JC
- JSV_SEND_JDXMOL - Static variable in class org.jmol.viewer.JC
- JSV_SETPEAKS - Static variable in class org.jmol.viewer.JC
- JSV_STRUCTURE - Static variable in class org.jmol.viewer.JC
- JSVApp - Class in jspecview.app
-
JSpecView Applet class.
- JSVApp(AppletFrame, boolean) - Constructor for class jspecview.app.JSVApp
- JSVAppInterface - Interface in jspecview.api
- JSVApplet - Class in jspecview.appletjs
-
Entry point for the web.
- JSVApplet(Map<String, Object>) - Constructor for class jspecview.appletjs.JSVApplet
- JSVAppletInterface - Interface in jspecview.api
- JSVAppletObject - Interface in jspecview.api.js
- JSVAppletPro - Class in jspecview.appletjs
-
A signed applet that has an Advanced...
- JSVAppletPro(Map<String, Object>) - Constructor for class jspecview.appletjs.JSVAppletPro
- JSVAppPro - Class in jspecview.app
- JSVAppPro(AppletFrame, boolean) - Constructor for class jspecview.app.JSVAppPro
- JSVDialog - Class in jspecview.dialog
- JSVDialog() - Constructor for class jspecview.dialog.JSVDialog
- JSVersion - Class in jspecview.common
- JSVersion() - Constructor for class jspecview.common.JSVersion
- JSVException - Exception Class in jspecview.exception
-
JSVException is the base class from which all exceptions in JSpecView is inherited.
- JSVException(String) - Constructor for exception class jspecview.exception.JSVException
-
Constructor that takes a string specifying exception details
- JSVExporter - Interface in jspecview.api
- JSVFileDropper - Interface in jspecview.api
- JSVFileHelper - Interface in jspecview.api
- JSVFileManager - Class in jspecview.common
- JSVFileManager() - Constructor for class jspecview.common.JSVFileManager
- JSVGenericPopup - Class in jspecview.popup
- JSVGenericPopup() - Constructor for class jspecview.popup.JSVGenericPopup
- JSViewer - Class in jspecview.common
-
This class encapsulates all general functionality of applet and app.
- JSViewer(ScriptInterface, boolean, boolean) - Constructor for class jspecview.common.JSViewer
- JSVInterface - Interface in org.jmol.api
-
and interface for JSpecView for the Jmol application
- JSVMainPanel - Interface in jspecview.api
- jsvp - Variable in class jspecview.app.GenericMouse
- jsvp - Variable in class jspecview.common.PanelData
- jsvp - Variable in class jspecview.common.PanelNode
- jsvp - Variable in class jspecview.dialog.JSVDialog
- JSVPanel - Interface in jspecview.api
- JSVPdfWriter - Interface in jspecview.api
- JSVPopupResourceBundle - Class in jspecview.popup
- JSVPopupResourceBundle() - Constructor for class jspecview.popup.JSVPopupResourceBundle
- jsvpPopupMenu - Variable in class jspecview.common.JSViewer
- JSVPrintDialog - Interface in jspecview.api
- JSVToJSmolInterface - Interface in jspecview.api.js
- JSVTree - Interface in jspecview.api
- JSVTreeNode - Interface in jspecview.api
- JSVTreePath - Interface in jspecview.api
- JSVViewPanel - Interface in jspecview.api
- JSVZipFileSequentialReader - Class in jspecview.common
-
Reads the entire contents of a ZIP file as though it were one straight file Skips and entry that contains '\0' Allows for a moderate amount of buffered reading via mark()
- JSVZipFileSequentialReader() - Constructor for class jspecview.common.JSVZipFileSequentialReader
- JSVZipInterface - Interface in jspecview.api
- JSVZipReader - Interface in jspecview.api
- JSVZipUtil - Class in jspecview.common
- JSVZipUtil() - Constructor for class jspecview.common.JSVZipUtil
- JTable - Class in org.jmol.awtjs.swing
- JTable(AbstractTableModel) - Constructor for class org.jmol.awtjs.swing.JTable
- JTextField - Class in org.jmol.awtjs.swing
- JTextField(String) - Constructor for class org.jmol.awtjs.swing.JTextField
- JTextPane - Class in org.jmol.awtjs.swing
-
A simple implementation of a Swing JTextPane.
- JTextPane() - Constructor for class org.jmol.awtjs.swing.JTextPane
- jumpBestFrame() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- JumpBestFrameAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
- jumpToSpectrum(Spectrum) - Method in class jspecview.common.PanelData
- jumpToSpectrumIndex(int, boolean) - Method in class jspecview.common.PanelData
- justifymeasurements - Static variable in class org.jmol.script.T
- Jvxl - Class in org.openscience.jvxl
- Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
- JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
- JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
- jvxlAppendEncodedNumber(SB, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- JvxlCoder - Class in org.jmol.jvxl.data
- JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
- jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlCreateHeader(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
Creates a two-line header for the XJVXL file.
- jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlCutoffRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlData - Variable in class org.jmol.shape.MeshCollection
- jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- JvxlData - Class in org.jmol.jvxl.data
- JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
- jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlDecodeBitSetRange(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
decode vertex data found within
element as created by jvxlEncodeVertexData (see above) - jvxlDecompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlEncodeBitSet(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEncodeBitSet0(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEncodeBitSetBuffer(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEncodeColorData(float[], float, float, int, int, boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFileSource - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlFractionAsCharacterRange(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], Lst<P3>, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetInfoData(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
- JvxlReader - Class in org.jmol.jvxl.readers
- jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
- jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
- jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
- jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
- JvxlWrite - Class in org.openscience.jvxl.simplewriter
- JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
- JvxlXmlReader - Class in org.jmol.jvxl.readers
- JZlib - Class in com.jcraft.jzlib
- JZlib() - Constructor for class com.jcraft.jzlib.JZlib
- jzSetDOS(OutputStream, Deflater, int, boolean) - Method in class com.jcraft.jzlib.DeflaterOutputStream
- jzt - Variable in class javajs.util.CompoundDocument
K
- ka - Variable in class org.jmol.minimize.MinAngle
- keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
- keepHydrogens - Variable in class jme.JME
- key - Variable in class org.jmol.minimize.MinObject
- KEY_MAX - Static variable in class javajs.util.CifDataParser
-
The maximum number of columns (data keys) passed to the parser or found in the file for a given loop_ or category.subkey listing.
- keybuf - Variable in class org.jmol.viewer.MouseState
- keyDown(KeyEvent, int) - Method in class jme.JME
- KeyJCheckBox - Class in org.jmol.console
- KeyJCheckBox(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
- KeyJCheckBoxMenuItem - Class in org.jmol.console
- KeyJCheckBoxMenuItem(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
- KeyJMenu - Class in org.jmol.console
- KeyJMenu(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenu
- KeyJMenuItem - Class in org.jmol.console
- KeyJMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenuItem
- KeyJRadioButtonMenuItem - Class in org.jmol.console
- KeyJRadioButtonMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
- keyPressed(int) - Method in class jspecview.application.CommandHistory
- keyPressed(int, int) - Method in class jspecview.common.PanelData
- keyPressed(int, int) - Method in interface org.jmol.api.EventManager
- keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
-
called by MouseManager.keyPressed
- keyPressed(KeyEvent) - Method in class jme.JME
- keyPressed(KeyEvent) - Method in class jspecview.app.GenericMouse
- keyPressed(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
- keyPressedEvent(int, char) - Method in class jspecview.application.MainFrame
- keyReleased(int) - Method in class jspecview.common.PanelData
- keyReleased(int) - Method in interface org.jmol.api.EventManager
- keyReleased(int) - Method in class org.jmol.viewer.ActionManager
- keyReleased(KeyEvent) - Method in class jme.JME
- keyReleased(KeyEvent) - Method in class jspecview.app.GenericMouse
- keyReleased(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
- keys - Static variable in class org.jmol.script.T
- keyTyped(int, int) - Method in class jspecview.common.PanelData
- keyTyped(int, int) - Method in interface org.jmol.api.EventManager
- keyTyped(int, int) - Method in class org.jmol.viewer.ActionManager
- keyTyped(KeyEvent) - Method in class jme.JME
- keyTyped(KeyEvent) - Method in class jspecview.app.GenericMouse
- keyTyped(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
- keyXy - Variable in class org.jmol.shapesurface.Isosurface
- kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- KioskFrame - Class in org.openscience.jmol.app.jsonkiosk
-
A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in http://molecularPlayground.org
- KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jsonkiosk.KioskFrame
- knownGroupID(String) - Static method in class org.jmol.modelsetbio.BioResolver
L
- label - Static variable in class org.jmol.script.T
- label - Variable in class org.jmol.shapespecial.Ellipsoid
- LABEL - Enum constant in enum class jspecview.common.ScriptToken
- LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- LABEL_DEFAULT_OFFSET - Static variable in class org.jmol.viewer.JC
- LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JC
- LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JC
- LABEL_EXPLICIT - Static variable in class org.jmol.viewer.JC
- LABEL_FLAGS - Static variable in class org.jmol.viewer.JC
- LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
- LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
- LABEL_OFFSET_MAX - Static variable in class org.jmol.viewer.JC
- LABEL_POINTER_BACKGROUND - Static variable in class org.jmol.viewer.JC
- LABEL_POINTER_NONE - Static variable in class org.jmol.viewer.JC
- LABEL_POINTER_ON - Static variable in class org.jmol.viewer.JC
- LABEL_ZPOS_FRONT - Static variable in class org.jmol.viewer.JC
- LABEL_ZPOS_GROUP - Static variable in class org.jmol.viewer.JC
- label1 - Variable in class org.jmol.console.GenericConsole
- labelColix - Variable in class org.jmol.modelset.Measurement
- labelColix - Variable in class org.jmol.render.LabelsRenderer
- labelFormat - Variable in class org.jmol.shape.Hover
- LabelNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
- labelpointerwidth - Static variable in class org.jmol.script.T
- labelPointerWidth - Variable in class org.jmol.viewer.GlobalSettings
- labels - Static variable in class org.jmol.console.GenericConsole
- labels - Variable in class org.jmol.shape.Axes
- labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
- Labels - Class in org.jmol.shape
- Labels() - Constructor for class org.jmol.shape.Labels
- labelSetter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- LabelSetter - Class in org.openscience.jmol.app.janocchio
- LabelSetter(NMR_Viewer, NoeTable, CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.LabelSetter
- LabelsRenderer - Class in org.jmol.render
- LabelsRenderer() - Constructor for class org.jmol.render.LabelsRenderer
- LabelToken - Class in org.jmol.modelset
- LabelToken() - Constructor for class org.jmol.modelset.LabelToken
- labelX - Variable in class jme.AtomDisplayLabel
- labelY - Variable in class jme.AtomDisplayLabel
- labToXyz(P3, P3) - Method in class javajs.img.GifEncoder
- language - Variable in class org.jmol.i18n.Language
- language - Static variable in class org.jmol.script.T
- language - Variable in class org.jmol.util.GenericApplet
- Language - Class in org.jmol.i18n
- languagetranslation - Static variable in class org.jmol.script.T
- last - Static variable in class org.jmol.script.T
- LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.C
- lastAtomIndex - Variable in class org.jmol.modelset.Group
- lastDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
- lastElement() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- lastFlowCommand - Variable in class org.jmol.script.ScriptCompiler
- lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
- lastIndexOf(String) - Method in class javajs.util.SB
- lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
- lastModelIndex - Variable in class org.jmol.atomdata.AtomData
- lastModelSet - Variable in class org.jmol.modelkit.ModelKit
- lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- lastNorm - Variable in class jspecview.dialog.JSVDialog
- lastPressTime - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- lastRepaintTime - Variable in class org.jmol.thread.JmolThread
- lastToken - Variable in class org.jmol.script.ScriptCompiler
- lastX - Variable in class jspecview.export.AMLExporter
- lastX - Variable in class jspecview.export.CMLExporter
- lastX - Variable in class jspecview.source.AnIMLReader
- latestMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- lattice - Static variable in class org.jmol.script.T
- lattice - Variable in class org.jmol.shape.Mesh
- LATTICE_VECTOR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- latticeOffset - Variable in class org.jmol.render.MeshRenderer
- latticeScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- latticeType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- launchMainFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- launchMainFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- layout - Variable in class jspecview.common.PrintLayout
-
The paper orientation ("portrait" or "landscape")
- layoutDialog() - Method in class jspecview.dialog.JSVDialog
- LayoutManager - Class in org.jmol.awtjs.swing
- LayoutManager() - Constructor for class org.jmol.awtjs.swing.LayoutManager
- layoutWindow(String) - Method in class org.jmol.console.AppletConsole
- layoutWindow(String) - Method in class org.jmol.console.GenericConsole
- layoutWindow(String) - Method in class org.jmol.consolejs.AppletConsole
- layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- lcaocartoon - Static variable in class org.jmol.script.T
- LcaoCartoon - Class in org.jmol.shapesurface
- LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
- LcaoCartoonRenderer - Class in org.jmol.rendersurface
- LcaoCartoonRenderer() - Constructor for class org.jmol.rendersurface.LcaoCartoonRenderer
- leadatom - Static variable in class org.jmol.script.T
- leadAtomIndex - Variable in class org.jmol.modelset.Group
- leadAtomIndices - Variable in class org.jmol.modelsetbio.BioPolymer
- leadAtomIndices - Variable in class org.jmol.renderbio.BackboneRenderer
- leadAtomIndices - Variable in class org.jmol.renderbio.CartoonRenderer
- leadAtomIndices - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- leadAtomIndices - Variable in class org.jmol.renderbio.RibbonsRenderer
- leadAtomIndices - Variable in class org.jmol.renderbio.RocketsRenderer
- leadAtomIndices - Variable in class org.jmol.renderbio.StrandsRenderer
- leadAtomIndices - Variable in class org.jmol.renderbio.TraceRenderer
- leadMidpoints - Variable in class org.jmol.modelsetbio.BioPolymer
- leadPoints - Variable in class org.jmol.modelsetbio.BioPolymer
- left - Variable in class jspecview.common.PanelData
- left - Static variable in class org.jmol.script.T
- LEFT - Static variable in class org.jmol.awtjs.swing.SwingConstants
- LEFT - Static variable in class org.jmol.viewer.binding.Binding
- leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- leftbrace - Static variable in class org.jmol.script.T
- leftDifference(Quat) - Method in class javajs.util.Quat
- leftdivide - Static variable in class org.jmol.script.T
- leftJustify(SB, String, String) - Static method in class javajs.util.PT
- leftMargin - Static variable in class jspecview.common.PanelData
- leftPanel - Variable in class jspecview.java.AwtDialog
- leftPanel - Variable in class jspecview.js2d.JsDialog
- leftparen - Static variable in class org.jmol.script.T
- leftsquare - Static variable in class org.jmol.script.T
- legacyautobonding - Static variable in class org.jmol.script.T
- legacyhaddition - Static variable in class org.jmol.script.T
- legacyjavafloat - Static variable in class org.jmol.script.T
- legacyJavaFloat - Variable in class org.jmol.viewer.GlobalSettings
- legend - Variable in class jspecview.common.PanelNode
- len - Variable in class com.jcraft.jzlib.InflaterInputStream
- length - Static variable in class org.jmol.script.T
- length() - Method in class javajs.util.BS
-
Returns the "logical size" of this
BitSet
: the index of the highest set bit in theBitSet
plus one. - length() - Method in class javajs.util.SB
- length() - Method in class javajs.util.T3
-
Returns the length of this vector.
- length() - Method in class javajs.util.V3d
-
Returns the length of this vector.
- length() - Method in interface org.jmol.api.GenericFileInterface
- lengthSquared() - Method in class javajs.util.T3
-
Returns the squared length of this vector.
- lengthSquared() - Method in class javajs.util.V3d
-
Returns the squared length of this vector.
- LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
- LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
- LEVEL_ERROR - Static variable in class org.jmol.util.Logger
- LEVEL_FATAL - Static variable in class org.jmol.util.Logger
- LEVEL_INFO - Static variable in class org.jmol.util.Logger
- LEVEL_MAX - Static variable in class org.jmol.util.Logger
- LEVEL_WARN - Static variable in class org.jmol.util.Logger
- LEXICAL_COMPARATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- LIGHT_GRAY - Static variable in class jspecview.common.ColorParameters
- lighting - Static variable in class org.jmol.script.T
- lighting - Variable in class org.jmol.shape.Mesh
- lightSource - Variable in class org.jmol.export.___Exporter
- LIME - Static variable in class org.jmol.util.C
- LimitedLineReader - Class in javajs.util
-
A simple class to read a designated number of bytes from a file and then return them line by line, skipping lines that start with #, and including the \n or \r characters at line ends.
- LimitedLineReader(BufferedReader, int) - Constructor for class javajs.util.LimitedLineReader
- line - Variable in class javajs.util.CifDataParser
-
from buffered reader
- line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- line - Variable in class org.jmol.jvxl.readers.JvxlReader
- line - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- line - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- line - Static variable in class org.jmol.script.T
- LINE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- LINE_SEGMENT - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
- lineCurrent - Variable in class org.jmol.script.ScriptCompiler
- linedata - Static variable in class org.jmol.script.T
- lineData - Variable in class org.jmol.shape.Mesh
- lineHeight - Variable in class org.jmol.modelset.Text
- lineIndices - Variable in class org.jmol.script.ScriptContext
- lines - Variable in class org.jmol.modelset.Text
- lines - Static variable in class org.jmol.script.T
- lineto(int, int) - Method in class javajs.export.PDFCreator
- lineTo(Object, int, int) - Method in class jspecview.common.PDFWriter
- lineTo(Object, int, int) - Method in class jspecview.java.AwtG2D
- lineTo(Object, int, int) - Method in class jspecview.js2d.JsG2D
- lineTo(Object, int, int) - Method in interface org.jmol.api.GenericGraphics
- lineTo(Object, int, int) - Method in class org.jmol.awt.AwtG2D
- lineTo(Object, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- LINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
- lineWidthMad - Variable in class org.jmol.export.___Exporter
- link - Static variable in class org.jmol.script.T
- LINK - Enum constant in enum class jspecview.common.ScriptToken
- LINK_TYPE_AROM - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_BITS - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_DELO - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_DOUBLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_GENERIC_LINK - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
types set by filter TOPOSE_TYPES in the format of one or more of {v, vw, hb} separated by "+"; default is v+hb
- LINK_TYPE_HBOND - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_OCTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_OTHER - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_PI - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_POLY - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_QUADRUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_QUINTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_SEPTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_SEXTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_SINGLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_TRIPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_VDW - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
-
Opens a web page in an external browser
- linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
-
Follows the reference in an link.
- linkedMesh - Variable in class org.jmol.shape.Mesh
- linkedMesh - Variable in class org.jmol.shape.MeshCollection
- linkSpectra(PanelData.LinkMode) - Method in class jspecview.common.PanelData
- linkTypes - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- list - Variable in class org.jmol.awtjs.swing.Container
- list - Static variable in class org.jmol.script.T
- list(SB) - Method in class org.jmol.shapespecial.Polyhedron
- LIST - Enum constant in enum class jspecview.common.IntegralData.IntMode
- listBS(BS) - Method in class org.jmol.script.ScriptEval
- listCommands - Variable in class org.jmol.viewer.Viewer
- ListDataReader - Class in javajs.util
-
VectorDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with Vector
arrays without any further adaptation. - ListDataReader() - Constructor for class javajs.util.ListDataReader
- listf - Static variable in class org.jmol.script.T
- listParameter(int, int, int) - Method in class org.jmol.script.ScriptParam
- listParameter4(int, int, int, boolean) - Method in class org.jmol.script.ScriptParam
- listSavedStates() - Method in class org.jmol.viewer.StateManager
- ListSelectionModel - Interface in org.jmol.awtjs.swing
- lo - Variable in class org.jmol.util.ColorEncoder
- load - Static variable in class org.jmol.script.T
- load(BufferedReader) - Method in class jspecview.application.DisplaySchemesProcessor
-
Loads the display schemes into memory and stores them in a
Vector
- load(InputStream) - Method in class jspecview.application.DisplaySchemesProcessor
- load(String) - Method in class jspecview.application.DisplaySchemesProcessor
-
Loads the display schemes into memory and stores them in a
Vector
- LOAD - Enum constant in enum class jspecview.common.ScriptToken
- LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JC
- loadAndRun(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- loadatomdatatolerance - Static variable in class org.jmol.script.T
- loadButton - Variable in class org.jmol.console.GenericConsole
- loadContent(String) - Method in interface org.jmol.api.JmolDropEditor
-
Deprecated.
- loadContent(String) - Method in class org.jmol.console.ScriptEditor
- loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- loadData() - Method in class jspecview.dialog.JSVDialog
- loadDefault() - Method in class jspecview.application.DisplaySchemesProcessor
-
Load a default DisplayScheme if xml file not found
- loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
- loadDOMNode(Object) - Method in interface org.jmol.api.JmolAppletInterface
- loadDOMNode(Object) - Method in class org.jmol.util.GenericApplet
- loadFile(String) - Method in interface org.jmol.api.JmolDropEditor
- loadFile(String) - Method in class org.jmol.console.ScriptEditor
- loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
-
When dropped, if the data are 2D, then read directly into JME.
- loadFileAsync(String, String, int, boolean) - Method in class org.jmol.script.ScriptEval
-
Allows asynchronous file loading from the LOAD or SCRIPT command.
- loadFileAsynchronously(Object, JSAppletObject, String, Object) - Method in interface javajs.api.js.J2SObjectInterface
- LOADFILECALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
- loadFileResourceAsync(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- loadFileResourceAsync(String) - Method in class org.jmol.script.ScriptEval
-
load a static file asynchronously
- loadformat - Static variable in class org.jmol.script.T
- loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- loadImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
-
Load an image
- loadImage(GenericPlatform, String, String, byte[], Object) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- loadImageData(Object, String, String, Object) - Method in class org.jmol.viewer.Viewer
-
NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage
- loadImaginary - Variable in class jspecview.common.JSViewer
- LOADIMAGINARY - Enum constant in enum class jspecview.common.ScriptToken
- loadInline(String) - Method in interface jspecview.api.JSVAppletInterface
-
Loads in-line JCAMP-DX data into the existing applet window
- loadInline(String) - Method in class jspecview.app.JSVApp
-
Loads in-line JCAMP-DX data into the existing applet window
- loadInline(String) - Method in class jspecview.appletjs.JSVApplet
- loadInline(String) - Method in class jspecview.application.MainFrame
- loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String) - Method in class org.jmol.api.JmolViewer
- loadInline(String) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(String) - Method in class org.jmol.viewer.Viewer
-
from Applet and external applications only
- loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String[]) - Method in class org.jmol.api.JmolViewer
- loadInline(String[]) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(String[]) - Method in class org.jmol.viewer.Viewer
-
external apps only
- loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
- loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
-
external apps and applet only
- loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String[], String) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(String, char) - Method in class org.jmol.api.JmolViewer
- loadInline(String, char) - Method in class org.jmol.viewer.Viewer
-
external apps only
- loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String, String) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(List<Object>, boolean) - Method in class org.jmol.api.JmolViewer
-
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
- loadInline(List<Object>, boolean) - Method in class org.jmol.viewer.Viewer
-
External applications only; does not preserve state -- intentionally!
- loadInlineAppend(String, boolean) - Method in class org.jmol.api.JmolViewer
- loadInlineAppend(String, boolean) - Method in class org.jmol.viewer.Viewer
-
used by applet and console
- loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
- loadInlineArray(String[], String, boolean) - Method in class org.jmol.util.GenericApplet
- loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
- loadInlineString(String, String, boolean) - Method in class org.jmol.util.GenericApplet
- loadligandformat - Static variable in class org.jmol.script.T
- LoadMeasureThread - Class in org.openscience.jmol.app.janocchio
- LoadMeasureThread() - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
- LoadMeasureThread(NMR_JmolPanel, String) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
- LoadMeasureThreadJSON - Class in org.openscience.jmol.app.janocchio
- LoadMeasureThreadJSON(NMR_JmolPanel, Map<String, Object>) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- loadModelFromFile(String, String, String[], Object, boolean, Map<String, Object>, SB, SB, int, String) - Method in class org.jmol.viewer.Viewer
-
Used by the ScriptEvaluator LOAD command to open one or more files.
- loadScript - Variable in class org.jmol.modelset.Model
- loadShape(int) - Method in class org.jmol.viewer.ShapeManager
- loadState - Variable in class org.jmol.modelset.Model
- LOADSTRUCT - Enum constant in enum class org.jmol.c.CBK
- loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- lobe - Static variable in class org.jmol.script.T
- Location - Class in com.sparshui.common
-
Represents a 2D location with float values.
- Location() - Constructor for class com.sparshui.common.Location
-
Cosntruct a default location.
- Location(float, float) - Constructor for class com.sparshui.common.Location
-
Construct a specific location.
- LocContact - Variable in class jspecview.source.AnIMLReader
- LOCCRC - Static variable in class javajs.api.GenericZipInputStream
- LOCEXT - Static variable in class javajs.api.GenericZipInputStream
- LOCFLG - Static variable in class javajs.api.GenericZipInputStream
- LOCHDR - Static variable in class javajs.api.GenericZipInputStream
- LOCHOW - Static variable in class javajs.api.GenericZipInputStream
- LOCLEN - Static variable in class javajs.api.GenericZipInputStream
- LOCNAM - Static variable in class javajs.api.GenericZipInputStream
- LocName - Variable in class jspecview.source.AnIMLReader
- LOCSIG - Static variable in class javajs.api.GenericZipInputStream
- LOCSIZ - Static variable in class javajs.api.GenericZipInputStream
- LOCTIM - Static variable in class javajs.api.GenericZipInputStream
- LOCVER - Static variable in class javajs.api.GenericZipInputStream
- log - Static variable in class org.jmol.script.T
- log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
-
Method to output a log.
- log(String) - Static method in class jme.JMEUtil.GWT
- log(String) - Method in interface org.jmol.atomdata.AtomDataServer
- log(String) - Method in class org.jmol.minimize.forcefield.ForceField
- log(String) - Method in class org.jmol.viewer.Viewer
- logcommands - Static variable in class org.jmol.script.T
- logCommands - Variable in class org.jmol.viewer.GlobalSettings
- logfile - Static variable in class org.jmol.script.T
- Logger - Class in org.jmol.util
-
Logger mechanism.
- LoggerInterface - Interface in org.jmol.util
-
Interface used for the logging mechanism.
- loggestures - Static variable in class org.jmol.script.T
- logGestures - Variable in class org.jmol.viewer.GlobalSettings
- logging - Variable in class javajs.img.ImageEncoder
- logInfo(String) - Method in class org.jmol.symmetry.CIPChirality
- loglevel - Static variable in class org.jmol.script.T
- logLevel() - Static method in class org.jmol.util.Logger
-
Indicates if the level is logged.
- logMessages - Variable in class org.jmol.script.ScriptCompiler
- lonepair - Static variable in class org.jmol.script.T
- longdate - Variable in class jspecview.export.AMLExporter
- longdate - Variable in class jspecview.export.CMLExporter
- longDate - Variable in class jspecview.source.JDXHeader
- LongDate - Variable in class jspecview.source.AnIMLReader
- longToByteArray(byte[], int, long) - Static method in class com.sparshui.common.utils.Converter
- lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEval
- lookupInterpolatedVoxelValue(T3, boolean) - Method in class org.jmol.jvxl.data.VolumeData
- lookupSpecialAtomID(String) - Method in class org.jmol.modelsetbio.BioResolver
- loop - Static variable in class org.jmol.script.T
- LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
- LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
- LOW - Static variable in class org.jmol.util.ColorEncoder
- lowPrecision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- lp - Static variable in class org.jmol.script.T
- Lst<V> - Class in javajs.util
-
created to remove ambiguities in add and remove
- Lst() - Constructor for class javajs.util.Lst
- lstDipoles - Variable in class org.jmol.shapespecial.Dipole
- lstNCS - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- lumo - Static variable in class org.jmol.script.T
M
- m - Variable in class javajs.util.Matrix
- m - Variable in class org.jmol.util.MeshSlicer
- m00 - Variable in class javajs.util.M34
-
The first element of the first row
- m01 - Variable in class javajs.util.M34
-
The second element of the first row.
- m02 - Variable in class javajs.util.M34
-
third element of the first row.
- m03 - Variable in class javajs.util.M4
-
The fourth element of the first row.
- m10 - Variable in class javajs.util.M34
-
The first element of the second row.
- m11 - Variable in class javajs.util.M34
-
The second element of the second row.
- m12 - Variable in class javajs.util.M34
-
The third element of the second row.
- m13 - Variable in class javajs.util.M4
-
The fourth element of the second row.
- m20 - Variable in class javajs.util.M34
-
The first element of the third row.
- m21 - Variable in class javajs.util.M34
-
The second element of the third row.
- m22 - Variable in class javajs.util.M34
-
The third element of the third row.
- m23 - Variable in class javajs.util.M4
-
The fourth element of the third row.
- M3 - Class in javajs.util
-
A single precision floating point 3 by 3 matrix.
- M3() - Constructor for class javajs.util.M3
-
Constructs and initializes a Matrix3f to all zeros.
- m30 - Variable in class javajs.util.M4
-
The first element of the fourth row.
- m31 - Variable in class javajs.util.M4
-
The second element of the fourth row.
- m32 - Variable in class javajs.util.M4
-
The third element of the fourth row.
- m33 - Variable in class javajs.util.M4
-
The fourth element of the fourth row.
- M34 - Class in javajs.util
-
A base class for both M3 and M4 to conserve code size.
- M34() - Constructor for class javajs.util.M34
- M4 - Class in javajs.util
-
A single precision floating point 4 by 4 matrix.
- M4() - Constructor for class javajs.util.M4
-
all zeros
- MAC_COMMAND - Static variable in class org.jmol.awtjs.Event
- MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
- macro - Static variable in class org.jmol.script.T
- macrodirectory - Static variable in class org.jmol.script.T
- mad - Variable in class org.jmol.modelset.Bond
- mad - Variable in class org.jmol.modelset.Measurement
- mad - Variable in class org.jmol.modelset.MeasurementData
- mad - Variable in class org.jmol.render.ShapeRenderer
- mad - Variable in class org.jmol.shape.AtomShape
- mad - Variable in class org.jmol.shapespecial.Dipole
- MAD_GLOBAL - Static variable in class org.jmol.modelset.Atom
- madAtom - Variable in class org.jmol.modelset.Atom
- madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JC
- mads - Variable in class org.jmol.renderbio.BackboneRenderer
- mads - Variable in class org.jmol.renderbio.CartoonRenderer
- mads - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- mads - Variable in class org.jmol.renderbio.RibbonsRenderer
- mads - Variable in class org.jmol.renderbio.RocketsRenderer
- mads - Variable in class org.jmol.renderbio.StrandsRenderer
- mads - Variable in class org.jmol.renderbio.TraceRenderer
- mads - Variable in class org.jmol.shape.AtomShape
- MAGENTA - Static variable in class org.jmol.util.C
- magneticshielding - Static variable in class org.jmol.script.T
- MagresReader - Class in org.jmol.adapter.readers.xtal
- MagresReader() - Constructor for class org.jmol.adapter.readers.xtal.MagresReader
- main(String[]) - Static method in class jme.JME
- main(String[]) - Static method in class jspecview.application.JSpecView
- main(String[]) - Static method in class jspecview.application.MainFrame
- main(String[]) - Static method in class jspecview.source.JDXDecompressorTest
- main(String[]) - Static method in class org.jmol.adapter.writers.CDXMLWriter
- main(String[]) - Static method in class org.jmol.quantum.NMRNoeMatrix
- main(String[]) - Static method in class org.jmol.symmetry.SpaceGroupFinder
- main(String[]) - Static method in class org.molecularplayground.MPJmolApp
- main(String[]) - Static method in class org.openscience.jmol.app.janocchio.Nmr
- main(String[]) - Static method in class org.openscience.jmol.app.Jmol
- main(String[]) - Static method in class org.openscience.jmol.app.JmolData
- main(String[]) - Static method in class org.openscience.jmol.app.jmolpanel.JmolJME
- main(String[]) - Static method in class org.openscience.jvxl.Jvxl
- main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- MAIN - Static variable in class org.jmol.thread.JmolThread
- mainFrame - Variable in class jspecview.application.ApplicationMenu
- mainFrame - Variable in class jspecview.application.AppToolBar
- MainFrame - Class in jspecview.application
-
The Main Class or Entry point of the JSpecView Application.
- MainFrame(JSpecView, Component, JSVInterface) - Constructor for class jspecview.application.MainFrame
-
Constructor
- mainPanel - Variable in class jspecview.common.JSViewer
- MainPopupResourceBundle - Class in org.jmol.popup
- MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
- mainSplitPane - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- majorVersion - Static variable in class jspecview.common.JSVersion
- majorVersion - Static variable in class org.jmol.viewer.JC
- makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
- makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
- makeConnections2(float, float, int, int, BS, BS, BS, boolean, boolean, float, SB) - Method in class org.jmol.modelset.ModelSet
- manager - Variable in class jspecview.dialog.JSVDialog
- manager - Variable in class jspecview.java.AwtDialog
- manager - Variable in class jspecview.js2d.JsDialog
- manifest - Static variable in class org.jmol.script.T
- map(Object, String, String, Map<String, Object>) - Static method in class org.jmol.console.GenericConsole
- mapAddKey(String) - Method in class org.jmol.util.JSONWriter
- mapAddKeyValue(String, Object, String) - Method in class org.jmol.util.JSONWriter
- mapAddKeyValueRaw(String, Object, String) - Method in class org.jmol.util.JSONWriter
-
Add a key:value pair where value is already quoted
- mapAddMapAllExcept(String, Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
- mapClose() - Method in class org.jmol.util.JSONWriter
- mapGet(String) - Method in class org.jmol.script.SV
- mapLattice - Variable in class org.jmol.jvxl.data.JvxlData
- mapLattice - Variable in class org.jmol.jvxl.readers.Parameters
- mapOpen() - Method in class org.jmol.util.JSONWriter
- mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
- mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
- mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
- mapPolyhedra(int, int, boolean, M4) - Method in class org.jmol.scriptext.SmilesExt
- mapproperty - Static variable in class org.jmol.script.T
- mapPut(String, SV) - Method in class org.jmol.script.SV
- mapString - Variable in class jme.AtomDisplayLabel
- mapUnique - Variable in class org.jmol.smiles.SmilesSearch
- marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MarchingCubes - Class in org.jmol.jvxl.calc
- MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
- MarchingCubes(VertexDataServer, VolumeData, Parameters, BS) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
- marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MarchingSquares - Class in org.jmol.jvxl.calc
- MarchingSquares(VertexDataServer, VolumeData, P4, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
- mark() - Method in class jme.JMEmol
- mark(int) - Method in class com.jcraft.jzlib.InflaterInputStream
- mark(int) - Method in class jspecview.common.JSVZipFileSequentialReader
- mark(long) - Method in class javajs.util.ArrayDataReader
- mark(long) - Method in class javajs.util.ListDataReader
- MARK - Enum constant in enum class jspecview.common.IntegralData.IntMode
- markLines(String, char) - Static method in class org.jmol.util.Parser
- markSupported() - Method in class com.jcraft.jzlib.InflaterInputStream
- markUsed - Variable in class jme.JME
- MAROON - Static variable in class org.jmol.util.C
- mass - Static variable in class org.jmol.script.T
- mat4 - Variable in class org.jmol.modelset.Model
-
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
- mat4 - Variable in class org.jmol.util.MeshSurface
- match(String) - Method in class org.jmol.symmetry.CIPData
-
Return a bit set corresponding to a SMARTS
- match(String) - Method in class org.jmol.symmetry.CIPDataSmiles
- matcher(String) - Method in class org.jmol.util.PatternMatcher.JSPattern
- matchesFilePath(String) - Method in class jspecview.source.JDXSource
- matchesPeakTypeModel(String, String) - Method in class jspecview.common.Spectrum
-
Find a matching spectrum by type (IR, 1HNMR,...) and model name
- mathExpressionCommand - Static variable in class org.jmol.script.T
- MathExt - Class in org.jmol.scriptext
- MathExt() - Constructor for class org.jmol.scriptext.MathExt
- mathfunc - Static variable in class org.jmol.script.T
- mathop - Static variable in class org.jmol.script.T
- mathproperty - Static variable in class org.jmol.script.T
- matrix - Static variable in class org.jmol.script.T
- Matrix - Class in javajs.util
-
streamlined and refined for Jmol by Bob Hanson from http://math.nist.gov/javanumerics/jama/ Jama = Java Matrix class.
- Matrix(double[][], int, int) - Constructor for class javajs.util.Matrix
-
Construct a matrix quickly without checking arguments.
- matrix3f - Static variable in class org.jmol.script.T
- matrix4f - Static variable in class org.jmol.script.T
- matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
- matrixCtoFNoOffset - Variable in class org.jmol.util.SimpleUnitCell
- matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
- matrixFtoCNoOffset - Variable in class org.jmol.util.SimpleUnitCell
- matrixRotate - Variable in class org.jmol.viewer.TransformManager
- matrixStereo - Variable in class org.jmol.viewer.TransformManager
- matrixTemp - Variable in class org.jmol.viewer.TransformManager
- matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
- matrixTest - Variable in class org.jmol.viewer.TransformManager
- matrixToScript(Object) - Static method in class org.jmol.util.Escape
- matrixTransform - Variable in class org.jmol.viewer.TransformManager
- matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
- matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- max - Static variable in class org.jmol.script.T
- MAX_ALPHA_SIZE - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
- MAX_CODE_LEN - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
- MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
- MAX_SELECTORS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- MAX_TYPE_SUPPORTED - Static variable in class org.jmol.quantum.QS
- MAX_WBITS - Static variable in class com.jcraft.jzlib.JZlib
- MAXABS - Static variable in class jspecview.common.Spectrum
- maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
- maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
- maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
- MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JC
- MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
- maxSerial - Variable in class org.jmol.adapter.readers.cif.CifReader
- maxset - Static variable in class org.jmol.script.T
- maxSphereCache - Static variable in class org.jmol.util.Shader
- maxXOnScale - Variable in class jspecview.common.ScaleData
-
the maximim X value on the scale, usually maxX
- maxYOnScale - Variable in class jspecview.common.ScaleData
- maybeGetBaseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- mayScript - Variable in class org.jmol.util.GenericApplet
- mc - Variable in class org.jmol.modelset.ModelSet
-
model count
- MdCrdReader - Class in org.jmol.adapter.readers.more
-
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
- MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
- MdTopReader - Class in org.jmol.adapter.readers.more
-
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
- MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
- measure - Static variable in class org.jmol.script.T
- Measure - Class in javajs.util
- Measure - Class in org.openscience.jmol.app.janocchio
- Measure() - Constructor for class javajs.util.Measure
- MEASURE - Enum constant in enum class org.jmol.c.CBK
- MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- measureallmodels - Static variable in class org.jmol.script.T
- MeasureCouple - Class in org.openscience.jmol.app.janocchio
- MeasureCouple(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureCouple
- MeasureDist - Class in org.openscience.jmol.app.janocchio
-
Calculates the difference between calculated and experimental values for coloring table
- MeasureDist(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureDist
- measureDistanceUnits - Variable in class org.jmol.viewer.GlobalSettings
- Measurement - Class in jspecview.common
-
The
Measurement
class stores an annotation that is a measurement - Measurement - Class in org.jmol.modelset
- Measurement() - Constructor for class jspecview.common.Measurement
- Measurement() - Constructor for class org.jmol.modelset.Measurement
- measurementCount - Variable in class org.jmol.shape.Measures
- MeasurementData - Class in jspecview.common
- MeasurementData - Class in org.jmol.modelset
- MeasurementData() - Constructor for class org.jmol.modelset.MeasurementData
- measurementlabels - Static variable in class org.jmol.script.T
- measurementnumbers - Static variable in class org.jmol.script.T
- MeasurementPending - Class in org.jmol.modelset
- MeasurementPending() - Constructor for class org.jmol.modelset.MeasurementPending
- measurements - Static variable in class org.jmol.script.T
- measurements - Variable in class org.jmol.shape.Measures
- Measurements - Enum constant in enum class jspecview.common.Annotation.AType
- measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- MeasurementsDialog - Class in jspecview.dialog
-
Dialog for managing the measurement list for a Spectrum within a GraphSet
- MeasurementsDialog() - Constructor for class jspecview.dialog.MeasurementsDialog
- measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
- MeasurementTable(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
Constructor
- measurementunits - Static variable in class org.jmol.script.T
- MeasureNoe - Class in org.openscience.jmol.app.janocchio
- MeasureNoe(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureNoe
- Measures - Class in org.jmol.shape
- Measures() - Constructor for class org.jmol.shape.Measures
- MeasuresRenderer - Class in org.jmol.render
- MeasuresRenderer() - Constructor for class org.jmol.render.MeasuresRenderer
- menu - Static variable in class org.jmol.script.T
- menuAddButtonGroup(SC) - Method in class org.jmol.awt.AwtPopupHelper
- menuAddButtonGroup(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuAddButtonGroup(SC) - Method in interface org.jmol.popup.PopupHelper
- menuAddSeparator(SC) - Method in class org.jmol.popup.GenericPopup
- menuAddSubMenu(SC, SC) - Method in class org.jmol.popup.GenericPopup
- menuCheckBoxCallback(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- menuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
- menuClearListeners(SC) - Method in class org.jmol.awt.AwtPopupHelper
- menuClearListeners(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuClearListeners(SC) - Method in interface org.jmol.popup.PopupHelper
- menuClickCallback(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
- menuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
- menuCreateCheckboxItem(SC, String, String, String, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
- menuCreateItem(SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
- menuCreatePopup(String, Object) - Method in class org.jmol.awt.AwtPopupHelper
- menuCreatePopup(String, Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuCreatePopup(String, Object) - Method in interface org.jmol.popup.PopupHelper
- menuEnable(SC, boolean) - Method in class org.jmol.popup.GenericPopup
- menuEnabled() - Method in class org.jmol.viewer.Viewer
- menuFocusCallback(String, String, boolean) - Method in class jspecview.java.AwtPopup
- menuFocusCallback(String, String, boolean) - Method in class jspecview.js2d.JsPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- menuGetId(SC) - Method in class org.jmol.popup.GenericPopup
- menuGetListPosition(SC) - Method in class org.jmol.popup.GenericPopup
- menuHidePopup(SC) - Method in class org.jmol.awt.AwtModelKitPopup
- menuHidePopup(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- menuHidePopup(SC) - Method in class org.jmol.modelkit.ModelKitPopup
- menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awt.AwtPopupHelper
- menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuInsertSubMenu(SC, SC, int) - Method in interface org.jmol.popup.PopupHelper
- menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- menuMap - Variable in class org.jmol.console.GenericConsole
- menuName - Variable in class org.jmol.popup.GenericPopup
- menuNewSubMenu(String, String) - Method in class org.jmol.popup.GenericPopup
- MENUON - Enum constant in enum class jspecview.common.ScriptToken
- menuRemoveAll(SC, int) - Method in class org.jmol.popup.GenericPopup
- menuSetAutoscrolls(SC) - Method in class org.jmol.popup.GenericPopup
- menuSetLabel(SC, String) - Method in class org.jmol.popup.GenericPopup
- menuShowPopup(SC, int, int) - Method in class jspecview.java.AwtPopup
- menuShowPopup(SC, int, int) - Method in class jspecview.js2d.JsPopup
-
could be frank menu or regular context menu
- menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtJmolPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtModelKitPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSJmolPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.popup.GenericPopup
- menuStructure - Variable in class org.jmol.api.JmolViewer
- menuText - Variable in class org.jmol.popup.JmolGenericPopup
- mep - Static variable in class org.jmol.script.T
- mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
- MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
- MepCalculation - Class in org.jmol.quantum
- MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
- merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- merge(MeshCollection) - Method in class org.jmol.shape.MeshCollection
-
called by ParallelProcessor at completion
- merge(MeshCollection) - Method in class org.jmol.shapesurface.LcaoCartoon
- merge(MeshCollection) - Method in class org.jmol.shapesurface.MolecularOrbital
- mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
- mergeBufferPixel(int, int, int) - Static method in class org.jmol.g3d.Graphics3D
- mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelSet
-
initial transfer of model data from old to new model set.
- mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
- mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
- merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- mesh - Variable in class org.jmol.render.MeshRenderer
- mesh - Static variable in class org.jmol.script.T
- Mesh - Class in org.jmol.shape
- Mesh() - Constructor for class org.jmol.shape.Mesh
-
always use Mesh().mesh1(thisID, colix, index)
- mesh1(Viewer, String, short, int) - Method in class org.jmol.shape.Mesh
- MeshCapper - Class in org.jmol.util
-
A class to properly cap a convoluted, closed slice of an isosurface inspired by: Computational Geometry: Algorithms and Applications Mark de Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
- MeshCapper() - Constructor for class org.jmol.util.MeshCapper
- MeshCapper.MeshCapperSorter - Class in org.jmol.util
- MeshCapperSorter() - Constructor for class org.jmol.util.MeshCapper.MeshCapperSorter
- meshColix - Variable in class org.jmol.shape.Mesh
- MeshCollection - Class in org.jmol.shape
- MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
- meshColor - Variable in class org.jmol.jvxl.data.JvxlData
- meshCount - Variable in class org.jmol.shape.MeshCollection
- meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MeshData - Class in org.jmol.jvxl.data
- MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
- MeshData.SortSet - Class in org.jmol.jvxl.data
- meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MeshDataServer - Interface in org.jmol.jvxl.api
- meshes - Variable in class org.jmol.shape.MeshCollection
- meshes - Variable in class org.jmol.shapebio.BioShape
- meshReady - Variable in class org.jmol.shapebio.BioShape
- MeshRenderer - Class in org.jmol.render
-
an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
- MeshRenderer() - Constructor for class org.jmol.render.MeshRenderer
- meshRibbon - Static variable in class org.jmol.script.T
- MeshRibbon - Class in org.jmol.shapebio
- MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
- MeshRibbonRenderer - Class in org.jmol.renderbio
- MeshRibbonRenderer() - Constructor for class org.jmol.renderbio.MeshRibbonRenderer
- meshscale - Static variable in class org.jmol.script.T
- meshSlabValue - Variable in class org.jmol.render.MeshRenderer
- MeshSlicer - Class in org.jmol.util
- MeshSlicer() - Constructor for class org.jmol.util.MeshSlicer
- MeshSurface - Class in org.jmol.util
- MeshSurface() - Constructor for class org.jmol.util.MeshSurface
- meshType - Variable in class org.jmol.util.MeshSurface
- message - Static variable in class org.jmol.script.T
- MESSAGE - Enum constant in enum class org.jmol.c.CBK
- MessagePackReader - Class in javajs.util
-
A simple MessagePack reader.
- MessagePackReader() - Constructor for class javajs.util.MessagePackReader
- MessagePackReader(GenericBinaryDocumentReader, boolean) - Constructor for class javajs.util.MessagePackReader
- messageQueue - Variable in class org.jmol.viewer.StatusManager
- messagestylechime - Static variable in class org.jmol.script.T
- MessageType() - Constructor for class com.sparshui.common.ClientProtocol.MessageType
- META_MASK - Static variable in class org.jmol.awtjs.Event
- mf - Variable in class org.jmol.util.JmolMolecule
- mi - Variable in class org.jmol.util.Point3fi
-
model index -- may be to a trajectory
- middle - Static variable in class org.jmol.script.T
- MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
- min - Static variable in class org.jmol.script.T
- MIN - Enum constant in enum class jspecview.common.IntegralData.IntMode
- MIN_ADDH - Static variable in class org.jmol.viewer.Viewer
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- MIN_GROUP_SELECT - Static variable in class org.jmol.viewer.Viewer
- MIN_HAVE_FIXED - Static variable in class org.jmol.viewer.Viewer
- MIN_MODELKIT - Static variable in class org.jmol.viewer.Viewer
- MIN_QUICK - Static variable in class org.jmol.viewer.Viewer
- MIN_SELECT_ONLY - Static variable in class org.jmol.viewer.Viewer
- MIN_SELECTED - Static variable in class org.jmol.viewer.Viewer
- MIN_SILENT - Static variable in class org.jmol.viewer.Viewer
- MIN_XX - Static variable in class org.jmol.viewer.Viewer
- MinAngle - Class in org.jmol.minimize
- minAngles - Variable in class org.jmol.minimize.Minimizer
- MinAtom - Class in org.jmol.minimize
- minAtoms - Variable in class org.jmol.minimize.Minimizer
- MinBond - Class in org.jmol.minimize
- minbonddistance - Static variable in class org.jmol.script.T
- minBonds - Variable in class org.jmol.minimize.Minimizer
- minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
- minGrid - Variable in class org.jmol.jvxl.data.VolumeData
- minHeight - Variable in class org.jmol.awtjs.swing.Component
- MINIMIZATION - Enum constant in enum class org.jmol.c.CBK
- minimizationcriterion - Static variable in class org.jmol.script.T
- minimizationmaxatoms - Static variable in class org.jmol.script.T
- minimizationOn() - Method in class org.jmol.minimize.Minimizer
- minimizationrefresh - Static variable in class org.jmol.script.T
- minimizationreportsteps - Static variable in class org.jmol.script.T
- minimizationsilent - Static variable in class org.jmol.script.T
- minimizationsteps - Static variable in class org.jmol.script.T
- MinimizationThread - Class in org.jmol.minimize
- MinimizationThread() - Constructor for class org.jmol.minimize.MinimizationThread
- minimize - Static variable in class org.jmol.script.T
- minimize(int, double, BS, BS, BS, int, String) - Method in class org.jmol.minimize.Minimizer
- minimize(JmolScriptEvaluator, int, float, BS, BS, BS, float, int) - Method in class org.jmol.viewer.Viewer
-
From the MINIMIZE command and other sources.
- MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JC
- minimizeEnd(BS, boolean) - Method in class org.jmol.modelkit.ModelKit
- Minimizer - Class in org.jmol.minimize
- Minimizer() - Constructor for class org.jmol.minimize.Minimizer
- MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
- minList - Variable in class org.jmol.minimize.MMConstraint
- minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
- minmaxmask - Static variable in class org.jmol.script.T
- MinObject - Class in org.jmol.minimize
- MinObject() - Constructor for class org.jmol.minimize.MinObject
- minpixelselradius - Static variable in class org.jmol.script.T
- MinPosition - Class in org.jmol.minimize
-
not implemented -- would be a force toward a given position in space
- minScreenDimension - Variable in class org.jmol.export._PovrayExporter
- minScreenDimension - Variable in class org.jmol.export._TachyonExporter
- minset - Static variable in class org.jmol.script.T
- MinTorsion - Class in org.jmol.minimize
- minTorsions - Variable in class org.jmol.minimize.Minimizer
- minus - Static variable in class org.jmol.script.T
- minusMinus - Static variable in class org.jmol.script.T
- minWidth - Variable in class org.jmol.awtjs.swing.Component
- minXOnScale - Variable in class jspecview.common.ScaleData
-
the minimum X value on the scale, usually minX
- minYOnScale - Variable in class jspecview.common.ScaleData
- misc - Static variable in class org.jmol.script.T
- mlp - Static variable in class org.jmol.script.T
- MlpCalculation - Class in org.jmol.quantum
- MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
- mm - Variable in class org.jmol.viewer.Viewer
- MMCifReader - Class in org.jmol.adapter.readers.cif
-
mmCIF files are recognized prior to class creation.
- MMCifReader() - Constructor for class org.jmol.adapter.readers.cif.MMCifReader
- MMCifValidationParser - Class in org.jmol.adapter.readers.cif
- MMCifValidationParser() - Constructor for class org.jmol.adapter.readers.cif.MMCifValidationParser
- MMConstraint - Class in org.jmol.minimize
- MMConstraint(int[], double) - Constructor for class org.jmol.minimize.MMConstraint
- MMTFReader - Class in org.jmol.adapter.readers.cif
-
JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md Note added 2024.01.19 Jose Duarte 2:03 PM (email) to MMTF-Users From July 2024 the PDB file archive will not be offered in the compressed MMTF format anymore.
- MMTFReader() - Constructor for class org.jmol.adapter.readers.cif.MMTFReader
- mo - Static variable in class org.jmol.script.T
- MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
- MOCalculation - Class in org.jmol.quantum
- MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
- moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- moData - Variable in class org.jmol.jvxl.readers.Parameters
- modAverage - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modAxes - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modDim - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modDim - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- modDim - Variable in class org.jmol.util.Vibration
-
modDim will be > 0 for modulation
- mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
- mode - Variable in class org.jmol.render.LabelsRenderer
- mode - Static variable in class org.jmol.script.T
- mode - Variable in class org.jmol.viewer.TransformManager
- MODE_CALC_2JHH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_3JCH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_3JHH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_ALL - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_INVALID - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_J - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_JHH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_NOE - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_MODEL - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
- MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
- MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- MODE_MASK - Static variable in class org.jmol.viewer.binding.Binding
- MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
- MODE_P_ALLOW_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
- MODE_P_CONVERT_TO_CARTESIAN - Static variable in class org.jmol.script.ScriptParam
- MODE_P_IMPLICIT_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
- MODE_P_INT_ONLY - Static variable in class org.jmol.script.ScriptParam
- MODE_P_NULL_ON_ERROR - Static variable in class org.jmol.script.ScriptParam
- MODE_P3 - Static variable in class org.jmol.script.ScriptParam
- MODE_P34 - Static variable in class org.jmol.script.ScriptParam
- MODE_P4 - Static variable in class org.jmol.script.ScriptParam
- MODE_PERSPECTIVE_PYMOL - Static variable in class org.jmol.viewer.TransformManager
- MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
- model - Variable in class jspecview.export.AMLExporter
- model - Variable in class jspecview.export.CMLExporter
- model - Variable in class org.jmol.modelset.Chain
- model - Variable in class org.jmol.modelsetbio.BioPolymer
- model - Static variable in class org.jmol.script.T
- model(int, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- Model - Class in org.jmol.modelset
- Model() - Constructor for class org.jmol.modelset.Model
- modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
- modelbased - Static variable in class org.jmol.script.T
- modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
- modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelSet
- modelFileNumbers - Variable in class org.jmol.modelset.ModelSet
- modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
- modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
- modelindex - Static variable in class org.jmol.script.T
- modelIndex - Variable in class org.jmol.atomdata.AtomData
- modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
- modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- modelIndex - Variable in class org.jmol.modelset.Model
- modelIndex - Variable in class org.jmol.modelset.Text
- modelIndex - Variable in class org.jmol.popup.JmolPopup
- modelIndex - Variable in class org.jmol.shape.Mesh
- modelIndex - Variable in class org.jmol.shape.MeshCollection
- modelIndex - Variable in class org.jmol.shapebio.BioShape
- modelIndex - Variable in class org.jmol.shapespecial.Polyhedron
- modelIndex - Variable in class org.jmol.util.JmolMolecule
- modelIndex - Variable in class org.jmol.util.Tensor
- modelIndex(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- modelInfo - Variable in class org.jmol.popup.JmolPopup
- modelInvRotation - Variable in class org.jmol.jvxl.readers.Parameters
- modelIsRawPDB() - Method in class org.jmol.modelset.Atom
- modelIsRawPDB() - Method in class org.jmol.smiles.SmilesAtom
- modelIsRawPDB() - Method in interface org.jmol.util.Node
- ModelKit - Class in org.jmol.modelkit
-
An abstract popup class that is instantiated for a given platform and context as one of:
- ModelKit() - Constructor for class org.jmol.modelkit.ModelKit
- MODELKIT - Enum constant in enum class org.jmol.c.CBK
- MODELKIT_ADDCONSTRAINT - Static variable in class org.jmol.viewer.JC
- MODELKIT_ADDHYDROGEN - Static variable in class org.jmol.viewer.JC
- MODELKIT_ADDHYDROGENS - Static variable in class org.jmol.viewer.JC
- MODELKIT_ALLOPERATORS - Static variable in class org.jmol.viewer.JC
- MODELKIT_APPLYFULL - Static variable in class org.jmol.viewer.JC
- MODELKIT_APPLYLOCAL - Static variable in class org.jmol.viewer.JC
- MODELKIT_ASSIGN_BOND - Static variable in class org.jmol.viewer.JC
- MODELKIT_ATOMPICKINGMODE - Static variable in class org.jmol.viewer.JC
- MODELKIT_ATOMTYPE - Static variable in class org.jmol.viewer.JC
- MODELKIT_AUTOBOND - Static variable in class org.jmol.viewer.JC
- MODELKIT_BONDINDEX - Static variable in class org.jmol.viewer.JC
- MODELKIT_BONDPICKINGMODE - Static variable in class org.jmol.viewer.JC
- MODELKIT_BONDTYPE - Static variable in class org.jmol.viewer.JC
- MODELKIT_BRANCH_ATOM_DRAGGED - Static variable in class org.jmol.viewer.JC
- MODELKIT_BRANCH_ATOM_PICKED - Static variable in class org.jmol.viewer.JC
- MODELKIT_CENTER - Static variable in class org.jmol.viewer.JC
- MODELKIT_CLICKTOSETELEMENT - Static variable in class org.jmol.viewer.JC
- MODELKIT_CONSTRAINT - Static variable in class org.jmol.viewer.JC
- MODELKIT_DATA - Static variable in class org.jmol.viewer.JC
- MODELKIT_DELETE_BOND - Static variable in class org.jmol.viewer.JC
- MODELKIT_DISTANCE - Static variable in class org.jmol.viewer.JC
- MODELKIT_DRAGATOM - Static variable in class org.jmol.viewer.JC
- MODELKIT_ELEMENT_KEY - Static variable in class org.jmol.viewer.JC
- MODELKIT_ELEMENT_KEY_ID - Static variable in class org.jmol.viewer.JC
- MODELKIT_ELEMENT_KEYS - Static variable in class org.jmol.viewer.JC
- MODELKIT_EXISTS - Static variable in class org.jmol.viewer.JC
- MODELKIT_FRAME_RESIZED - Static variable in class org.jmol.viewer.JC
- MODELKIT_HIDDEN - Static variable in class org.jmol.viewer.JC
- MODELKIT_HIDEMENU - Static variable in class org.jmol.viewer.JC
- MODELKIT_HIGHLIGHT - Static variable in class org.jmol.viewer.JC
- MODELKIT_HOVERLABEL - Static variable in class org.jmol.viewer.JC
- MODELKIT_INITIALIZE_MODEL - Static variable in class org.jmol.viewer.JC
- MODELKIT_INVARIANT - Static variable in class org.jmol.viewer.JC
- MODELKIT_ISMOLECULAR - Static variable in class org.jmol.viewer.JC
- MODELKIT_KEY - Static variable in class org.jmol.viewer.JC
- MODELKIT_MINIMIZING - Static variable in class org.jmol.viewer.JC
- MODELKIT_MODE - Static variable in class org.jmol.viewer.JC
- MODELKIT_NEW_MODEL_ATOM_KEYS - Static variable in class org.jmol.viewer.JC
- MODELKIT_OFFSET - Static variable in class org.jmol.viewer.JC
- MODELKIT_REMOVEALLCONSTRAINTS - Static variable in class org.jmol.viewer.JC
- MODELKIT_REMOVECONSTRAINT - Static variable in class org.jmol.viewer.JC
- MODELKIT_RESET - Static variable in class org.jmol.viewer.JC
- MODELKIT_RETAINLOCAL - Static variable in class org.jmol.viewer.JC
- MODELKIT_ROTATE_BOND_ATOM_INDEX - Static variable in class org.jmol.viewer.JC
- MODELKIT_ROTATEBONDINDEX - Static variable in class org.jmol.viewer.JC
- MODELKIT_SCREENXY - Static variable in class org.jmol.viewer.JC
- MODELKIT_SET_ELEMENT_KEYS - Static variable in class org.jmol.viewer.JC
- MODELKIT_SHOWSYMOPINFO - Static variable in class org.jmol.viewer.JC
- MODELKIT_SYMMETRY - Static variable in class org.jmol.viewer.JC
- MODELKIT_SYMOP - Static variable in class org.jmol.viewer.JC
- MODELKIT_UDPATE_KEY_STATE - Static variable in class org.jmol.viewer.JC
- MODELKIT_UNITCELL - Static variable in class org.jmol.viewer.JC
- MODELKIT_UPDATE_ATOM_KEYS - Static variable in class org.jmol.viewer.JC
- MODELKIT_UPDATE_MODEL_KEYS - Static variable in class org.jmol.viewer.JC
- MODELKIT_VIBRATION - Static variable in class org.jmol.viewer.JC
- MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JC
- MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JC
- modelkitmode - Static variable in class org.jmol.script.T
- ModelKitPopup - Class in org.jmol.modelkit
-
An abstract popup class that is instantiated for a given platform and context as one of:
- ModelKitPopup() - Constructor for class org.jmol.modelkit.ModelKitPopup
- ModelKitPopupResourceBundle - Class in org.jmol.modelkit
- ModelKitPopupResourceBundle(String, Properties) - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
- ModelLoader - Class in org.jmol.modelset
- ModelLoader(Viewer, String, SB, Object, ModelSet, BS) - Constructor for class org.jmol.modelset.ModelLoader
- modelMap - Variable in class org.jmol.adapter.readers.cif.CifReader
- modelName - Variable in class org.jmol.atomdata.AtomData
- modelNames - Variable in class org.jmol.modelset.ModelSet
- modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- modelNumberParameter(int) - Method in class org.jmol.script.ScriptParam
- modelNumbers - Variable in class org.jmol.modelset.ModelSet
- modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelSet
- modelRadius - Variable in class org.jmol.viewer.TransformManager
- modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
- ModelSet - Class in org.jmol.modelset
- ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
- modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
- modelSetName - Variable in class org.jmol.modelset.ModelSet
- modelSetProperties - Variable in class org.jmol.modelset.ModelSet
- modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
- modelStartEnd - Variable in class org.jmol.adapter.smarter.Structure
- modelType - Variable in class jspecview.source.AnIMLReader
- modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
- modeMultipleBond - Variable in class org.jmol.viewer.GlobalSettings
- modifiersWhenPressed10 - Variable in class jspecview.app.GenericMouse
- modify - Static variable in class org.jmol.script.T
- MODIFY_ASSIGN_ATOM - Static variable in class org.jmol.viewer.Viewer
- MODIFY_ASSIGN_BOND - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_ATOM - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_ATOMS - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_BONDS - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_MODEL - Static variable in class org.jmol.viewer.Viewer
- MODIFY_SET_COORD - Static variable in class org.jmol.viewer.Viewer
- modifyorcreate - Static variable in class org.jmol.script.T
- modo - Static variable in class org.jmol.script.T
- modScale - Variable in class org.jmol.util.Vibration
- modt1 - Static variable in class org.jmol.script.T
- modt2 - Static variable in class org.jmol.script.T
- modt3 - Static variable in class org.jmol.script.T
- modulateoccupancy - Static variable in class org.jmol.script.T
- modulation - Static variable in class org.jmol.script.T
- Modulation - Class in org.jmol.util
-
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
- Modulation(char, char, double[], String, double[]) - Constructor for class org.jmol.util.Modulation
-
Each atomic modulation involves a fractional coordinate wave vector q, a Fourier power n, a modulation axis (x, y, or, z), and specified parameters that depend upon the type of function.
- modulationscale - Static variable in class org.jmol.script.T
- modulationScale - Variable in class org.jmol.viewer.GlobalSettings
- ModulationSet - Class in org.jmol.util
-
A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
- ModulationSet() - Constructor for class org.jmol.util.ModulationSet
- MODULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- modx - Static variable in class org.jmol.script.T
- modxyz - Static variable in class org.jmol.script.T
- mody - Static variable in class org.jmol.script.T
- modz - Static variable in class org.jmol.script.T
- MOEnergySorter() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
- MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
- mol - Variable in class jme.JME
- Mol2Reader - Class in org.jmol.adapter.readers.more
-
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
- Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
- Mol3DReader - Class in org.jmol.adapter.readers.molxyz
-
3D only
- Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
- MoldenReader - Class in org.jmol.adapter.readers.quantum
-
A molecular structure and orbital reader for MolDen files.
- MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
- molecular - Static variable in class org.jmol.script.T
- MolecularOrbital - Class in org.jmol.shapesurface
- MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
- MolecularOrbitalRenderer - Class in org.jmol.rendersurface
- MolecularOrbitalRenderer() - Constructor for class org.jmol.rendersurface.MolecularOrbitalRenderer
- molecule - Static variable in class org.jmol.script.T
- MOLECULE - Enum constant in enum class org.jmol.c.PAL
- MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND_STEREO - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_FORMULA - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- moleculeCount - Variable in class org.jmol.modelset.BondCollection
- moleculeCount - Variable in class org.jmol.modelset.Model
- moleculeID - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- moleculeIndex - Variable in class org.jmol.util.JmolMolecule
- molecules - Variable in class org.jmol.modelset.BondCollection
- moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
- molFile() - Method in class jme.JME
- molform - Variable in class jspecview.export.AMLExporter
- molform - Variable in class jspecview.export.CMLExporter
- molForm - Variable in class jspecview.source.AnIMLReader
- MolReader - Class in org.jmol.adapter.readers.molxyz
-
A reader for MDLI mol and sdf files.
- MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
- mols - Variable in class jme.JME
- MOLWriter - Class in org.jmol.adapter.writers
- MOLWriter() - Constructor for class org.jmol.adapter.writers.MOLWriter
- monitorenergy - Static variable in class org.jmol.script.T
- monomer - Static variable in class org.jmol.script.T
- Monomer - Class in org.jmol.modelsetbio
-
A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
- Monomer() - Constructor for class org.jmol.modelsetbio.Monomer
- MONOMER - Enum constant in enum class org.jmol.c.PAL
- monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
- monomerCount - Variable in class org.jmol.renderbio.BackboneRenderer
- monomerCount - Variable in class org.jmol.renderbio.CartoonRenderer
- monomerCount - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- monomerCount - Variable in class org.jmol.renderbio.RibbonsRenderer
- monomerCount - Variable in class org.jmol.renderbio.RocketsRenderer
- monomerCount - Variable in class org.jmol.renderbio.StrandsRenderer
- monomerCount - Variable in class org.jmol.renderbio.TraceRenderer
- monomerCount - Variable in class org.jmol.shape.AtomShape
- monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
- monomers - Variable in class org.jmol.modelsetbio.BioPolymer
- monomers - Variable in class org.jmol.renderbio.BackboneRenderer
- monomers - Variable in class org.jmol.renderbio.CartoonRenderer
- monomers - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- monomers - Variable in class org.jmol.renderbio.RibbonsRenderer
- monomers - Variable in class org.jmol.renderbio.RocketsRenderer
- monomers - Variable in class org.jmol.renderbio.StrandsRenderer
- monomers - Variable in class org.jmol.renderbio.TraceRenderer
- monomers - Variable in class org.jmol.shapebio.BioShape
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- MopacArchiveReader - Class in org.jmol.adapter.readers.simple
-
Mopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cell
- MopacArchiveReader() - Constructor for class org.jmol.adapter.readers.simple.MopacArchiveReader
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.CsfReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
-
Reads Mopac 2007 GRAPHF output files
- MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
- MopacReader - Class in org.jmol.adapter.readers.simple
-
Reads Mopac 93, 6, 7, 2002, or 2009 output files
- MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
- MOReader - Class in org.jmol.adapter.readers.quantum
-
General methods for reading molecular orbital data, including embedded output from the NBO program.
- MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
- moreLabels(Map<String, String>) - Method in class org.openscience.jmol.app.janocchio.NmrGuiMap
-
See NMR_JmolPanel where "NMR." is processed, and ./Properties/Nmr.properties where they are defined
- moreLabels(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
-
Add more labels if desired
- morph - Static variable in class org.jmol.script.T
- morph(float) - Method in class org.jmol.viewer.AnimationManager
- morphTrajectories(int, int, float) - Method in class org.jmol.modelset.ModelSet
- moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
- motionDisabled - Variable in class org.molecularplayground.MPJmolApp
- moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
- mouse - Static variable in class org.jmol.script.T
- Mouse - Class in org.jmol.awtjs2d
-
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
- Mouse(double, Viewer, Object) - Constructor for class org.jmol.awtjs2d.Mouse
- MOUSE_DOWN - Static variable in class org.jmol.awtjs.Event
- MOUSE_DRAG - Static variable in class org.jmol.awtjs.Event
- MOUSE_ENTER - Static variable in class org.jmol.awtjs.Event
- MOUSE_EXIT - Static variable in class org.jmol.awtjs.Event
- MOUSE_LEFT - Static variable in class org.jmol.awtjs.Event
- MOUSE_MIDDLE - Static variable in class org.jmol.awtjs.Event
- MOUSE_MOVE - Static variable in class org.jmol.awtjs.Event
- MOUSE_NONE - Static variable in class org.jmol.viewer.JC
- MOUSE_RIGHT - Static variable in class org.jmol.awtjs.Event
- MOUSE_UP - Static variable in class org.jmol.awtjs.Event
- MOUSE_WHEEL - Static variable in class org.jmol.awtjs.Event
- mouseAction(int, long, int, int, int, int) - Method in class jspecview.common.PanelData
- mouseAction(int, long, int, int, int, int) - Method in interface org.jmol.api.EventManager
- mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
- mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
- mouseClicked(MouseEvent) - Method in class jme.JME
- mouseClicked(MouseEvent) - Method in class jspecview.app.GenericMouse
- mouseClicked(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseClicked(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseDown(MouseEvent, int, int) - Method in class jme.JME
- mouseDrag(MouseEvent, int, int) - Method in class jme.JME
- mousedragfactor - Static variable in class org.jmol.script.T
- mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
- mouseDragged(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- mouseDragged(MouseEvent) - Method in class jme.JME
- mouseDragged(MouseEvent) - Method in class jspecview.app.GenericMouse
- mouseDragged(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseEntered(MouseEvent) - Method in class jme.JME
- mouseEntered(MouseEvent) - Method in class jspecview.app.GenericMouse
- mouseEntered(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseEnterExit(long, int, int, boolean) - Method in class jspecview.common.PanelData
- mouseEnterExit(long, int, int, boolean) - Method in interface org.jmol.api.EventManager
- mouseEnterExit(long, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
- mouseExited(MouseEvent) - Method in class jme.JME
- mouseExited(MouseEvent) - Method in class jspecview.app.GenericMouse
- mouseExited(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseListener - Variable in class org.jmol.awtjs.swing.Component
- mouseMove(MouseEvent, int, int) - Method in class jme.JME
- mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- mouseMoved(MouseEvent) - Method in class jme.JME
- mouseMoved(MouseEvent) - Method in class jspecview.app.GenericMouse
- mouseMoved(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mousePressed(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- mousePressed(MouseEvent) - Method in class jme.JME
- mousePressed(MouseEvent) - Method in class jspecview.app.GenericMouse
- mousePressed(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mousePressed(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseReleased(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- mouseReleased(MouseEvent) - Method in class jme.JME
- mouseReleased(MouseEvent) - Method in class jspecview.app.GenericMouse
- mouseReleased(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseReleased(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseShift - Variable in class jme.JME
- MouseState - Class in org.jmol.viewer
- mouseUp(MouseEvent, int, int) - Method in class jme.JME
- mousewheelfactor - Static variable in class org.jmol.script.T
- mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
- mouseWheelMoved(MouseWheelEvent) - Method in class jspecview.app.GenericMouse
- mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseX - Variable in class jspecview.common.PanelData
- mouseY - Variable in class jspecview.common.PanelData
- movableBitSet - Variable in class org.jmol.viewer.Viewer
- movableX - Variable in class org.jmol.modelset.Text
- movableXPercent - Variable in class org.jmol.modelset.Text
- movableY - Variable in class org.jmol.modelset.Text
- movableYPercent - Variable in class org.jmol.modelset.Text
- movableZ - Variable in class org.jmol.modelset.Text
- movableZPercent - Variable in class org.jmol.modelset.Text
- move - Static variable in class org.jmol.script.T
- move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.Viewer
- MOVE - Static variable in class com.sparshui.common.TouchState
- MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
- moveAtoms(M4, M3, M3, V3, BS, P3, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- moveAtoms(M4, M3, M3, V3, P3, boolean, BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- moveAtomWithHydrogens(int, int, int, int, P3, BS) - Method in class org.jmol.viewer.Viewer
- moved - Variable in class org.jmol.viewer.ActionManager
- moved(long, int, int, int) - Method in class jspecview.app.GenericMouse
- MOVED - Static variable in class org.jmol.awtjs.Event
- moveMinConstrained(int, P3, BS) - Method in class org.jmol.modelkit.ModelKit
- movePossible - Variable in class jme.JME
- moveRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
- moveto - Static variable in class org.jmol.script.T
- moveto(int, int) - Method in class javajs.export.PDFCreator
- moveTo(JmolScriptEvaluator, float, P3, V3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.Viewer
- MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- moveToPyMOL(JmolScriptEvaluator, float, float[]) - Method in class org.jmol.viewer.TransformManager
- movetoThread - Variable in class org.jmol.viewer.TransformManager
- MoveToThread - Class in org.jmol.thread
- MoveToThread() - Constructor for class org.jmol.thread.MoveToThread
- moveUpdate(float) - Method in class org.jmol.viewer.Viewer
- movie - Static variable in class org.jmol.script.T
- mp - Variable in class jspecview.export.AMLExporter
- mp - Variable in class jspecview.export.CMLExporter
- mPending - Variable in class org.jmol.shape.Measures
- MPJmolApp - Class in org.molecularplayground
- MPJmolApp() - Constructor for class org.molecularplayground.MPJmolApp
- MPJmolApp(int) - Constructor for class org.molecularplayground.MPJmolApp
- mrc - Static variable in class org.jmol.script.T
- ms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ms - Variable in class org.jmol.modelset.Measurement
- ms - Variable in class org.jmol.modelset.Model
-
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
- ms - Variable in class org.jmol.modelset.ModelLoader
- ms - Variable in class org.jmol.render.ShapeRenderer
- ms - Variable in class org.jmol.shape.Shape
- ms - Variable in class org.jmol.viewer.Viewer
- MSCifParser - Class in org.jmol.adapter.readers.cif
- MSCifParser() - Constructor for class org.jmol.adapter.readers.cif.MSCifParser
- msg - Variable in class org.jmol.jvxl.data.JvxlData
- msInfo - Variable in class org.jmol.modelset.ModelSet
- MSInterface - Interface in org.jmol.adapter.smarter
-
Modulated Structure Reader Interface
- msms - Static variable in class org.jmol.script.T
- MSRdr - Class in org.jmol.adapter.readers.cif
-
generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth, Legendre; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
- MSRdr() - Constructor for class org.jmol.adapter.readers.cif.MSRdr
- mul - Static variable in class org.jmol.script.T
- mul(float) - Method in class javajs.util.Quat
- mul(M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to the result of multiplying itself with matrix m1.
- mul(M4) - Method in class javajs.util.M4
-
Sets the value of this matrix to the result of multiplying itself with matrix m1.
- mul(Matrix) - Method in class javajs.util.Matrix
-
Linear algebraic matrix multiplication, A * B
- mul2(M3, M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to the result of multiplying the two argument matrices together.
- mul2(M4, M4) - Method in class javajs.util.M4
-
Sets the value of this matrix to the result of multiplying the two argument matrices together.
- mul3 - Static variable in class org.jmol.script.T
- mul33(float) - Method in class javajs.util.M34
- mulQ(Quat) - Method in class javajs.util.Quat
- MULTI_POINT_DRAG_GESTURE - Static variable in class com.sparshui.GestureType
- MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JC
- MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JC
- MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JC
- MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JC
- multipart - Variable in class jme.JME
- MULTIPLE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- multiplebondbananas - Static variable in class org.jmol.script.T
- multiplebondradiusfactor - Static variable in class org.jmol.script.T
- multiplebondspacing - Static variable in class org.jmol.script.T
- multiprocessor - Static variable in class org.jmol.script.T
- mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
- mustFinalizeModelSet - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
- mustResumeEval - Variable in class org.jmol.script.ScriptContext
- mutate - Static variable in class org.jmol.script.T
- mutate(BS, String, String[], String, float[]) - Method in class org.jmol.modelsetbio.BioModelSet
- mxyz - Variable in class org.jmol.util.ModulationSet
-
the modulated magnetic spin
- myAtoms - Variable in class org.jmol.util.ContactPair
- mydeflater - Variable in class com.jcraft.jzlib.DeflaterOutputStream
- MyFileFilter - Class in org.openscience.jmol.app.janocchio
- MyFileFilter(String[], String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
- MyFileFilter(String, String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
- myFrame - Variable in class jme.JME
- myinflater - Variable in class com.jcraft.jzlib.InflaterInputStream
- myName - Variable in class org.jmol.script.SV
- myName - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- myParams - Variable in class jspecview.common.MeasurementData
- myParams - Variable in class jspecview.dialog.JSVDialog
- myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- myType - Variable in class org.jmol.shape.Shape
- myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
- myVisibilityFlag - Variable in class org.jmol.render.ShapeRenderer
N
- n - Variable in class javajs.util.Matrix
- n(int, int) - Static method in class org.jmol.script.T
- N_GROUPS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- N_ITERS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- NA - Enum constant in enum class jspecview.common.IntegralData.IntMode
- nada - Static variable in class org.jmol.script.T
- NADA - Enum constant in enum class org.jmol.c.VDW
- name - Variable in class jspecview.common.Parameters
- name - Variable in class org.jmol.awtjs.swing.Component
- name - Variable in class org.jmol.minimize.forcefield.ForceField
- name - Static variable in class org.jmol.script.T
- name - Variable in class org.jmol.symmetry.UnitCell
- name - Variable in class org.jmol.thread.JmolThread
- name - Variable in class org.jmol.viewer.binding.Binding
- name - Variable in class org.jmol.viewer.MouseState
- namedSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- nameOf(int) - Static method in class org.jmol.script.T
-
note: nameOf is a very inefficient mechanism for getting the name of a token.
- NamfisReader - Class in org.openscience.jmol.app.janocchio
- NamfisReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisReader
- NamfisSaver - Class in org.openscience.jmol.app.janocchio
- NamfisSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisSaver
- nativeLanguage - Variable in class org.jmol.i18n.Language
- natoms - Variable in class jme.JMEmol
- nAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
- nAtoms - Variable in class org.jmol.minimize.MMConstraint
- nAtoms0 - Variable in class org.jmol.adapter.readers.cif.CifReader
- NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager
- navfps - Static variable in class org.jmol.script.T
- navFps - Variable in class org.jmol.viewer.TransformManager
- navigate - Static variable in class org.jmol.script.T
- navigateAxis(V3, float) - Method in interface org.jmol.api.JmolNavigatorInterface
- navigateAxis(V3, float) - Method in class org.jmol.navigate.Navigator
- navigateAxis(V3, float) - Method in class org.jmol.viewer.TransformManager
-
scripted entry point for navigation
- navigateAxis(V3, float) - Method in class org.jmol.viewer.Viewer
- navigateKey(int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
- navigateKey(int, int) - Method in class org.jmol.navigate.Navigator
- navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in interface org.jmol.api.JmolNavigatorInterface
- navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.navigate.Navigator
- navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.viewer.TransformManager
- navigatePt(P3) - Method in class org.jmol.viewer.Viewer
- navigatesurface - Static variable in class org.jmol.script.T
- navigating - Variable in class org.jmol.viewer.TransformManager
- navigationCenter - Variable in class org.jmol.viewer.TransformManager
- navigationdepth - Static variable in class org.jmol.script.T
- navigationDepthPercent - Variable in class org.jmol.viewer.TransformManager
- navigationmode - Static variable in class org.jmol.script.T
- navigationOffset - Variable in class org.jmol.viewer.TransformManager
- navigationperiodic - Static variable in class org.jmol.script.T
- navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
- navigationslab - Static variable in class org.jmol.script.T
- navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager
- navigationspeed - Static variable in class org.jmol.script.T
- Navigator - Class in org.jmol.navigate
-
Navigator is a user input mechanism that utilizes the keypad to drive through the model.
- Navigator() - Constructor for class org.jmol.navigate.Navigator
- navMode - Variable in class org.jmol.viewer.TransformManager
- navOn - Variable in class org.jmol.viewer.TransformManager
- navTranslatePercent(float, float) - Method in class org.jmol.viewer.Viewer
- navTranslatePercentOrTo(float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
- navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.navigate.Navigator
- navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.viewer.TransformManager
-
seconds invalid input: '<' 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"
- navx - Static variable in class org.jmol.script.T
- navX - Variable in class org.jmol.viewer.TransformManager
- navy - Static variable in class org.jmol.script.T
- navY - Variable in class org.jmol.viewer.TransformManager
- NAVY - Static variable in class org.jmol.util.C
- navz - Static variable in class org.jmol.script.T
- navZ - Variable in class org.jmol.viewer.TransformManager
- nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
- nbo - Static variable in class org.jmol.script.T
- NBO - Class in org.jmol.shapesurface
- NBO() - Constructor for class org.jmol.shapesurface.NBO
- NBO_CONFIG - Static variable in class org.jmol.viewer.JC
- NBO_MODEL - Static variable in class org.jmol.viewer.JC
- NBO_RUN - Static variable in class org.jmol.viewer.JC
- NBO_SEARCH - Static variable in class org.jmol.viewer.JC
- NBO_TYPES - Static variable in class org.jmol.viewer.JC
- NBO_VIEW - Static variable in class org.jmol.viewer.JC
- nbocharges - Static variable in class org.jmol.script.T
- nbonds - Variable in class jme.JMEmol
- nBonds - Variable in class org.jmol.minimize.MinAtom
- NBOParser - Class in org.jmol.adapter.readers.quantum
- NBOParser() - Constructor for class org.jmol.adapter.readers.quantum.NBOParser
- NBORenderer - Class in org.jmol.rendersurface
- NBORenderer() - Constructor for class org.jmol.rendersurface.NBORenderer
- nBytes - Variable in class javajs.util.BinaryDocument
- nBytes - Variable in class org.jmol.jvxl.data.JvxlData
- nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nci - Static variable in class org.jmol.script.T
- NciCalculation - Class in org.jmol.quantum
- NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
- nCoef - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- nContours - Variable in class org.jmol.jvxl.data.JvxlData
- nData - Variable in class org.jmol.jvxl.readers.JvxlReader
- nData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- nData - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
- ndots - Static variable in class org.jmol.render.FontLineShapeRenderer
- ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
- nEdges - Variable in class org.jmol.jvxl.data.JvxlData
- needRecentering - Variable in class jme.JMEmol
- needTranslucent - Variable in class org.jmol.render.MeshRenderer
- negate() - Method in class javajs.util.Quat
- negativeAtomCount - Variable in class org.jmol.jvxl.readers.JvxlReader
- negativeAtomCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- negativeAtomCount - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nElements - Variable in class org.jmol.util.JmolMolecule
- nError - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- NetworkConfiguration - Class in com.sparshui.common
-
Defines the port the server will be listening for connections on.
- NetworkConfiguration() - Constructor for class com.sparshui.common.NetworkConfiguration
- new3(float, float, float) - Static method in class javajs.util.P3
- new3(float, float, float) - Static method in class javajs.util.V3
- new3(int, int, int) - Static method in class javajs.util.P3i
- new4(float, float, float, float) - Static method in class javajs.util.A4
-
Constructs and initializes an AxisAngle4f from the specified x, y, z, and angle.
- new4(float, float, float, float) - Static method in class javajs.util.P4
- new4(float, float, float, float) - Static method in class javajs.util.Quat
-
Note that q0 is the last parameter here
- newA(float[]) - Static method in class javajs.util.P3
- newA(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- newA16(float[]) - Static method in class javajs.util.M4
-
Constructs and initializes a Matrix4f from the specified 16 element array.
- newA9(float[]) - Static method in class javajs.util.M3
-
Constructs and initializes a Matrix3f from the specified 9 element array.
- newAA(A4) - Static method in class javajs.util.A4
-
Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
- newAA(A4) - Static method in class javajs.util.Quat
- newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- newAndSetBit(int) - Static method in class org.jmol.util.BSUtil
- newAntialiasing - Variable in class org.jmol.util.GData
- newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Create a new atoms set, clearing the atom map
- newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- newAtomSetClear(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Create a new atom set, optionally clearing the atom map.
- newBinding(Viewer, String) - Static method in class org.jmol.viewer.binding.Binding
- newBitSet2(int, int) - Static method in class org.jmol.util.BSUtil
- newBS(BS) - Static method in class org.jmol.modelset.BondSet
- newBufferedImage(Object, int, int) - Method in class jspecview.java.AwtPlatform
- newBufferedImage(Object, int, int) - Method in class jspecview.js2d.JsPlatform
- newBufferedImage(Object, int, int) - Method in interface org.jmol.api.GenericPlatform
- newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
- newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs.Platform
- newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs2d.Platform
- newByte2(int) - Static method in class javajs.util.AU
- newBZip2InputStream(InputStream) - Method in interface javajs.api.GenericZipTools
- newBZip2InputStream(InputStream) - Method in class javajs.util.ZipTools
- newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- newDocument(int, int, boolean) - Method in class javajs.export.PDFCreator
- newDouble2(int) - Static method in class javajs.util.AU
- newDouble3n(int) - Static method in class javajs.util.AU
- newEcho(Viewer, Font, String, short, int, int, float) - Static method in class org.jmol.modelset.Text
- newF(float) - Static method in class org.jmol.script.SV
- newFile(String) - Method in class jspecview.java.AwtPlatform
- newFile(String) - Method in class jspecview.js2d.JsPlatform
- newFile(String) - Method in interface org.jmol.api.GenericPlatform
- newFile(String) - Method in class org.jmol.awt.Platform
- newFile(String) - Method in class org.jmol.awtjs2d.Platform
- newFileSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- newFileSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- newFloat2(int) - Static method in class javajs.util.AU
- newFloat3(int, int) - Static method in class javajs.util.AU
- newFont(String, boolean, boolean, float) - Method in class jspecview.java.AwtPlatform
- newFont(String, boolean, boolean, float) - Method in class jspecview.js2d.JsPlatform
- newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.FontManager
- newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
- newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs2d.Platform
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface javajs.api.js.J2SObjectInterface
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.common.PDFWriter
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.java.AwtG2D
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.js2d.JsG2D
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface org.jmol.api.GenericGraphics
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awt.AwtG2D
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awtjs2d.JsG2D
- newGZIPInputStream(InputStream) - Method in interface javajs.api.GenericZipTools
- newGZIPInputStream(InputStream) - Method in class javajs.util.ZipTools
- newGZIPInputStream(InputStream) - Method in interface jspecview.api.JSVZipInterface
- newGZIPInputStream(InputStream) - Method in class jspecview.common.JSVZipUtil
- newI(int) - Static method in class org.jmol.script.SV
- newI(int) - Static method in class org.jmol.util.Rgb16
- newID(String) - Static method in class org.jmol.awtjs.swing.Component
- newInt2(int) - Static method in class javajs.util.AU
- newInt3(int, int) - Static method in class javajs.util.AU
- newInt4(int) - Static method in class javajs.util.AU
- newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJMenu(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- newJMenu(String) - Method in class org.jmol.console.JmolConsole
- newJMenu(String) - Method in class org.jmol.consolejs.AppletConsole
- newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJMenuItem(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- newJMenuItem(String) - Method in class org.jmol.console.JmolConsole
- newJMenuItem(String) - Method in class org.jmol.consolejs.AppletConsole
- newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJSVZipFileSequentialReader(InputStream, String[], String) - Method in interface jspecview.api.JSVZipInterface
- newJSVZipFileSequentialReader(InputStream, String[], String) - Method in class jspecview.common.JSVZipUtil
- newLabel(Viewer, Font, String, short, short, int, float) - Static method in class org.jmol.modelset.Text
- newLatticePts - Variable in class org.jmol.util.BZone
- newLine - Static variable in class jspecview.export.JDXExporter
- newList() - Static method in class org.qcschema.QCSchemaUnits
- newM(M3) - Static method in class javajs.util.Quat
- newM3(M3) - Static method in class javajs.util.M3
-
Constructs a new matrix with the same values as the Matrix3f parameter.
- newM4(M4) - Static method in class javajs.util.M4
-
Constructs a new matrix with the same values as the Matrix4f parameter.
- newMeasure(Viewer, Font, short) - Static method in class org.jmol.modelset.Text
- newMeasurementData(String, Lst<Object>) - Method in class org.jmol.viewer.Viewer
- newMesh(boolean, T3[], int, int[][], T3[], int) - Static method in class org.jmol.util.MeshSurface
- newModel(int) - Method in class org.jmol.adapter.readers.cif.CifReader
- newMolecule - Variable in class jme.JME
- newMV(M3, T3) - Static method in class javajs.util.M4
-
Constructs and initializes a Matrix4f from the rotation matrix and translation.
- newN(int) - Static method in class javajs.util.BS
-
Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range
0
throughnbits-1
. - newN(int) - Static method in class javajs.util.SB
- newOffScreenImage(int, int) - Method in class jspecview.java.AwtPlatform
- newOffScreenImage(int, int) - Method in class jspecview.js2d.JsPlatform
- newOffScreenImage(int, int) - Method in interface org.jmol.api.GenericPlatform
- newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
- newOffScreenImage(int, int) - Method in class org.jmol.awtjs.Platform
- newOffScreenImage(int, int) - Method in class org.jmol.awtjs2d.Platform
- newP(T3) - Static method in class javajs.util.P3
- newP4(P4) - Static method in class javajs.util.Quat
- newParams(float[], float) - Static method in class org.jmol.util.SimpleUnitCell
- newPlanes - Variable in class org.jmol.util.BZone
- newPt(P4) - Static method in class javajs.util.P4
- newQ(Quat) - Static method in class javajs.util.Quat
- newS(String) - Static method in class javajs.util.SB
- newS(String) - Static method in class org.jmol.script.SV
- newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
- newSg() - Method in class org.jmol.shapesurface.Isosurface
- newShort2(int) - Static method in class javajs.util.AU
- newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
- newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
- newSpectrum(Lst<Spectrum>) - Method in class jspecview.common.ViewData
- newSpectrum(Spectrum, Coordinate[], String) - Static method in class jspecview.common.Spectrum
-
copy spectrum with new coordinates
- newStereo(SmilesSearch) - Static method in class org.jmol.smiles.SmilesStereo
- newT(T3, boolean) - Static method in class javajs.util.Matrix
- newT(T) - Static method in class org.jmol.script.SV
- newToolbar(String[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- newTreePath(Object[]) - Method in interface jspecview.api.JSVTree
- newTreePath(Object[]) - Method in class jspecview.application.AwtTree
- newTreePath(Object[]) - Method in class jspecview.tree.SimpleTree
- newV(int, Object) - Static method in class org.jmol.script.SV
- newV(T3) - Static method in class javajs.util.V3
- newVA(T3, float) - Static method in class javajs.util.Quat
- newVA(V3, float) - Static method in class javajs.util.A4
-
Constructs and initializes an AxisAngle4f from the specified axis and angle.
- newVertex(P3, V3, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- newVertexBitSet() - Static method in class org.jmol.util.Normix
- newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
- newVsub(T3, T3) - Static method in class javajs.util.V3
- newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
- newWindow(boolean) - Method in interface jspecview.api.AppletFrame
- newWindow(boolean) - Method in class jspecview.appletjs.JSVApplet
- newWindowHeight - Variable in class org.jmol.util.GData
- newWindowWidth - Variable in class org.jmol.util.GData
- newXYCoords - Variable in class jspecview.export.AMLExporter
- newXYCoords - Variable in class jspecview.export.CMLExporter
- newZipInputStream(InputStream) - Method in interface javajs.api.GenericZipTools
- newZipInputStream(InputStream) - Method in class javajs.util.ZipTools
- next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- next - Variable in class org.jmol.jvxl.readers.JvxlReader
- next - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- next - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- next - Static variable in class org.jmol.script.T
- next() - Method in class jspecview.source.JDXDecompressor
- next() - Method in interface org.jmol.api.AtomIndexIterator
- next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- next() - Method in interface org.jmol.modelset.BondIterator
- next() - Method in class org.jmol.symmetry.UnitCellIterator
- nextAtomSet() - Method in class org.jmol.adapter.readers.cif.CifReader
- nextClearBit(int) - Method in class javajs.util.BS
-
Returns the index of the first bit that is set to
false
that occurs on or after the specified starting index. - nextData(StringTokenizer, String) - Static method in class jme.JMEmol
- nextData(StringTokenizer, String) - Static method in class jme.JMEUtil
- nextElement() - Method in class jspecview.tree.SimpleTreeEnumeration
- nextElement() - Method in class org.jmol.bspt.CubeIterator
-
normal iterator method
- nextEvent() - Method in class jspecview.source.XMLParser
- nextFileName(String, int) - Method in class org.jmol.console.GenericConsole
- nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
- nextFileName(String, int) - Method in class org.jmol.consolejs.AppletConsole
- nextIndex() - Method in interface org.jmol.modelset.BondIterator
- nextRandom8Bit() - Method in class org.jmol.util.Shader
-
Implements RANDU algorithm for random noise in lighting/shading.
- nextSetBit(int) - Method in class javajs.util.BS
-
Returns the index of the first bit that is set to
true
that occurs on or after the specified starting index. - nextStartTag() - Method in class jspecview.source.XMLParser
- nextTag() - Method in class jspecview.source.XMLParser
- nextToken() - Method in class jspecview.common.ScriptTokenizer
- nextValue() - Method in class jspecview.source.XMLParser
- nextView() - Method in class jspecview.common.PanelData
-
Displays the next view zoomed
- nextVoxel() - Method in class org.jmol.jvxl.readers.JvxlReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nFast - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- nFrankList - Variable in class org.jmol.popup.JmolGenericPopup
- nGaussians - Variable in class org.jmol.quantum.MOCalculation
- nihresolverformat - Static variable in class org.jmol.script.T
- nIn - Variable in class org.jmol.util.Shader
- nioClosed(JsonNioServer) - Method in class org.molecularplayground.MPJmolApp
- nioClosed(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- nioClosed(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- nioSync(Viewer, Map<String, Object>) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
-
process touch or gesture commands driven by hardware.
- nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
- nList - Variable in class org.jmol.shapecgo.CGOMesh
- nmols - Variable in class jme.JME
- nmr - Static variable in class org.jmol.script.T
- Nmr - Class in org.openscience.jmol.app.janocchio
- Nmr(String[]) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
- Nmr(String[], NmrPlugin) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
- NMR_DC - Static variable in class org.jmol.modelset.Measurement
- NMR_DisplayPanel - Class in org.openscience.jmol.app.janocchio
- NMR_JC - Static variable in class org.jmol.modelset.Measurement
- NMR_JmolPanel - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- NMR_JmolPanel.DetachAppletAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.JumpBestFrameAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.LabelNmrAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ReadNamfisAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ReadNmrAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ReattachAppletAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ViewCoupleTableAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ViewNoeTableAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.WriteNamfisAction - Class in org.openscience.jmol.app.janocchio
- NMR_NOE_OR_J - Static variable in class org.jmol.modelset.Measurement
- NMR_NOT - Static variable in class org.jmol.modelset.Measurement
- NMR_Viewer - Class in org.openscience.jmol.app.janocchio
-
Implements some lost interfaces.
- NMR_Viewer(Map<String, Object>) - Constructor for class org.openscience.jmol.app.janocchio.NMR_Viewer
- NmrApplet - Class in org.openscience.jmol.app.janocchio
- NmrApplet() - Constructor for class org.openscience.jmol.app.janocchio.NmrApplet
- NMRCalculation - Class in org.jmol.quantum
- NMRCalculation() - Constructor for class org.jmol.quantum.NMRCalculation
- NmrGuiMap - Class in org.openscience.jmol.app.janocchio
- NmrGuiMap() - Constructor for class org.openscience.jmol.app.janocchio.NmrGuiMap
- nmrMaxY - Variable in class jspecview.common.JSViewer
- NmrMolecule - Class in org.openscience.jmol.app.janocchio
- NmrMolecule(NMR_JmolPanel, BS, String[], boolean) - Constructor for class org.openscience.jmol.app.janocchio.NmrMolecule
- NMRNoeMatrix - Class in org.jmol.quantum
-
Class for calculating NOE intensities by full matrix relaxation approach.
- NMRNoeMatrix.NOEParams - Class in org.jmol.quantum
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- NmrPlugin - Class in org.openscience.jmol.app.janocchio
- NmrPlugin() - Constructor for class org.openscience.jmol.app.janocchio.NmrPlugin
- nmrpredictformat - Static variable in class org.jmol.script.T
- NmrReader - Class in org.openscience.jmol.app.janocchio
- NmrReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrReader
- NmrResourceHandler - Class in org.openscience.jmol.app.janocchio
-
Provides access to resources (for example, strings and images).
- NmrSaver - Class in org.openscience.jmol.app.janocchio
- NmrSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrSaver
- nmrType(String) - Static method in class org.jmol.modelset.Measurement
- nmrurlformat - Static variable in class org.jmol.script.T
- NO_AUTOPLAY - Static variable in interface org.jmol.api.JmolScriptManager
- NO_CONVERT - Enum constant in enum class jspecview.common.Spectrum.IRMode
- NO_SCRIPT - Static variable in interface org.jmol.api.JmolScriptManager
- NO_SUCH_PAGE - Static variable in class jspecview.common.JSViewer
- noArgs - Static variable in class org.jmol.script.T
- nobackshell - Static variable in class org.jmol.script.T
- nocenter - Variable in class jme.JME
- noColor - Variable in class org.jmol.export.__CartesianExporter
- nocontourlines - Static variable in class org.jmol.script.T
- noCopy(int, int) - Method in class org.jmol.script.ScriptEval
- nocross - Static variable in class org.jmol.script.T
- noCross - Variable in class org.jmol.shapespecial.Dipole
- Node - Interface in org.jmol.util
- nodebug - Static variable in class org.jmol.script.T
- nodelay - Static variable in class org.jmol.script.T
- noDelay - Variable in class org.jmol.viewer.GlobalSettings
-
ensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1
- nodes - Variable in class org.jmol.util.JmolMolecule
- nodots - Static variable in class org.jmol.script.T
- noeColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NoeColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
- NoeColourSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- noedges - Static variable in class org.jmol.script.T
- noeMatrix - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- noeParameterSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NoeParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
- NoeParameterSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- NOEParams() - Constructor for class org.jmol.quantum.NMRNoeMatrix.NOEParams
- noeTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- NoeTable - Class in org.openscience.jmol.app.janocchio
- NoeTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.NoeTable
-
Constructor
- nofill - Static variable in class org.jmol.script.T
- noFrankEcho - Variable in class org.jmol.viewer.Viewer
- noGraphicsAllowed - Variable in class org.jmol.viewer.Viewer
- nohead - Static variable in class org.jmol.script.T
- noHead - Variable in class org.jmol.shapespecial.DrawMesh
- NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
- NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
- noHydrogens - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- NOJMOL - Enum constant in enum class org.jmol.c.VDW
- noLabelAtom - Variable in class jme.AtomDisplayLabel
- noload - Static variable in class org.jmol.script.T
- nomesh - Static variable in class org.jmol.script.T
- noMinimize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- nonArrayString(Object) - Static method in class javajs.util.PT
-
Checks to see if an object is an array (including typed arrays), and if it is, returns null; otherwise it returns the string equivalent of that object.
- none - Static variable in class org.jmol.script.T
- NONE - Enum constant in enum class javajs.util.Encoding
- NONE - Enum constant in enum class jspecview.common.Annotation.AType
- NONE - Enum constant in enum class jspecview.common.PanelData.LinkMode
- NONE - Enum constant in enum class org.jmol.c.PAL
- NONE - Enum constant in enum class org.jmol.c.STER
- NONE - Enum constant in enum class org.jmol.c.STR
- NONE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- NONE - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
- NONE - Static variable in interface javajs.api.GenericCifDataParser
- NONE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- NONE - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- noneSelected - Variable in class org.jmol.viewer.SelectionManager
-
a flag to indicate that labels and fonts should be set to default values; set only by SELECT NONE;
- nonisomericSmiles() - Method in class jme.JME
- noPack - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- noplane - Static variable in class org.jmol.script.T
- nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- NORM_NBO - Static variable in class org.jmol.quantum.MOCalculation
- NORM_NONE - Static variable in class org.jmol.quantum.MOCalculation
- NORM_NWCHEM - Static variable in class org.jmol.quantum.MOCalculation
- NORM_STANDARD - Static variable in class org.jmol.quantum.MOCalculation
- normal - Static variable in class org.jmol.script.T
- NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
- normalCount - Variable in class org.jmol.util.MeshSurface
- normalise(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
-
Normalises the y values of a spectrum to a certain range
- normalize() - Method in class javajs.util.T3
-
Normalizes this vector in place.
- normalize() - Method in class javajs.util.V3d
-
Normalizes this vector in place.
- normalize12ths(V3) - Static method in class org.jmol.symmetry.SymmetryOperation
- normalizeIntegral() - Method in class jspecview.common.PanelData
- normalizeOperationToCentroid(int, M4, P3[], int, int) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.
- normalizeSimulation(double) - Method in class jspecview.source.JDXDataObject
- normals - Variable in class org.jmol.util.MeshSurface
- normalsTemp - Variable in class org.jmol.util.MeshSurface
- Normix - Class in org.jmol.util
-
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
- Normix() - Constructor for class org.jmol.util.Normix
- NORMIX_NULL - Static variable in class org.jmol.util.Normix
- normixCount - Static variable in class org.jmol.util.GData
- normixCount - Variable in class org.jmol.util.MeshSurface
- normixes - Variable in class org.jmol.render.MeshRenderer
- normixes - Variable in class org.jmol.shape.Mesh
- normType - Variable in class org.jmol.quantum.MOCalculation
- NORTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
- NOT - Enum constant in enum class org.jmol.c.HB
- NOT - Enum constant in enum class org.jmol.c.STR
- NOT_LOADED - Enum constant in enum class org.jmol.c.FIL
- NOT_SORTED - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- note - Variable in class org.jmol.modelset.MeasurementData
- NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JC
- notfrontonly - Static variable in class org.jmol.script.T
- notify(int, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
- notify(int, Object[]) - Method in class org.jmol.console.ScriptEditor
- notifyAtomPositionsChanged(int, BS, M4) - Method in class org.jmol.viewer.ShapeManager
- notifyAtoms(String, BS[]) - Method in class org.jmol.viewer.ShapeManager
- notifyAudioEnded(Object) - Method in interface org.jmol.api.JmolAppletInterface
- notifyAudioEnded(Object) - Method in class org.jmol.util.GenericApplet
- notifyAudioStatus(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
-
called from JmolAudio
- notifyCallback(CBK, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
- notifyCallback(CBK, Object[]) - Method in class org.jmol.console.GenericConsole
- notifyCallback(CBK, Object[]) - Method in class org.jmol.util.GenericApplet
- notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifyCallback(CBK, Object[]) - Method in interface org.openscience.jmol.app.JmolPlugin
- notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
- notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
- notifyEnabled(CBK) - Method in interface org.jmol.api.JmolCallbackListener
- notifyEnabled(CBK) - Method in class org.jmol.console.GenericConsole
- notifyEnabled(CBK) - Method in class org.jmol.util.GenericApplet
- notifyEnabled(CBK) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifyEndOfRendering() - Method in class jspecview.java.AwtPlatform
- notifyEndOfRendering() - Method in class jspecview.js2d.JsPlatform
- notifyEndOfRendering() - Method in interface org.jmol.api.GenericPlatform
- notifyEndOfRendering() - Method in class org.jmol.awt.Platform
- notifyEndOfRendering() - Method in class org.jmol.awtjs2d.Platform
- notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
- notifyListeners(Object) - Method in class jspecview.common.PanelData
- notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
- notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
- notifyPeakPickedListeners(PeakPickEvent) - Method in class jspecview.common.PanelData
-
Notifies CoordinatePickedListeners
- notifyResumeStatus() - Method in interface org.jmol.api.JmolScriptEvaluator
- notifyResumeStatus() - Method in class org.jmol.script.ScriptEval
- notifyScriptEditor(int, Object[]) - Method in class org.jmol.viewer.Viewer
- notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
- notifyScriptTermination(String) - Method in class org.jmol.console.ScriptEditor
- notifyStatusReady(boolean) - Method in class org.jmol.api.JmolViewer
- notifyStatusReady(boolean) - Method in class org.jmol.viewer.Viewer
- notifySubSpectrumChange(int, Spectrum) - Method in class jspecview.common.PanelData
- notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
- notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
- notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
- notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
- notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
- notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
- notInCentroid(ModelSet, BS, int[]) - Method in interface org.jmol.api.SymmetryInterface
- notInCentroid(ModelSet, BS, int[]) - Method in class org.jmol.symmetry.Symmetry
- notriangles - Static variable in class org.jmol.script.T
- nOut - Variable in class org.jmol.util.Shader
- now - Static variable in class org.jmol.script.T
- npoints - Variable in class jspecview.export.AMLExporter
- npoints - Variable in class jspecview.export.CMLExporter
- npoints - Variable in class jspecview.source.AnIMLReader
- nPoints - Variable in class org.jmol.jvxl.data.VolumeData
- nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
- nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
- nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
- nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nProcessors - Static variable in class org.jmol.viewer.Viewer
- nRes - Variable in class org.jmol.modelsetbio.ProteinStructure
- nSets - Variable in class org.jmol.util.MeshSurface
- nSkipX - Variable in class org.jmol.jvxl.readers.JvxlReader
- nSkipX - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- nSkipX - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nSkipY - Variable in class org.jmol.jvxl.readers.JvxlReader
- nSkipY - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- nSkipY - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nSkipZ - Variable in class org.jmol.jvxl.readers.JvxlReader
- nSkipZ - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- nSkipZ - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
- nSurfaces - Variable in class org.jmol.jvxl.readers.JvxlReader
- nSurfaces - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- nSurfaces - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- nTab - Variable in class org.jmol.console.GenericConsole
- nTokens - Variable in class org.jmol.script.ScriptCompiler
- nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
- nucleic - Static variable in class org.jmol.script.T
- NUCLEIC - Enum constant in enum class org.jmol.c.PAL
- NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
- NucleicMonomer - Class in org.jmol.modelsetbio
- NucleicPolymer - Class in org.jmol.modelsetbio
- NucleicRenderer - Class in org.jmol.renderbio
-
extends CartoonRenderer for nucleics
- NucleicRenderer() - Constructor for class org.jmol.renderbio.NucleicRenderer
- nucleusX - Variable in class jspecview.source.JDXDataObject
- nucleusY - Variable in class jspecview.source.JDXDataObject
- nullDeletedAtoms - Static variable in class org.jmol.viewer.Viewer
- nullPeakInfo - Static variable in class jspecview.common.PeakInfo
- nullString - Variable in class javajs.util.CifDataParser
-
string to return for CIF data value .
- NUM_OVERSHOOT_BYTES - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- number - Variable in class jme.JME
- numberAtoms() - Method in class jme.JMEmol
- numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptError
- numCached - Variable in class org.jmol.modelset.BondCollection
- numSet - Variable in class org.jmol.modelset.MeasurementPending
- numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- nUnnamed - Variable in class org.jmol.shape.MeshCollection
- nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
- NWChemReader - Class in org.jmol.adapter.readers.quantum
-
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
- NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
- nX - Variable in class org.jmol.quantum.QuantumCalculation
- nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
- nY - Variable in class org.jmol.quantum.QuantumCalculation
- nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
- nZ - Variable in class org.jmol.quantum.QuantumCalculation
O
- o(int, Object) - Static method in class org.jmol.script.T
- o(String, Object) - Static method in class org.jmol.i18n.GT
- oabc - Variable in class org.jmol.jvxl.data.VolumeData
- oabc - Variable in class org.jmol.util.MeshSurface
- obFreq - Variable in class jspecview.export.AMLExporter
- obFreq - Variable in class jspecview.export.CMLExporter
- obFreq - Variable in class jspecview.source.AnIMLReader
- obj - Static variable in class org.jmol.script.T
- OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
- OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
- OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
- OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
- OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
- OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
- OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
- OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
- object - Static variable in class org.jmol.script.T
- objectNameParameter(int) - Method in class org.jmol.script.ScriptParam
- objects - Variable in class org.jmol.shape.TextShape
- obNucleus - Variable in class jspecview.export.AMLExporter
- obNucleus - Variable in class jspecview.export.CMLExporter
- obNucleus - Variable in class jspecview.source.AnIMLReader
- OBSCURE - Enum constant in enum class jspecview.common.ScriptToken
- obscureTitleFromUser - Variable in class jspecview.common.JSViewer
- oc - Variable in class org.jmol.adapter.writers.CMLWriter
- oc - Variable in class org.jmol.util.JSONWriter
- OC - Class in javajs.util
-
A generic output method.
- OC() - Constructor for class javajs.util.OC
- OC(String) - Constructor for class javajs.util.OC
- occupancies - Variable in class org.jmol.modelset.AtomCollection
- occupancy - Static variable in class org.jmol.script.T
- OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
- OdysseyReader - Class in org.jmol.adapter.readers.spartan
- OdysseyReader() - Constructor for class org.jmol.adapter.readers.spartan.OdysseyReader
- off - Static variable in class org.jmol.script.T
- OFF - Enum constant in enum class jspecview.common.IntegralData.IntMode
- officialRelease - Static variable in class org.jmol.viewer.JC
- offset - Static variable in class org.jmol.script.T
- offset - Variable in class org.jmol.util.MeshSurface
- offset(BS, int, int) - Static method in class org.jmol.util.BSUtil
-
offset the bitset in place by the specified number of bits starting at a given position
- OFFSET - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
- offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
- offsetPt - Variable in class org.jmol.shapespecial.Dipole
- offsets - Variable in class org.jmol.modelsetbio.Monomer
- offsets - Variable in class org.jmol.shape.Labels
- offsetside - Static variable in class org.jmol.script.T
- offsetSide - Variable in class org.jmol.shapespecial.Dipole
- offsetX - Variable in class org.jmol.modelset.Text
- offsetY - Variable in class org.jmol.modelset.Text
- ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
- OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
- OLIVE - Static variable in class org.jmol.util.C
- omega - Static variable in class org.jmol.script.T
- on - Static variable in class org.jmol.script.T
- ON - Enum constant in enum class jspecview.common.IntegralData.IntMode
- once - Static variable in class org.jmol.script.T
- ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
- ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
- onFailure(Throwable) - Method in class jme.JMEUtil.JSME_RunAsyncCallback
- onFailure(Throwable) - Method in interface jme.JMEUtil.RunAsyncCallback
-
Called when, for some reason, the necessary code cannot be loaded.
- onFailure(Throwable) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
-
Called when, for some reason, the necessary code cannot be loaded.
- onFocus() - Method in class jspecview.js2d.JsDialog
- only - Static variable in class org.jmol.script.T
- onSuccess() - Method in interface jme.JMEUtil.RunAsyncCallback
-
Called once the necessary code for it has been loaded.
- onSuccess(String) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
-
Called once the necessary code for it has been loaded.
- onWarning(String) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
- oops(Exception) - Method in class org.jmol.minimize.MinimizationThread
- oops(Exception) - Method in class org.jmol.navigate.Navigator
- oops(Exception) - Method in class org.jmol.thread.JmolThread
- opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
- opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
- opAnd - Static variable in class org.jmol.script.T
- opAND - Static variable in class org.jmol.script.T
- opaque - Static variable in class org.jmol.script.T
- OPAQUE_MASK - Static variable in class org.jmol.util.C
- open() - Method in class org.jmol.console.ScriptEditor
- openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
- openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
- openBufferedReader(String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
- openConnection(URL) - Method in class javajs.util.AjaxURLStreamHandler
- openDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String) - Method in class jspecview.common.JSViewer
- openDocument(SB) - Static method in class javajs.util.XmlUtil
- openDocument(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
- openDOM(Object) - Method in class org.jmol.api.JmolViewer
- openDOM(Object) - Method in class org.jmol.viewer.Viewer
-
applet DOM method -- does not preserve state
- openExportChannel(double, String, boolean) - Method in class org.jmol.viewer.Viewer
- openFile(String) - Method in class jspecview.appletjs.JSVApplet
-
possibly called from JSmolJSV.js upon start up
- openFile(String) - Method in class org.jmol.api.JmolViewer
- openFile(String) - Method in class org.jmol.util.GenericApplet
-
possibly called from JSmolApplet.js upon start up
- openFile(String) - Method in class org.jmol.viewer.Viewer
-
for JmolSimpleViewer -- external applications only (and no-script JavaScript)
- openFile(String, boolean) - Method in class jspecview.common.JSViewer
-
Opens and displays a file
- openFileAsync(String) - Method in class org.jmol.api.JmolViewer
- openFileAsync(String, int, String) - Method in interface org.jmol.api.JmolScriptManager
- openFileAsync(String, int, String) - Method in class org.jmol.script.ScriptManager
-
From file dropping.
- openFileAsyncSpecial(String, int) - Method in interface javajs.api.JSInterface
- openFileAsyncSpecial(String, int) - Method in class jspecview.appletjs.JSVApplet
- openFileAsyncSpecial(String, int) - Method in class jspecview.common.JSViewer
- openFileAsyncSpecial(String, int) - Method in class org.jmol.api.JmolViewer
- openFileAsyncSpecial(String, int) - Method in class org.jmol.util.GenericApplet
- openFileAsyncSpecial(String, int) - Method in class org.jmol.viewer.Viewer
-
opens a file as a model, a script, or a surface via the creation of a script that is queued.
- openFileAsyncSpecialType(String, int, String) - Method in interface javajs.api.JSInterface
- openFileAsyncSpecialType(String, int, String) - Method in class jspecview.appletjs.JSVApplet
- openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.api.JmolViewer
- openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.util.GenericApplet
- openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.viewer.Viewer
- openFileFromDialog(boolean, boolean, String, String) - Method in class jspecview.common.JSViewer
- openFiles(String[]) - Method in class org.jmol.api.JmolViewer
- openFiles(String[]) - Method in class org.jmol.viewer.Viewer
-
for JmolSimpleViewer -- external applications only
- openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
- openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
- openReader(String, Object) - Method in class org.jmol.api.JmolViewer
-
Opens the file and creates the model set, given the reader.
- openReader(String, String, Object) - Method in class org.jmol.api.JmolViewer
-
Opens the file and creates the model set, given the reader.
- openReader(String, String, Object) - Method in class org.jmol.viewer.Viewer
-
Opens the file, given an already-created reader.
- openSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
- openStringInline(String) - Method in class org.jmol.api.JmolViewer
- openStringInline(String) - Method in class org.jmol.viewer.Viewer
-
only used by file dropper.
- openStringInlineParamsAppend(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
-
Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
- openTag(SB, String) - Static method in class javajs.util.XmlUtil
- openTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- openTagAttr(SB, String, Object[]) - Static method in class javajs.util.XmlUtil
- openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
- opEQ - Static variable in class org.jmol.script.T
- operations - Variable in class org.jmol.symmetry.SpaceGroup
- opGE - Static variable in class org.jmol.script.T
- opGT - Static variable in class org.jmol.script.T
- opIf - Static variable in class org.jmol.script.T
- opIsLong - Variable in class org.jmol.symmetry.SymmetryOperation
- opLE - Static variable in class org.jmol.script.T
- opLIKE - Static variable in class org.jmol.script.T
- opLT - Static variable in class org.jmol.script.T
- opNE - Static variable in class org.jmol.script.T
- opNot - Static variable in class org.jmol.script.T
- opOr - Static variable in class org.jmol.script.T
- oPt - Variable in class org.jmol.script.ScriptMathProcessor
- OptimadeReader - Class in org.jmol.adapter.readers.xtal
-
A (preliminary) reader for OPTIMADE resources.
- OptimadeReader() - Constructor for class org.jmol.adapter.readers.xtal.OptimadeReader
- optimize2D - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- optionKey - Variable in class jspecview.dialog.JSVDialog
- optionKey - Variable in class jspecview.java.AwtDialog
- optionKey - Variable in class jspecview.js2d.JsDialog
- options - Variable in class jspecview.common.PanelData
- options - Variable in class jspecview.dialog.JSVDialog
- options - Variable in class jspecview.java.AwtDialog
- options - Variable in class jspecview.js2d.JsDialog
- options - Static variable in class org.jmol.script.T
- options - Variable in class org.jmol.shapespecial.Ellipsoid
- options(String) - Method in class jme.JME
- optionsSaved - Variable in class jspecview.common.PanelData
- opToggle - Static variable in class org.jmol.script.T
- optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- optParameterAsString(int) - Method in class org.jmol.script.ScriptParam
- opXor - Static variable in class org.jmol.script.T
- or(BS) - Method in class javajs.util.BS
-
Performs a logical OR of this bit set with the bit set argument.
- ORANGE - Static variable in class org.jmol.util.C
- orbital - Static variable in class org.jmol.script.T
- orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- Orbitals - Class in org.openscience.jmol.app.webexport
- Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
- orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
- orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- OrcaReader - Class in org.jmol.adapter.readers.quantum
-
Reads ORCA input and output files
- OrcaReader - Class in org.jmol.adapter.readers.simple
-
Reads ORCA input and output files
- OrcaReader() - Constructor for class org.jmol.adapter.readers.quantum.OrcaReader
- OrcaReader() - Constructor for class org.jmol.adapter.readers.simple.OrcaReader
- order - Variable in class org.jmol.adapter.smarter.Bond
- order - Variable in class org.jmol.minimize.MinBond
- order - Variable in class org.jmol.util.Edge
- ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
- ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_HEX - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_QUAD - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_QUINT - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PYMOL_MULT - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PYMOL_SINGLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_STEREO_EITHER - Static variable in class org.jmol.api.JmolAdapter
- ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
- ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
- ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
- org.apache.tools.bzip2 - package org.apache.tools.bzip2
- org.jmol.adapter.readers.cif - package org.jmol.adapter.readers.cif
- org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
- org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
- org.jmol.adapter.readers.pdb - package org.jmol.adapter.readers.pdb
- org.jmol.adapter.readers.pymol - package org.jmol.adapter.readers.pymol
- org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
- org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
- org.jmol.adapter.readers.spartan - package org.jmol.adapter.readers.spartan
- org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
- org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
- org.jmol.adapter.smarter - package org.jmol.adapter.smarter
- org.jmol.adapter.writers - package org.jmol.adapter.writers
- org.jmol.api - package org.jmol.api
- org.jmol.api.js - package org.jmol.api.js
- org.jmol.appletjs - package org.jmol.appletjs
- org.jmol.atomdata - package org.jmol.atomdata
- org.jmol.awt - package org.jmol.awt
- org.jmol.awtjs - package org.jmol.awtjs
- org.jmol.awtjs.swing - package org.jmol.awtjs.swing
- org.jmol.awtjs2d - package org.jmol.awtjs2d
- org.jmol.bspt - package org.jmol.bspt
-
Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
- org.jmol.c - package org.jmol.c
- org.jmol.console - package org.jmol.console
- org.jmol.consolejs - package org.jmol.consolejs
- org.jmol.dialog - package org.jmol.dialog
- org.jmol.dssx - package org.jmol.dssx
- org.jmol.export - package org.jmol.export
- org.jmol.g3d - package org.jmol.g3d
-
Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
- org.jmol.geodesic - package org.jmol.geodesic
- org.jmol.i18n - package org.jmol.i18n
- org.jmol.image - package org.jmol.image
- org.jmol.inchi - package org.jmol.inchi
- org.jmol.io - package org.jmol.io
- org.jmol.jsv - package org.jmol.jsv
- org.jmol.jvxl.api - package org.jmol.jvxl.api
- org.jmol.jvxl.calc - package org.jmol.jvxl.calc
- org.jmol.jvxl.data - package org.jmol.jvxl.data
- org.jmol.jvxl.readers - package org.jmol.jvxl.readers
- org.jmol.minimize - package org.jmol.minimize
- org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
- org.jmol.modelkit - package org.jmol.modelkit
- org.jmol.modelset - package org.jmol.modelset
- org.jmol.modelsetbio - package org.jmol.modelsetbio
- org.jmol.multitouch - package org.jmol.multitouch
- org.jmol.multitouch.jni - package org.jmol.multitouch.jni
- org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
- org.jmol.navigate - package org.jmol.navigate
- org.jmol.popup - package org.jmol.popup
- org.jmol.quantum - package org.jmol.quantum
- org.jmol.quantum.mo - package org.jmol.quantum.mo
- org.jmol.render - package org.jmol.render
- org.jmol.renderbio - package org.jmol.renderbio
- org.jmol.rendercgo - package org.jmol.rendercgo
- org.jmol.renderspecial - package org.jmol.renderspecial
- org.jmol.rendersurface - package org.jmol.rendersurface
- org.jmol.script - package org.jmol.script
- org.jmol.scriptext - package org.jmol.scriptext
- org.jmol.shape - package org.jmol.shape
- org.jmol.shapebio - package org.jmol.shapebio
- org.jmol.shapecgo - package org.jmol.shapecgo
- org.jmol.shapespecial - package org.jmol.shapespecial
- org.jmol.shapesurface - package org.jmol.shapesurface
- org.jmol.smiles - package org.jmol.smiles
-
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
- org.jmol.symmetry - package org.jmol.symmetry
- org.jmol.thread - package org.jmol.thread
- org.jmol.translation - package org.jmol.translation
- org.jmol.util - package org.jmol.util
- org.jmol.viewer - package org.jmol.viewer
- org.jmol.viewer.binding - package org.jmol.viewer.binding
- org.molecularplayground - package org.molecularplayground
- org.openscience.jmol.app - package org.openscience.jmol.app
- org.openscience.jmol.app.janocchio - package org.openscience.jmol.app.janocchio
- org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
- org.openscience.jmol.app.jmolpanel.console - package org.openscience.jmol.app.jmolpanel.console
- org.openscience.jmol.app.jsonkiosk - package org.openscience.jmol.app.jsonkiosk
- org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
- org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
- org.openscience.jvxl - package org.openscience.jvxl
- org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
- org.qcschema - package org.qcschema
- orientation - Variable in class org.jmol.modelset.Model
- orientation - Static variable in class org.jmol.script.T
- Orientation - Class in org.jmol.modelset
- Orientation(Viewer, boolean, float[]) - Constructor for class org.jmol.modelset.Orientation
- origin - Variable in class jspecview.export.AMLExporter
- origin - Variable in class jspecview.export.CMLExporter
- origin - Variable in class jspecview.source.JDXHeader
- origin - Variable in class jspecview.source.AnIMLReader
- origin - Variable in class org.jmol.jvxl.data.VolumeData
- origin - Variable in class org.jmol.jvxl.readers.Parameters
- origin - Static variable in class org.jmol.script.T
- origin - Variable in class org.jmol.shapespecial.Dipole
- originBohr - Variable in class org.jmol.quantum.QuantumCalculation
- originPoint - Variable in class org.jmol.shape.Axes
- OS_AMIGA - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_ATARI - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_CPM - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_MACOS - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_MSDOS - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_OS2 - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_QDOS - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_RISCOS - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_TOPS20 - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_UNIX - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_UNKNOWN - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_VMCMS - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_VMS - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_WIN32 - Static variable in class com.jcraft.jzlib.GZIPHeader
- OS_ZSYSTEM - Static variable in class com.jcraft.jzlib.GZIPHeader
- out - Variable in class javajs.img.ImageEncoder
- out - Variable in class javajs.util.BinaryDocument
- out - Variable in class jspecview.export.AMLExporter
- out - Variable in class jspecview.export.CMLExporter
- out - Variable in class jspecview.export.SVGExporter
- out - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- out - Variable in class org.jmol.export.___Exporter
- out - Variable in class org.jmol.jvxl.readers.JvxlReader
- out - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- out - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- out - Static variable in class org.jmol.script.T
- output - Variable in class org.jmol.console.GenericConsole
- output(String) - Method in class org.jmol.console.ScriptEditor
- output(String) - Method in class org.jmol.export.___Exporter
- output(String) - Method in class org.jmol.export._StlExporter
- output(String) - Method in class org.jmol.util.GenericApplet
- output(T3) - Method in class org.jmol.export.___Exporter
- output(T3) - Method in class org.jmol.export._IdtfExporter
- output(T3) - Method in class org.jmol.export._MayaExporter
- output(T3) - Method in class org.jmol.export._ObjExporter
- output(T3) - Method in class org.jmol.export._PovrayExporter
- output(T3) - Method in class org.jmol.export._TachyonExporter
- output(T3) - Method in class org.jmol.export._VrmlExporter
- output(T3) - Method in class org.jmol.export.JSExporter
- outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
- outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
- outputAttr(String, float, float, float) - Method in class org.jmol.export._StlExporter
- outputAttr(String, float, float, float) - Method in class org.jmol.export._VrmlExporter
- outputAttr(String, float, float, float) - Method in class org.jmol.export._X3dExporter
- outputAttrPt(String, T3) - Method in class org.jmol.export._StlExporter
- outputAttrPt(String, T3) - Method in class org.jmol.export._VrmlExporter
- outputAttrPt(String, T3) - Method in class org.jmol.export._X3dExporter
- outputBuffer - Variable in class org.jmol.script.ScriptContext
- outputBuffer - Variable in class org.jmol.script.ScriptEval
- outputBytes(byte[]) - Method in class javajs.util.AjaxURLConnection
- outputChildClose() - Method in class org.jmol.export._StlExporter
- outputChildClose() - Method in class org.jmol.export._VrmlExporter
- outputChildClose() - Method in class org.jmol.export._X3dExporter
- outputChildShapeClose() - Method in class org.jmol.export._VrmlExporter
- outputChildShapeClose() - Method in class org.jmol.export._X3dExporter
- outputChildShapeStart() - Method in class org.jmol.export._VrmlExporter
- outputChildShapeStart() - Method in class org.jmol.export._X3dExporter
- outputChildStart() - Method in class org.jmol.export._StlExporter
- outputChildStart() - Method in class org.jmol.export._VrmlExporter
- outputChildStart() - Method in class org.jmol.export._X3dExporter
- outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
- outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._StlExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._X3dExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
- outputCloseTag() - Method in class org.jmol.export._VrmlExporter
- outputCloseTag() - Method in class org.jmol.export._X3dExporter
- outputColorIndices(int[][], int, BS, int, Map<Short, Integer>, short[], short[]) - Method in class org.jmol.export._VrmlExporter
- outputColors(Lst<Short>) - Method in class org.jmol.export._VrmlExporter
- outputComment(String) - Method in class org.jmol.export.___Exporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export.__CartesianExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._IdtfExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._MayaExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._VrmlExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export.JSExporter
- outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
- outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
- outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._IdtfExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._MayaExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._ObjExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._VrmlExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.JSExporter
- outputCylinderChildScaled(short, byte) - Method in class org.jmol.export._VrmlExporter
- outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._PovrayExporter
- outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._TachyonExporter
- outputDefChildFaceSet(String) - Method in class org.jmol.export._VrmlExporter
- outputDefChildFaceSet(String) - Method in class org.jmol.export._X3dExporter
- outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._PovrayExporter
- outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._TachyonExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.__CartesianExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._IdtfExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._MayaExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._ObjExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._VrmlExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.JSExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export.JSExporter
- outputFaceSetClose() - Method in class org.jmol.export._VrmlExporter
- outputFaceSetClose() - Method in class org.jmol.export._X3dExporter
- outputFaceSetStart() - Method in class org.jmol.export._VrmlExporter
- outputFaceSetStart() - Method in class org.jmol.export._X3dExporter
- outputFileName - Variable in class org.jmol.dialog.Dialog
- outputFooter() - Method in class org.jmol.export.___Exporter
- outputFooter() - Method in class org.jmol.export._IdtfExporter
- outputFooter() - Method in class org.jmol.export._TachyonExporter
- outputFooter() - Method in class org.jmol.export._VrmlExporter
- outputFooter() - Method in class org.jmol.export._X3dExporter
- outputFooter() - Method in class org.jmol.export.JSExporter
- outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._StlExporter
- outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
- outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._X3dExporter
- outputHeader() - Method in class org.jmol.export.___Exporter
- outputHeader() - Method in class org.jmol.export._IdtfExporter
- outputHeader() - Method in class org.jmol.export._MayaExporter
- outputHeader() - Method in class org.jmol.export._ObjExporter
- outputHeader() - Method in class org.jmol.export._PovrayExporter
- outputHeader() - Method in class org.jmol.export._StlExporter
- outputHeader() - Method in class org.jmol.export._TachyonExporter
- outputHeader() - Method in class org.jmol.export._VrmlExporter
- outputHeader() - Method in class org.jmol.export._X3dExporter
- outputHeader() - Method in class org.jmol.export.JSExporter
- outputIndices(int[][], int[], int, BS, int) - Method in class org.jmol.export.__CartesianExporter
- outputInitialTransform() - Method in class org.jmol.export._VrmlExporter
- outputJmolPerspective() - Method in class org.jmol.export.___Exporter
- OutputManagerAwt - Class in org.jmol.viewer
- OutputManagerAwt() - Constructor for class org.jmol.viewer.OutputManagerAwt
- OutputManagerJS - Class in org.jmol.viewer
- OutputManagerJS() - Constructor for class org.jmol.viewer.OutputManagerJS
- outputNormals(Lst<String>) - Method in class org.jmol.export._VrmlExporter
- outputQuaternionFrame(P3, P3, P3, P3, float, float, float) - Method in class org.jmol.export._VrmlExporter
- outputRotation(A4) - Method in class org.jmol.export._StlExporter
- outputRotation(A4) - Method in class org.jmol.export._VrmlExporter
- outputRotation(A4) - Method in class org.jmol.export._X3dExporter
- outputShapeClose() - Method in class org.jmol.export._VrmlExporter
- outputShapeClose() - Method in class org.jmol.export._X3dExporter
- outputShapeStart() - Method in class org.jmol.export._VrmlExporter
- outputShapeStart() - Method in class org.jmol.export._X3dExporter
- outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export.__CartesianExporter
- outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export._VrmlExporter
- outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
- outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
- outputString(String) - Method in class javajs.util.AjaxURLConnection
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.___Exporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._IdtfExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._MayaExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._PovrayExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._TachyonExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.JSExporter
- outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
- outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export.__CartesianExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._IdtfExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._MayaExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._ObjExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._VrmlExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._X3dExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export.JSExporter
- outputToFile(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
- outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._VrmlExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__CartesianExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._IdtfExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._MayaExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._PovrayExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._TachyonExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._X3dExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.JSExporter
- outputUseChildClose(String) - Method in class org.jmol.export._VrmlExporter
- outputUseChildClose(String) - Method in class org.jmol.export._X3dExporter
- outputVertex(T3, T3) - Method in class org.jmol.export.___Exporter
- outputVertex(T3, T3) - Method in class org.jmol.export._PovrayExporter
- outputVertex(T3, T3) - Method in class org.jmol.export._TachyonExporter
- outputVertices(T3[], int, T3) - Method in class org.jmol.export.___Exporter
- outSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- OUTSOCKET - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OUTSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- oValue(Object) - Static method in class org.jmol.script.SV
- overlaps(double, double) - Method in class jspecview.common.Measurement
- OVERLAY - Enum constant in enum class jspecview.common.ScriptToken
- OVERLAY_DIALOG - Static variable in class jspecview.common.JSViewer
- OVERLAY_OFFSET - Static variable in class jspecview.common.JSViewer
- OverlayLegend - Enum constant in enum class jspecview.common.Annotation.AType
- OverlayLegendDialog - Class in jspecview.dialog
-
Dialog for showing the legend or key for overlaid plots in a
JSVPanel
. - OverlayLegendDialog() - Constructor for class jspecview.dialog.OverlayLegendDialog
- OVERLAYSTACKED - Enum constant in enum class jspecview.common.ScriptToken
- owner - Variable in class jspecview.export.AMLExporter
- owner - Variable in class jspecview.export.CMLExporter
- owner - Variable in class jspecview.source.JDXHeader
- owner - Variable in class jspecview.source.AnIMLReader
P
- P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
- P - Static variable in class org.jmol.quantum.QS
- P_CHECK - Static variable in class org.jmol.util.MeshSurface
- P_CONTOUR - Static variable in class org.jmol.util.MeshSurface
- P_EXPLICIT_COLOR - Static variable in class org.jmol.util.MeshSurface
- P2nReader - Class in org.jmol.adapter.readers.pdb
-
P2N file reader.
- P2nReader() - Constructor for class org.jmol.adapter.readers.pdb.P2nReader
- P3 - Class in javajs.util
-
A 3 element point that is represented by single precision floating point x,y,z coordinates.
- P3() - Constructor for class javajs.util.P3
- P3i - Class in javajs.util
-
A 3 element point that is represented by signed integer x,y,z coordinates.
- P3i() - Constructor for class javajs.util.P3i
- p3Screens - Variable in class org.jmol.render.AxesRenderer
- p3Screens - Variable in class org.jmol.render.BbcageRenderer
- p3Screens - Variable in class org.jmol.render.UccageRenderer
- p3Screens - Variable in class org.jmol.render.MeshRenderer
- P4 - Class in javajs.util
-
A 4 element point that is represented by single precision floating point x,y,z,w coordinates.
- P4() - Constructor for class javajs.util.P4
- PAC - Enum constant in enum class jspecview.common.ExportType
- pack() - Method in interface jspecview.api.PlatformDialog
- pack() - Method in class org.jmol.awtjs.swing.JDialog
- packageJSON(String, String) - Static method in class javajs.util.PT
- packed - Static variable in class org.jmol.script.T
- PAGE_EXISTS - Static variable in class jspecview.common.JSViewer
- paint(Graphics) - Method in class jme.JME
- paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
- paintComponent(Graphics) - Method in class jspecview.java.AwtPanel
-
Overrides paintComponent in class JPanel in order to draw the spectrum
- paintComponent(Object) - Method in interface jspecview.api.JSVPanel
- paintComponent(Object) - Method in class jspecview.java.AwtPanel
- paintComponent(Object) - Method in class jspecview.js2d.JsPanel
-
Overrides paintComponent in class JPanel in order to draw the spectrum
- paintMolecularArea(BufferedImage) - Method in class jme.JME
- PAL - Enum Class in org.jmol.c
-
Enum for animation mode.
- PALETTE_ALTLOC - Static variable in enum class org.jmol.c.PAL
- PALETTE_AMINO - Static variable in enum class org.jmol.c.PAL
- PALETTE_CHAIN - Static variable in enum class org.jmol.c.PAL
- PALETTE_CPK - Static variable in enum class org.jmol.c.PAL
- PALETTE_ENERGY - Static variable in enum class org.jmol.c.PAL
- PALETTE_FIXEDTEMP - Static variable in enum class org.jmol.c.PAL
- PALETTE_FORMAL_CHARGE - Static variable in enum class org.jmol.c.PAL
- PALETTE_GROUP - Static variable in enum class org.jmol.c.PAL
- PALETTE_INSERTION - Static variable in enum class org.jmol.c.PAL
- PALETTE_JMOL - Static variable in enum class org.jmol.c.PAL
- PALETTE_MOLECULE - Static variable in enum class org.jmol.c.PAL
- PALETTE_MONOMER - Static variable in enum class org.jmol.c.PAL
- PALETTE_NONE - Static variable in enum class org.jmol.c.PAL
- PALETTE_NUCLEIC - Static variable in enum class org.jmol.c.PAL
- PALETTE_PARTIAL_CHARGE - Static variable in enum class org.jmol.c.PAL
- PALETTE_POLYMER - Static variable in enum class org.jmol.c.PAL
- PALETTE_PROPERTY - Static variable in enum class org.jmol.c.PAL
- PALETTE_RASMOL - Static variable in enum class org.jmol.c.PAL
- PALETTE_SHAPELY - Static variable in enum class org.jmol.c.PAL
- PALETTE_STRAIGHTNESS - Static variable in enum class org.jmol.c.PAL
- PALETTE_STRUCTURE - Static variable in enum class org.jmol.c.PAL
- PALETTE_SURFACE - Static variable in enum class org.jmol.c.PAL
- PALETTE_TEMP - Static variable in enum class org.jmol.c.PAL
- PALETTE_TYPE - Static variable in enum class org.jmol.c.PAL
- PALETTE_VARIABLE - Static variable in enum class org.jmol.c.PAL
- PALETTE_VOLATILE - Static variable in enum class org.jmol.c.PAL
- paletteID - Variable in class org.jmol.modelset.Atom
- paletteIDs - Variable in class org.jmol.shape.AtomShape
- palindrome - Static variable in class org.jmol.script.T
- panel() - Method in class org.openscience.jmol.app.webexport.Test
- PanelData - Class in jspecview.common
-
JSVPanel class draws a plot from the data contained a instance of a
Graph
. - PanelData(JSVPanel, JSViewer) - Constructor for class jspecview.common.PanelData
- PanelData.LinkMode - Enum Class in jspecview.common
- panelEvent(Object) - Method in interface jspecview.api.PanelListener
- panelEvent(Object) - Method in class jspecview.app.JSVApp
-
called by notifyPeakPickedListeners in JSVPanel
- panelEvent(Object) - Method in class jspecview.application.MainFrame
- PanelListener - Interface in jspecview.api
- panelNode - Variable in class jspecview.application.AwtTreeNode
- panelNode - Variable in class jspecview.tree.SimpleTreeNode
- PanelNode - Class in jspecview.common
- PanelNode(String, String, JDXSource, JSVPanel) - Constructor for class jspecview.common.PanelNode
- panelNodes - Variable in class jspecview.common.JSViewer
- paper - Variable in class jspecview.common.PrintLayout
-
The size of the paper to be printed on
- paperHeight - Variable in class jspecview.common.PrintLayout
- paperWidth - Variable in class jspecview.common.PrintLayout
- parabolicInterpolation(Coordinate[], int) - Static method in class jspecview.common.Coordinate
-
see https://ccrma.stanford.edu/~jos/sasp/Quadratic_Interpolation_Spectral_Peaks.html
- parallel - Static variable in class org.jmol.script.T
- PARAM_COUNT - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_M33 - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_M4 - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_OXYZ - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_SCALE - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_SLOP - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_STD - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_SUPERCELL - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_VAX - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_VBX - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_VCX - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_VCZ - Static variable in class org.jmol.util.SimpleUnitCell
- paramAsStr(int) - Method in class org.jmol.script.ScriptParam
- paramAsStr(int) - Method in class org.jmol.scriptext.ScriptExt
- parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptEval
- parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptEval
- parameterExpressionSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
- parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptEval
- parameterExpressionToken(int) - Method in class org.jmol.script.ScriptEval
- parameters - Variable in class jspecview.common.JSViewer
- parameters - Static variable in class org.jmol.script.T
- Parameters - Class in jspecview.common
- Parameters - Class in org.jmol.jvxl.readers
- Parameters() - Constructor for class jspecview.common.Parameters
- Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
- params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- params - Variable in class org.jmol.jvxl.readers.SurfaceReader
- params(int, int) - Method in class com.jcraft.jzlib.Deflater
- paramsCentroid - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- paramsLattice - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- paramTypes - Static variable in class org.jmol.script.T
- parBorU - Variable in class org.jmol.util.Tensor
- parent - Variable in class jspecview.source.JDXDataObject
- parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
- parent - Variable in class org.jmol.awtjs.swing.Component
- parentContext - Variable in class org.jmol.script.ScriptContext
- parse(String, boolean) - Method in class javajs.util.JSJSONParser
-
Could return Integer, Float, Boolean, String, Mapinvalid input: '<'String, Object>, Lst
- parseCartesianField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
- parseCartesianField() - Method in class org.jmol.adapter.readers.cif.CifReader
- parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
- parseDataBlockParameters(String[], String, String, int[], int[]) - Method in interface javajs.api.GenericCifDataParser
- parseDataBlockParameters(String[], String, String, int[], int[]) - Method in class javajs.util.CifDataParser
-
Process a data block, with or without a loop_.
- parsedContext - Variable in class org.jmol.console.ScriptEditor
- parsedData - Variable in class org.jmol.console.ScriptEditor
- parseDSV(String, double, double) - Static method in class jspecview.common.Coordinate
-
Parses data stored in x, y format
- parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseFloat() - Method in class org.jmol.jvxl.readers.JvxlReader
- parseFloat() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseFloat() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseFloat(String) - Static method in class javajs.util.PT
- parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.JvxlReader
- parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseFloatArray(String) - Static method in class javajs.util.PT
- parseFloatArrayBsData(String[], BS, float[]) - Static method in class org.jmol.util.Parser
- parseFloatArrayData(String[], float[]) - Static method in class javajs.util.PT
-
parses a string array for floats.
- parseFloatArrayDataN(String[], float[], int) - Static method in class javajs.util.PT
-
parses a string array for floats.
- parseFloatArrayFromMatchAndField(String, BS, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
-
the major lifter here.
- parseFloatArrayInfested(String[], float[]) - Static method in class javajs.util.PT
- parseFloatArrayNext(String, int[], float[], String, String) - Static method in class javajs.util.PT
- parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
- parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseFloatChecked(String, int, int[], boolean) - Static method in class javajs.util.PT
-
A float parser that is 30% faster than Float.parseFloat(x) and also accepts x.yD+-n
- parseFloatField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
- parseFloatField() - Method in class org.jmol.adapter.readers.cif.CifReader
- parseFloatFraction(String) - Static method in class javajs.util.PT
-
parse a float or "float/float"
- parseFloatNext(String, int[]) - Static method in class javajs.util.PT
- parseFloatRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
- parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseFloatRange(String, int, int[]) - Static method in class javajs.util.PT
- parseFloatStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseFloatStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
- parseFloatStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseFloatStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseFloatStrict(String) - Static method in class javajs.util.PT
- parseInitScript(String) - Method in class jspecview.common.JSViewer
-
Parses the JavaScript call parameters and executes them accordingly
- parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseInt() - Method in class org.jmol.jvxl.readers.JvxlReader
- parseInt() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseInt() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseInt(String) - Static method in class javajs.util.PT
- parseIntAt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseIntChecked(String, int, int[]) - Static method in class javajs.util.PT
- parseIntField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
- parseIntField() - Method in class org.jmol.adapter.readers.cif.CifReader
- parseIntFieldTok(byte) - Method in class org.jmol.adapter.readers.cif.BCIFReader
-
Get a specific column's item for this category on this row.
- parseIntFieldTok(byte) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- parseIntNext(String) - Method in class org.jmol.jvxl.readers.JvxlReader
- parseIntNext(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseIntNext(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseIntNext(String, int[]) - Static method in class javajs.util.PT
- parseIntRadix(String, int) - Static method in class javajs.util.PT
- parseIntRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseIntRange(String, int, int[]) - Static method in class javajs.util.PT
- parseIntStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseIntStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
- parseIntStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- parseIntStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- parseJSON(String) - Method in class org.jmol.viewer.Viewer
- parseJSONArray(String) - Method in class org.jmol.viewer.Viewer
- parseJSONMap(String) - Method in class org.jmol.viewer.Viewer
- parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.BCIFReader
-
This is the callback the that the MMCifReader and CifReader process.....() methods call initially.
- parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
-
sets up arrays and variables for tokenizer.getData() after the first tag of the loop has been checked.
- parseMap(String, boolean) - Method in class javajs.util.JSJSONParser
-
requires { "key":"value", "key":"value",....}
- parsePrecision(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Track the precision (count of y digits in "xx.yyyy") for setting cellSlop.
- parser - Variable in class jspecview.source.AnIMLReader
- Parser - Class in org.jmol.util
- Parser() - Constructor for class org.jmol.util.Parser
- parseScript(String, int) - Method in class org.jmol.console.ScriptEditor
- parseStringInfestedFloatArray(String, BS, float[]) - Static method in class org.jmol.util.Parser
-
parses a "dirty" string for floats.
- parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseToken(String) - Static method in class javajs.util.PT
- parseTokenChecked(String, int, int[]) - Static method in class javajs.util.PT
- parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseTokenNext(String, int[]) - Static method in class javajs.util.PT
- parseTokenRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseTokenRange(String, int, int[]) - Static method in class javajs.util.PT
- parseTokenStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseTrimmed(String) - Static method in class javajs.util.PT
- parseTrimmedAt(String, int) - Static method in class javajs.util.PT
- parseTrimmedChecked(String, int, int) - Static method in class javajs.util.PT
- parseTrimmedRange(String, int, int) - Static method in class javajs.util.PT
- PARTIAL_CHARGE - Enum constant in enum class org.jmol.c.PAL
- PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
- PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JC
- partialcharge - Static variable in class org.jmol.script.T
- partialCharge - Variable in class org.jmol.adapter.smarter.Atom
- partialCharge - Variable in class org.jmol.minimize.MinAtom
- partialdots - Static variable in class org.jmol.script.T
- particleradius - Static variable in class org.jmol.script.T
- pass2Flag01 - Variable in class org.jmol.g3d.Graphics3D
- pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
- pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- path - Static variable in class org.jmol.script.T
- path - Static variable in class org.openscience.jmol.app.janocchio.Nmr
- PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
AtomSetCollectionReader.readData() will close any BufferedReader
- PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
- pathforallfiles - Static variable in class org.jmol.script.T
- pathlength - Variable in class jspecview.export.AMLExporter
- pathlength - Variable in class jspecview.export.CMLExporter
- pathlength - Variable in class jspecview.source.AnIMLReader
- pattern - Static variable in class org.jmol.script.T
- PatternMatcher - Class in org.jmol.util
- PatternMatcher() - Constructor for class org.jmol.util.PatternMatcher
- PatternMatcher.JSPattern - Class in org.jmol.util
-
Super-simplified for JavaScript
- pause - Static variable in class org.jmol.script.T
- pauseExecution(boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- pauseExecution(boolean) - Method in class org.jmol.script.ScriptEval
- pauseScript(Viewer, boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
- pbuf - Variable in class org.jmol.g3d.Graphics3D
- pbufT - Variable in class org.jmol.g3d.Graphics3D
- pc - Variable in class org.jmol.script.ScriptContext
- pc - Variable in class org.jmol.script.ScriptEval
- pc - Variable in class org.jmol.util.MeshSurface
-
polygon count
- pc0 - Variable in class org.jmol.script.ScriptContext
- pcEnd - Variable in class org.jmol.script.ScriptContext
- pcResume - Variable in class org.jmol.script.ScriptEval
- pcs - Variable in class org.jmol.util.MeshSurface
-
polygon color index "colix" array
- pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- pd - Variable in class jspecview.app.GenericMouse
- pd() - Method in class jspecview.common.JSViewer
- pd() - Method in class jspecview.common.PanelNode
- pdb - Static variable in class org.jmol.script.T
- PDB_ANNOTATIONS - Static variable in class org.jmol.viewer.JC
- PDB_CARTOONS - Static variable in interface org.jmol.api.JmolScriptManager
- pdbaddhydrogens - Static variable in class org.jmol.script.T
- pdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
-
pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid.
- pdbgetheader - Static variable in class org.jmol.script.T
- pdbheader - Static variable in class org.jmol.script.T
- pdbID - Variable in class org.jmol.adapter.readers.cif.CifReader
- pdbID - Variable in class org.jmol.modelset.Model
- PdbReader - Class in org.jmol.adapter.readers.pdb
-
PDB file reader.
- PdbReader() - Constructor for class org.jmol.adapter.readers.pdb.PdbReader
- pdbsequential - Static variable in class org.jmol.script.T
- PDBWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
- PDBWriter() - Constructor for class org.jmol.adapter.writers.PDBWriter
- PDF - Enum constant in enum class jspecview.common.ExportType
- PDFCreator - Class in javajs.export
- PDFCreator() - Constructor for class javajs.export.PDFCreator
- PdfEncoder - Class in javajs.img
-
A relatively primitive PDF generator that just makes a document with an image in it.
- PdfEncoder() - Constructor for class javajs.img.PdfEncoder
- PDFWriter - Class in jspecview.common
-
A class that creates the PDF document specific to JSpecView using javajs.export.PDFCreator.
- PDFWriter() - Constructor for class jspecview.common.PDFWriter
- PEAK - Enum constant in enum class jspecview.common.ScriptToken
- PEAKCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
- peakCount - Variable in class jspecview.source.JDXSource
- PeakData - Class in jspecview.common
-
a data structure for peak lists
- PeakData(Annotation.AType, Spectrum) - Constructor for class jspecview.common.PeakData
- PeakInfo - Class in jspecview.common
- PeakInfo() - Constructor for class jspecview.common.PeakInfo
- PeakInfo(String) - Constructor for class jspecview.common.PeakInfo
- PeakList - Enum constant in enum class jspecview.common.Annotation.AType
- PEAKLIST - Enum constant in enum class jspecview.common.ScriptToken
- PeakListDialog - Class in jspecview.dialog
-
Dialog for managing the peak listing for a Spectrum within a GraphSet
- PeakListDialog() - Constructor for class jspecview.dialog.PeakListDialog
- peakListInterpolation - Variable in class jspecview.common.Parameters
- peakListThreshold - Variable in class jspecview.common.Parameters
- PeakPickEvent - Class in jspecview.common
- PeakPickEvent(Object, Coordinate, PeakInfo) - Constructor for class jspecview.common.PeakPickEvent
- peakTabColor - Variable in class jspecview.common.PanelData
- PEAKTABCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- peakTabsOn - Variable in class jspecview.common.PanelData
- PEAKTABSON - Enum constant in enum class jspecview.common.ScriptToken
- peek() - Method in class jspecview.source.XMLParser
- peekToken() - Method in interface javajs.api.GenericCifDataParser
- peekToken() - Method in class javajs.util.CifDataParser
-
Just look at the next token.
- per - Static variable in class org.jmol.script.T
- percent - Static variable in class org.jmol.script.T
- percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
- percentvdwatom - Static variable in class org.jmol.script.T
- period - Static variable in class org.jmol.script.T
- PeriodicVolumeFileReader - Class in org.jmol.jvxl.readers
- PeriodicVolumeFileReader() - Constructor for class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- perpendicular - Static variable in class org.jmol.script.T
- perper - Static variable in class org.jmol.script.T
- perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- perspectivedepth - Static variable in class org.jmol.script.T
- perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
- perspectivemodel - Static variable in class org.jmol.script.T
- perspectiveModel - Variable in class org.jmol.viewer.TransformManager
- perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
- perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
- PfaatBinding - Class in org.jmol.viewer.binding
- PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
- phase - Static variable in class org.jmol.script.T
- phi - Static variable in class org.jmol.script.T
- phongexponent - Static variable in class org.jmol.script.T
- PhosphorusMonomer - Class in org.jmol.modelsetbio
- PhosphorusMonomer() - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
- PhosphorusPolymer - Class in org.jmol.modelsetbio
- PICK - Enum constant in enum class org.jmol.c.CBK
- PICK_COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
- pickedMesh - Variable in class org.jmol.shape.MeshCollection
- pickedModel - Variable in class org.jmol.shape.MeshCollection
- pickedPt - Variable in class org.jmol.shape.MeshCollection
- pickedVertex - Variable in class org.jmol.shape.MeshCollection
- picking - Static variable in class org.jmol.script.T
- PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
- PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_LIGAND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MODEL - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
- PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
- PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
- PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MK_RESET - Static variable in class org.jmol.viewer.ActionManager
- PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
- PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
- PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SYMOP - Static variable in class org.jmol.viewer.ActionManager
- pickingspinrate - Static variable in class org.jmol.script.T
- pickingstyle - Static variable in class org.jmol.script.T
- PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
-
picking styles
- PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
- picklabel - Static variable in class org.jmol.script.T
- pidOf(Object) - Static method in enum class org.jmol.c.PAL
- ping() - Method in class jme.JME
- PINK - Static variable in class org.jmol.util.C
- pis - Variable in class org.jmol.util.MeshSurface
-
polygon indexes
- pivot - Static variable in class org.jmol.script.T
- pivot2 - Static variable in class org.jmol.script.T
- pixelLocation(Location) - Static method in class com.sparshui.common.Location
- pixels - Variable in class javajs.img.ImageEncoder
- PLAIN_MESSAGE - Static variable in class jspecview.dialog.DialogManager
- planarparam - Static variable in class org.jmol.script.T
- plane - Static variable in class org.jmol.script.T
- PLANE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- planeParameter(int, boolean) - Method in class org.jmol.script.ScriptParam
- planeValue(T) - Method in class org.jmol.script.ScriptParam
- Platform - Class in org.jmol.awt
- Platform - Class in org.jmol.awtjs
-
WebGL interface
- Platform - Class in org.jmol.awtjs2d
-
JavaScript 2D canvas version requires Ajax-based URL stream processing.
- Platform() - Constructor for class org.jmol.awt.Platform
- Platform() - Constructor for class org.jmol.awtjs.Platform
- Platform() - Constructor for class org.jmol.awtjs2d.Platform
- PlatformDialog - Interface in jspecview.api
- platformspeed - Static variable in class org.jmol.script.T
- PlatformViewer - Interface in org.jmol.api
- play - Static variable in class org.jmol.script.T
- playAudio(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
- playAudio(JSmolAppletObject, Map<String, Object>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- playAudio(Viewer, Map<String, Object>) - Method in class org.jmol.util.JmolAudio
-
WAV only for application
- playrev - Static variable in class org.jmol.script.T
- plLabel - Variable in class jspecview.source.AnIMLReader
- plot - Static variable in class org.jmol.script.T
- plot3d - Static variable in class org.jmol.script.T
- Plot3D - Class in org.jmol.shapesurface
- Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
- Plot3DRenderer - Class in org.jmol.rendersurface
- Plot3DRenderer() - Constructor for class org.jmol.rendersurface.Plot3DRenderer
- plotAreaColor - Variable in class jspecview.common.PanelData
- PLOTAREACOLOR - Enum constant in enum class jspecview.common.ScriptToken
- PLOTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- plotColors - Variable in class jspecview.common.ColorParameters
- PLOTCOLORS - Enum constant in enum class jspecview.common.ScriptToken
- plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
- plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.util.GData
- plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in interface org.jmol.api.JmolRendererInterface
- plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.export.Export3D
- plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.g3d.Graphics3D
- plotPixelClippedP3i(P3i) - Method in interface org.jmol.api.JmolRendererInterface
- plotPixelClippedP3i(P3i) - Method in class org.jmol.export.Export3D
- plotPixelClippedP3i(P3i) - Method in class org.jmol.g3d.Graphics3D
- plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
- plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.util.GData
- pluginFile - Variable in class org.openscience.jmol.app.JmolApp
- pluginFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- plus - Static variable in class org.jmol.script.T
- plusPlus - Static variable in class org.jmol.script.T
- pmesh - Static variable in class org.jmol.script.T
- Pmesh - Class in org.jmol.shapesurface
- Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
- PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
- PmeshRenderer - Class in org.jmol.rendersurface
- PmeshRenderer() - Constructor for class org.jmol.rendersurface.PmeshRenderer
- PMeshWriter - Class in org.jmol.shapesurface
-
A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
- PMeshWriter() - Constructor for class org.jmol.shapesurface.PMeshWriter
- PNG - Enum constant in enum class jspecview.common.ExportType
- pngBytes - Variable in class javajs.img.PngEncoder
- PngEncoder - Class in javajs.img
-
Modified by Bob Hanson hansonr@stolaf.edu to be a subclass of ImageEncoder and to use javajs.util.OutputChannel instead of just returning bytes.
- PngEncoder() - Constructor for class javajs.img.PngEncoder
- pngjCache - Variable in class org.jmol.viewer.FileManager
- PO - Class in org.jmol.translation
-
Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.
- PO() - Constructor for class org.jmol.translation.PO
- pocket - Static variable in class org.jmol.script.T
- point - Static variable in class org.jmol.script.T
- POINT - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- point3f - Static variable in class org.jmol.script.T
- Point3fi - Class in org.jmol.util
-
the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
- Point3fi() - Constructor for class org.jmol.util.Point3fi
- point4f - Static variable in class org.jmol.script.T
- pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
- pointer - Variable in class org.jmol.modelset.Text
- pointerPt - Variable in class org.jmol.modelset.Text
- pointgroup - Static variable in class org.jmol.script.T
- pointGroup - Variable in class org.jmol.modelset.AtomCollection
- pointgroupdistancetolerance - Static variable in class org.jmol.script.T
- pointgrouplineartolerance - Static variable in class org.jmol.script.T
- PointIterator - Class in org.jmol.bspt
- PointIterator() - Constructor for class org.jmol.bspt.PointIterator
- pointPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d, boolean) - Static method in class org.jmol.minimize.Util
-
calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
- points - Variable in class org.jmol.jvxl.readers.Parameters
- points - Variable in class org.jmol.modelset.MeasurementData
- points - Variable in class org.jmol.quantum.QuantumCalculation
- pointScale - Variable in class org.jmol.shapespecial.Polyhedron
- pointSize - Variable in class org.jmol.jvxl.data.JvxlData
- pointSize - Variable in class org.jmol.jvxl.readers.Parameters
- POINTSONLY - Enum constant in enum class jspecview.common.ScriptToken
- pointsperangstrom - Static variable in class org.jmol.script.T
- pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
- pointT - Variable in class org.jmol.render.FontLineShapeRenderer
- pointT2 - Variable in class org.jmol.render.FontLineShapeRenderer
- pointT3 - Variable in class org.jmol.render.FontLineShapeRenderer
- polarnitro - Variable in class jme.JME
- polygon - Static variable in class org.jmol.script.T
- POLYGON - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
- polygonCount0 - Variable in class org.jmol.util.MeshSurface
- polyhedra - Static variable in class org.jmol.script.T
- Polyhedra - Class in org.jmol.shapespecial
- Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
- POLYHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
- PolyhedraRenderer - Class in org.jmol.renderspecial
- PolyhedraRenderer() - Constructor for class org.jmol.renderspecial.PolyhedraRenderer
- Polyhedron - Class in org.jmol.shapespecial
- polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
- polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
- polyhedronStereo - Variable in class org.jmol.smiles.SmilesSearch
-
indicates that we have [XxPHn] with no connected atoms
- polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in interface org.jmol.api.SmilesMatcherInterface
- polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in class org.jmol.smiles.SmilesMatcher
-
Generate a topological SMILES string from a set of faces
- polymer - Static variable in class org.jmol.script.T
- POLYMER - Enum constant in enum class org.jmol.c.PAL
- polymerlength - Static variable in class org.jmol.script.T
- polySmiles - Variable in class org.jmol.shapespecial.Polyhedron
- polySmilesCenter - Variable in class org.jmol.smiles.SmilesGenerator
- pop - Static variable in class org.jmol.script.T
- popHoldRepaint(boolean, String) - Method in interface org.jmol.api.JmolRepaintManager
- popHoldRepaint(boolean, String) - Method in class org.jmol.render.RepaintManager
- popHoldRepaint(String) - Method in class org.jmol.api.JmolViewer
- popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
- popMatrix() - Method in class org.jmol.export._StlExporter
- popMatrix() - Method in class org.jmol.export._VrmlExporter
- popMatrix() - Method in class org.jmol.export._X3dExporter
- popStack(int) - Method in class org.jmol.viewer.StateManager
-
Remove the last item on the specified stack, and save the current state to the other stack provided that state is not null.
- popState() - Method in class org.jmol.util.CommandHistory
- popState() - Method in class org.jmol.viewer.Viewer
- populateVariables() - Method in class jspecview.source.AnIMLReader
- populationDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- PopulationDisplay - Class in org.openscience.jmol.app.janocchio
- PopulationDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.PopulationDisplay
-
Constructor
- PopupHelper - Interface in org.jmol.popup
- popupMenu - Variable in class org.jmol.popup.GenericPopup
- PopupResource - Class in org.jmol.popup
- PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
- port - Variable in class org.openscience.jmol.app.JmolApp
-
The data model.
- port - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- PORTRAIT - Static variable in class jspecview.common.JSViewer
- position - Variable in class jspecview.common.PrintLayout
-
The position of the graph on the paper ("center", "default", "fit to page")
- postByteArray(String, byte[]) - Method in interface javajs.api.BytePoster
- postByteArray(String, byte[]) - Static method in class jspecview.common.JSVFileManager
- postByteArray(String, byte[]) - Method in class jspecview.common.JSViewer
- postByteArray(String, byte[]) - Method in class org.jmol.viewer.FileManager
- postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
- povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
- povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
-
A dialog for controling the creation of a povray input file from a Chemframe and a display.
- PovrayDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Creates a dialog for getting info related to output frames in povray format.
- povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- PpmEncoder - Class in javajs.img
-
see http://netpbm.sourceforge.net/doc/ppm.html
- PpmEncoder() - Constructor for class javajs.img.PpmEncoder
- PqrReader - Class in org.jmol.adapter.readers.pdb
-
PQR file reader.
- PqrReader() - Constructor for class org.jmol.adapter.readers.pdb.PqrReader
- precision - Variable in class jspecview.common.MeasurementData
- precision - Variable in class jspecview.common.Parameters
- precision - Variable in class jspecview.common.ScaleData
-
The precision (number of decimal places) of the X and Y values
- precision - Variable in class jspecview.dialog.JSVDialog
- precision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
maximum of the decimal length of unit cell lengths and fractional coordinates
- precision - Variable in class org.jmol.adapter.writers.XtlWriter
- PrecisionRenderer - Class in org.jmol.g3d
-
Note added 4/2015 BH: Well, it turns out that the calculation of the intermediate pixel z value in all methods involving rasterization of lines is incorrect and has been incorrect since Jmol's inception.
- PrecisionRenderer() - Constructor for class org.jmol.g3d.PrecisionRenderer
- predefinedset - Static variable in class org.jmol.script.T
- predefinedStatic - Static variable in class org.jmol.viewer.JC
- predefinedVariable - Static variable in class org.jmol.viewer.JC
- preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PreferencesDialog - Class in jspecview.application
-
Dialog to change the preferences for the application.
- PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
- PreferencesDialog(Frame, JSViewer, String, boolean, DisplaySchemesProcessor) - Constructor for class jspecview.application.PreferencesDialog
-
Initialises the
PreferencesDialog
- PreferencesDialog(JmolPanel, JFrame, GuiMap, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- prepareBinaryOutput(SV) - Method in class org.jmol.scriptext.CmdExt
- prepareNextLine() - Method in class javajs.util.CifDataParser
-
sets the string for parsing to be from the next line when the token buffer is empty, and if ';' is at the beginning of that line, extends the string to include that full multiline string.
- preprocessSemiString() - Method in class javajs.util.CifDataParser
-
Encapsulate a multi-line ; ....
- preprocessString() - Method in class javajs.util.CifDataParser
-
Preprocess the string on a line starting with a semicolon to produce a string with a \1 ...
- preprocessString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
initial processing; returns a string bounded by \1
- preservestate - Static variable in class org.jmol.script.T
- preserveState - Variable in class org.jmol.modelset.AtomCollection
- preserveState - Variable in class org.jmol.viewer.GlobalSettings
- pressed(long, int, int, int, boolean) - Method in class jspecview.app.GenericMouse
- PRESSED - Static variable in class org.jmol.awtjs.Event
- pressedCount - Variable in class org.jmol.viewer.ActionManager
- prev - Static variable in class org.jmol.script.T
- prevBondCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
- PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
- PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
- previousMeshID - Variable in class org.jmol.shape.MeshCollection
- previousMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- previousView() - Method in class jspecview.common.PanelData
-
Displays the previous view zoomed
- previousX - Variable in class org.jmol.viewer.TransformManager
- previousY - Variable in class org.jmol.viewer.TransformManager
- prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
- primitiveToCrystal - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- print - Static variable in class org.jmol.script.T
- print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
added print command, so that it can be used by RasmolScriptHandler
- print(Graphics, PageFormat, int) - Method in class jspecview.java.AwtPanel
-
Implements method print in interface printable
- print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- print(Object, double, double, double, double, double, double, boolean, int) - Method in class jspecview.common.PanelData
- print(String) - Method in interface jspecview.api.JSVAppletInterface
- print(String) - Method in class jspecview.app.JSVApp
- print(String) - Method in class jspecview.appletjs.JSVApplet
- print(String) - Method in class jspecview.application.MainFrame
- print(String) - Method in class jspecview.common.JSViewer
- PRINT - Enum constant in enum class jspecview.common.ScriptToken
- printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
- printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- printFilePath(Object, int, int, String) - Method in class jspecview.common.PanelData
- printGraphPosition - Variable in class jspecview.common.PanelData
- printingFontName - Variable in class jspecview.common.PanelData
- printJobTitle - Variable in class jspecview.common.PanelData
- PrintLayout - Class in jspecview.common
-
PrintLayout
class stores all the information needed from thePrintLayoutDialog
- PrintLayout(PanelData) - Constructor for class jspecview.common.PrintLayout
- printPanel(PrintLayout, OutputStream, String) - Method in interface jspecview.api.JSVPanel
- printPanel(PrintLayout, OutputStream, String) - Method in class jspecview.java.AwtPanel
-
Send a print job of the spectrum to the default printer on the system
- printPanel(PrintLayout, OutputStream, String) - Method in class jspecview.js2d.JsPanel
-
Send a print job of the spectrum to the default printer on the system
- printPdf(GenericGraphics, PrintLayout) - Method in class jspecview.common.PanelData
-
from jspecview.export.PDFCreator -- does not use iText --
- printPDF(JSViewer, String) - Method in interface jspecview.export.ExportInterface
- printVersion(Object, int) - Method in class jspecview.common.PanelData
- privat - Static variable in class org.jmol.script.T
- privateFuncs - Variable in class org.jmol.script.ScriptContext
- privateFuncs - Variable in class org.jmol.script.ScriptEval
- privateKey - Variable in class org.jmol.export.___Exporter
- privateKey - Variable in class org.jmol.viewer.OutputManagerAwt
- privateKey - Variable in class org.jmol.viewer.OutputManagerJS
- probe - Static variable in class org.jmol.script.T
- probes - Variable in class org.jmol.jvxl.readers.Parameters
- probeValues - Variable in class org.jmol.jvxl.readers.Parameters
- probeValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- process - Static variable in class org.jmol.script.T
- process() - Method in class org.jmol.quantum.MepCalculation
- process() - Method in class org.jmol.quantum.MOCalculation
- process() - Method in class org.jmol.quantum.NciCalculation
- process() - Method in class org.jmol.quantum.QuantumCalculation
- process(int, boolean) - Method in class jspecview.source.AnIMLReader
-
Process the audit XML events
- process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
-
Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
- process(int, int, float) - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
- process(Lst<Spectrum>, Spectrum.IRMode) - Static method in class jspecview.common.Spectrum
- processAssemblyGenBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processAtom(Atom, String, char, String, int, int, char, boolean, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
-
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
- processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.BCIFReader
-
The primare method initiating this reader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.xtal.CmdfReader
- processBinaryDocument() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processBlock(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- processCellParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
-
unit cell parameters -- two options, so we use MOD 6
- processChange(List<TouchPoint>, TouchPoint) - Method in interface com.sparshui.gestures.Gesture
-
Process a touch point change in the gesture.
- processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
-
incorporates double-click gesture
- processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
a general name definition field.
- processCitationListBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
- processClick(String) - Method in class jspecview.dialog.DialogManager
-
processing click event from platform DialogManager
- processCompBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processEndMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- processEndTag(int) - Method in class jspecview.source.AnIMLReader
- processEntry() - Method in class org.jmol.adapter.readers.cif.MSCifParser
- processError(int) - Method in class com.sparshui.server.ServerToClientProtocol
-
Send an error message to the client.
- processErrors(String) - Method in class jspecview.source.AnIMLReader
- processEvent(int, int, int, int, long) - Method in class jspecview.app.GenericMouse
- processEvent(int, int, int, int, long) - Method in interface org.jmol.api.GenericMouseInterface
- processEvent(int, int, int, int, long) - Method in class org.jmol.awtjs2d.Mouse
- processEvent(int, Event) - Method in interface com.sparshui.client.SparshClient
-
This method processes events from the Gesture Server.
- processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
- processEvents(int, Lst<Event>) - Method in class com.sparshui.server.ServerToClientProtocol
-
Instruct the client to process the events that have been generated by a group.
- processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- processKey(int, int, boolean) - Method in class org.jmol.console.GenericConsole
- processKeyEvent(Object) - Method in interface javajs.api.JSInterface
- processKeyEvent(Object) - Method in interface jspecview.api.JSVPanel
- processKeyEvent(Object) - Method in class jspecview.app.GenericMouse
- processKeyEvent(Object) - Method in class jspecview.appletjs.JSVApplet
- processKeyEvent(Object) - Method in class jspecview.java.AwtPanel
- processKeyEvent(Object) - Method in class jspecview.js2d.JsPanel
- processKeyEvent(Object) - Method in interface org.jmol.api.GenericMouseInterface
- processKeyEvent(Object) - Method in class org.jmol.awtjs2d.Mouse
- processKeyEvent(Object) - Method in class org.jmol.util.GenericApplet
- processKeyEvent(Object) - Method in class org.jmol.viewer.Viewer
- processLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
-
processes loop_ blocks of interest or skips the data
- processLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
-
creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.
- processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- processMKPropertyItem(String, boolean) - Method in class org.jmol.modelkit.ModelKit
- processModelData(String, String, String, String, String, float, float, boolean) - Method in class jspecview.source.JDXReader
- processModelData(String, String, String, String, String, float, float, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- processModelData(String, String, String, String, String, float, float, boolean) - Method in interface org.jmol.api.JmolJDXMOLReader
- processMouseEvent(int, int, int, int, long) - Method in interface javajs.api.JSInterface
- processMouseEvent(int, int, int, int, long) - Method in interface jspecview.api.JSVPanel
- processMouseEvent(int, int, int, int, long) - Method in class jspecview.appletjs.JSVApplet
- processMouseEvent(int, int, int, int, long) - Method in class jspecview.common.JSViewer
-
called by JSmol.js mouse event
- processMouseEvent(int, int, int, int, long) - Method in class jspecview.java.AwtPanel
- processMouseEvent(int, int, int, int, long) - Method in class jspecview.js2d.JsPanel
-
called only by JavaScript
- processMouseEvent(int, int, int, int, long) - Method in class org.jmol.util.GenericApplet
- processMouseEvent(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
- processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.multitouch.ActionManagerMT
- processMultitouchEvent(int, int, int, int, P3, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
- processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.viewer.ActionManager
-
Specific to ActionManagerMT -- for processing SparshUI gestures
- processNextMeasure(MeasurementData, Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
- processNextMeasure(MeasurementData, Measurement) - Method in class org.jmol.modelset.MeasurementData
-
if this is the client, then this method is called by MeasurementData when a measurement is ready
- processNextMeasure(MeasurementData, Measurement) - Method in class org.jmol.shape.Measures
- processNioMessage(byte[]) - Method in class org.molecularplayground.MPJmolApp
- processNioMessage(byte[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- processNioMessage(byte[]) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- processPeakPickEvent(Object, boolean) - Method in class jspecview.common.JSViewer
-
this method is called as a result of the user clicking on a peak (eventObject instanceof PeakPickEvent) or from PEAK command execution
- processPoints() - Method in class org.jmol.quantum.MOCalculation
- processPoints() - Method in class org.jmol.quantum.QuantumCalculation
- processPt(T3) - Method in class org.jmol.quantum.QuantumCalculation
- ProcessRecord(String, String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
process _topol_node.id 1
- processRequest(SparshClient) - Method in class com.sparshui.client.ClientToServerProtocol
-
Processes a request from the Gesture Server
- processSemiString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Sets a multiline semicolon-eclipsed string to be parsed from the beginning, allowing for CIF 2.0-type prefixed text lines and removing line folding.
- processSequence() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
get canonical 1-letter DNA/RNA sequence code from 3-letter code.
- processService(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
-
service is expected to return a value in the "ret" key
- processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
- processStartMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
identifies ranges for HELIX and TURN
- processStructConnLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processStructOperListBlock(boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
identifies sheet ranges
- processStructSiteBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
identifies structure sites
- processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.CifReader
- processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
- processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processSymop(String, boolean) - Method in class org.jmol.modelkit.ModelKit
- processSync(String, int) - Method in interface org.jmol.api.JmolJSpecView
- processSync(String, int) - Method in class org.jmol.jsv.JSpecView
- processTableEvent(String, int, int, boolean) - Method in class jspecview.dialog.DialogManager
-
processing table cell click event from platform DialogManager; takes two hits in AWT -- one a row, the other a column
- processTag(int) - Method in class jspecview.source.AnIMLReader
-
Process the XML events.
- processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- processTwoPointGesture(float[][][]) - Method in interface javajs.api.JSInterface
- processTwoPointGesture(float[][][]) - Method in interface jspecview.api.JSVPanel
- processTwoPointGesture(float[][][]) - Method in class jspecview.app.GenericMouse
- processTwoPointGesture(float[][][]) - Method in class jspecview.appletjs.JSVApplet
- processTwoPointGesture(float[][][]) - Method in class jspecview.common.JSViewer
- processTwoPointGesture(float[][][]) - Method in class jspecview.java.AwtPanel
- processTwoPointGesture(float[][][]) - Method in class jspecview.js2d.JsPanel
- processTwoPointGesture(float[][][]) - Method in interface org.jmol.api.GenericMouseInterface
- processTwoPointGesture(float[][][]) - Method in class org.jmol.awtjs2d.Mouse
-
called by JSmol as processTwoPointGesture(canvas.touches);
- processTwoPointGesture(float[][][]) - Method in class org.jmol.util.GenericApplet
- processTwoPointGesture(float[][][]) - Method in class org.jmol.viewer.Viewer
- processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cif.CifReader
-
the PDB transformation matrix cartesian --> fractional key and field have been set already
- processUpdate(String) - Method in class org.jmol.util.JmolAudio
- processWindowClosing(String) - Method in class jspecview.dialog.DialogManager
-
processing window closing event from platform DialogManager
- processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
from eval write command only includes option to write set of files
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
the current state
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
- processXML(int, int) - Method in class jspecview.source.AnIMLReader
- processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.more.CDXReader
- processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- programInfo - Variable in class org.jmol.atomdata.AtomData
- projectOntoAxis(P3, P3, V3, V3) - Static method in class javajs.util.Measure
-
project point onto a line containing ptA and having axis unitVector axisUnitVector, returning the result in point and a vector from ptA to pt in vectorProjection
- prompt - Static variable in class org.jmol.script.T
- prompt(String, String, String[], boolean) - Method in class jspecview.java.AwtPlatform
- prompt(String, String, String[], boolean) - Method in class jspecview.js2d.JsPlatform
- prompt(String, String, String[], boolean) - Method in interface org.jmol.api.GenericPlatform
- prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
- prompt(String, String, String[], boolean) - Method in class org.jmol.awtjs2d.Platform
- prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
- PROP_ATOMS_DELETED - Static variable in class org.jmol.viewer.JC
- PROP_ATOMS_MOVED - Static variable in class org.jmol.viewer.JC
- PROP_DELETE_MODEL_ATOMS - Static variable in class org.jmol.viewer.JC
- properties - Variable in class jspecview.common.JSViewer
- properties - Variable in class org.jmol.modelset.Model
- property - Variable in class org.jmol.modelset.Measurement
- property - Variable in class org.jmol.modelset.MeasurementData
- property - Static variable in class org.jmol.script.T
- PROPERTY - Enum constant in enum class org.jmol.c.PAL
- propertyatomnumbercolumncount - Static variable in class org.jmol.script.T
- propertyatomnumberfield - Static variable in class org.jmol.script.T
- propertyChange(PropertyChangeEvent) - Method in class org.jmol.dialog.FilePreview
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
- propertycolorscheme - Static variable in class org.jmol.script.T
- propertydatacolumncount - Static variable in class org.jmol.script.T
- propertydatafield - Static variable in class org.jmol.script.T
- propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
- PROPERTYFLAGS - Static variable in class org.jmol.script.T
- PropertyManager - Class in org.jmol.viewer
-
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
- PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
- propselector - Static variable in class org.jmol.script.T
- protein - Static variable in class org.jmol.script.T
- proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
- ProteinStructure - Class in org.jmol.modelsetbio
- ProteinStructure() - Constructor for class org.jmol.modelsetbio.ProteinStructure
- proteinStructureTainted - Variable in class org.jmol.modelset.ModelSet
- PS_CLOSEPATH - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_LINETO - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_MOVETO - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_NEWPATH - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_SETLINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_SHOWPAGE - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_STROKE - Static variable in class org.jmol.shapecgo.CGOMesh
- psi - Static variable in class org.jmol.script.T
- psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
- PsiReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Psi3 output files.
- PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
- pt - Variable in enum class org.jmol.c.VDW
- pt - Variable in class org.jmol.util.ContactPair
- PT - Class in javajs.util
-
a combination of Parsing and Text-related utility classes
- PT() - Constructor for class javajs.util.PT
- PT_INT_LABEL - Static variable in class jspecview.common.Measurement
- PT_ON_LINE - Static variable in class jspecview.common.Measurement
- PT_ON_LINE1 - Static variable in class jspecview.common.Measurement
- PT_ON_LINE2 - Static variable in class jspecview.common.Measurement
- PT_XY1 - Static variable in class jspecview.common.Measurement
- PT_XY2 - Static variable in class jspecview.common.Measurement
- pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
- pt0 - Variable in class org.jmol.modelsetbio.AlphaPolymer
-
Specifically for mmTF bitset setting of structures
- pt0 - Variable in class org.jmol.render.FontLineShapeRenderer
- pt0 - Variable in class org.jmol.renderspecial.DrawRenderer
- pt0i - Variable in class org.jmol.render.FontLineShapeRenderer
- pt0i - Variable in class org.jmol.renderspecial.DrawRenderer
- pt1 - Variable in class org.jmol.render.FontLineShapeRenderer
- pt1 - Variable in class org.jmol.renderspecial.DrawRenderer
- pt1f - Variable in class org.jmol.render.MeshRenderer
- pt1i - Variable in class org.jmol.render.MeshRenderer
- pt2 - Variable in class org.jmol.renderspecial.DrawRenderer
- pt2f - Variable in class org.jmol.render.MeshRenderer
- pt2i - Variable in class org.jmol.render.FontLineShapeRenderer
- pt2i - Variable in class org.jmol.render.MeshRenderer
- pt3i - Variable in class org.jmol.render.MeshRenderer
- pt4Value(SV) - Static method in class org.jmol.script.SV
- ptCenter - Variable in class org.jmol.shape.Mesh
- pTemp - Variable in class org.jmol.render.LabelsRenderer
- ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ptMark - Variable in class javajs.util.DataReader
- ptNewSetModifier - Variable in class org.jmol.script.ScriptCompiler
- pts - Variable in class org.jmol.modelset.Measurement
- ptSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
- ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- ptTest1 - Variable in class org.jmol.viewer.TransformManager
- ptTest2 - Variable in class org.jmol.viewer.TransformManager
- ptTest3 - Variable in class org.jmol.viewer.TransformManager
- ptToIJK(T3, int) - Static method in class org.jmol.util.SimpleUnitCell
-
Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}
- ptValue(SV) - Static method in class org.jmol.script.SV
- ptValue(SV, BS) - Method in class org.jmol.script.ScriptMathProcessor
- purine - Static variable in class org.jmol.script.T
- PURINE_MASK - Static variable in class org.jmol.viewer.JC
- PURPLE - Static variable in class org.jmol.util.C
- push - Static variable in class org.jmol.script.T
- pushContextDown(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- pushContextDown(String) - Method in class org.jmol.script.ScriptEval
- pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
- pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
- pushHoldRepaint(String) - Method in interface org.jmol.api.JmolRepaintManager
- pushHoldRepaint(String) - Method in class org.jmol.render.RepaintManager
- pushHoldRepaintWhy(String) - Method in class org.jmol.viewer.Viewer
- pushMatrix() - Method in class org.jmol.export._StlExporter
- pushMatrix() - Method in class org.jmol.export._VrmlExporter
- pushMatrix() - Method in class org.jmol.export._X3dExporter
- pushPop(SV, SV) - Method in class org.jmol.script.SV
-
Script variables are pushed after cloning, because the name comes with them when we do otherwise they are not mutable anyway.
- pushState() - Method in class org.jmol.viewer.Viewer
- pushState(String) - Method in class org.jmol.util.CommandHistory
- put(int, int) - Method in class org.jmol.util.Int2IntHash
- putBox(int, float[]) - Method in class org.jmol.shape.Labels
- putByte(int) - Method in class javajs.img.ImageEncoder
- putCoord(V3d, double[]) - Static method in class org.jmol.minimize.Util
- putInfo(String, Map<String, Object>, String, Object) - Static method in class jspecview.common.Parameters
- putLabel(int, Text) - Method in class org.jmol.shape.Labels
- putP(T3) - Method in class javajs.util.T3
- putString(String) - Method in class javajs.img.ImageEncoder
- PWmatReader - Class in org.jmol.adapter.readers.xtal
-
crude PWmat atom.config reader http://pwmatus.com/manual
- PWmatReader() - Constructor for class org.jmol.adapter.readers.xtal.PWmatReader
- PWMATWriter - Class in org.jmol.adapter.writers
-
A writer for PWMAT atom.config files.
- PWMATWriter() - Constructor for class org.jmol.adapter.writers.PWMATWriter
- Pwr2 - Static variable in class org.jmol.util.TriangleData
- pymol - Static variable in class org.jmol.script.T
- PYMOL_LABEL_OFFSET_ABS_ANG - Static variable in class org.jmol.modelset.Text
- PYMOL_LABEL_OFFSET_ABS_PIX - Static variable in class org.jmol.modelset.Text
- PYMOL_LABEL_OFFSET_JMOL - Static variable in class org.jmol.modelset.Text
- PYMOL_LABEL_OFFSET_PIX - Static variable in class org.jmol.modelset.Text
- PYMOL_LABEL_OFFSET_REL - Static variable in class org.jmol.modelset.Text
- PYMOL_LABEL_OFFSET_REL_ANG - Static variable in class org.jmol.modelset.Text
- PYMOL_LABEL_OFFSET_REL_PIX - Static variable in class org.jmol.modelset.Text
- PymolAtomReader - Interface in org.jmol.api
- pymolOffset - Variable in class org.jmol.modelset.Text
- PyMOLReader - Class in org.jmol.adapter.readers.pymol
-
PyMOL PSE (binary Python session) file reader.
- PyMOLReader() - Constructor for class org.jmol.adapter.readers.pymol.PyMOLReader
- pyrimidine - Static variable in class org.jmol.script.T
- PYRIMIDINE_MASK - Static variable in class org.jmol.viewer.JC
Q
- q0 - Variable in class javajs.util.Quat
- q1 - Variable in class javajs.util.Quat
- q2 - Variable in class javajs.util.Quat
- q3 - Variable in class javajs.util.Quat
- QchemReader - Class in org.jmol.adapter.readers.quantum
-
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
- QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
- QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
- QCJSONReader - Class in org.jmol.adapter.readers.quantum
-
A molecular structure and orbital reader for MolDen files.
- QCJSONReader() - Constructor for class org.jmol.adapter.readers.quantum.QCJSONReader
- QCJSONWriter - Class in org.jmol.adapter.writers
-
A very experimental class for writing QCJSON files.
- QCJSONWriter() - Constructor for class org.jmol.adapter.writers.QCJSONWriter
- QCJSONWriter.SparseArray - Class in org.jmol.adapter.writers
- QCSchemaUnits - Class in org.qcschema
-
A general Java class for working with QCShema units and array types.
- QCSchemaUnits() - Constructor for class org.qcschema.QCSchemaUnits
- qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
- qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
- QS - Class in org.jmol.quantum
-
Constants and static methods for quantum shells.
- QS() - Constructor for class org.jmol.quantum.QS
- QUADRIC - Static variable in class org.jmol.shapecgo.CGOMesh
- qualifiedValue() - Method in class jspecview.source.XMLParser
-
for <xxxx> value </xxxx>
- quality - Variable in class javajs.img.ImageEncoder
- qualityJ - Variable in class org.jmol.dialog.Dialog
- qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- QualityListener(boolean, JSlider) - Constructor for class org.jmol.dialog.Dialog.QualityListener
- qualityP - Variable in class org.jmol.dialog.Dialog
- qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
-
gets the value at the color boundary for this color range fraction
- quantize4(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
- QuantumCalculation - Class in org.jmol.quantum
- QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
- QuantumPlaneCalculation - Class in org.jmol.quantum
-
Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
- QuantumPlaneCalculation() - Constructor for class org.jmol.quantum.QuantumPlaneCalculation
- Quat - Class in javajs.util
- Quat() - Constructor for class javajs.util.Quat
- quaternion - Static variable in class org.jmol.script.T
- quaternionframe - Static variable in class org.jmol.script.T
- query - Variable in class jme.JME
- QUESTION_MESSAGE - Static variable in class jspecview.dialog.DialogManager
- queueOnHold - Variable in class org.jmol.viewer.Viewer
- queueThreadFinished(int) - Method in interface org.jmol.api.JmolScriptManager
- queueThreadFinished(int) - Method in class org.jmol.script.ScriptManager
- quiet - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- quit - Static variable in class org.jmol.script.T
R
- r - Variable in class org.jmol.quantum.SlaterData
- r - Variable in class org.jmol.util.Rgb16
- R3 - Static variable in class org.jmol.minimize.forcefield.ForceField
- R4 - Static variable in class org.jmol.minimize.forcefield.ForceField
- R5 - Static variable in class org.jmol.minimize.forcefield.ForceField
- rad - Static variable in class org.jmol.script.T
- RAD_COV_BODR_2014_02_22 - Static variable in class org.jmol.util.Elements
- RAD_COV_IONIC_OB1_100_1 - Static variable in class org.jmol.util.Elements
- RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
- radiansPerDegree - Static variable in class javajs.util.Measure
- radiansPerDegree - Static variable in class org.jmol.viewer.JC
- radical - Static variable in class org.jmol.script.T
- radii - Variable in class org.jmol.util.ContactPair
- radius - Variable in class org.jmol.adapter.smarter.Atom
- radius - Variable in class org.jmol.adapter.smarter.Bond
- radius - Static variable in class org.jmol.script.T
- RADIUS_GLOBAL - Static variable in class org.jmol.modelset.Atom
- RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
- RADIUS_MAX - Static variable in class org.jmol.shape.Shape
- radiusData - Variable in class org.jmol.atomdata.AtomData
- radiusData - Variable in class org.jmol.modelset.MeasurementData
- RadiusData - Class in org.jmol.atomdata
- RadiusData(float[], float, RadiusData.EnumType, VDW) - Constructor for class org.jmol.atomdata.RadiusData
- RadiusData.EnumType - Enum Class in org.jmol.atomdata
- ramachandran - Static variable in class org.jmol.script.T
- random - Static variable in class org.jmol.script.T
- randomPoint() - Static method in class org.jmol.shapespecial.Draw
- randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
- range - Static variable in class org.jmol.script.T
- rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
- rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
- rangeselected - Static variable in class org.jmol.script.T
- rangeSelected - Variable in class org.jmol.viewer.GlobalSettings
- Raromatic - Static variable in class org.jmol.minimize.forcefield.ForceField
- rasmol - Static variable in class org.jmol.script.T
- RASMOL - Enum constant in enum class org.jmol.c.PAL
- RASMOL - Enum constant in enum class org.jmol.c.VDW
- RASMOL - Static variable in class org.jmol.util.ColorEncoder
- RasmolBinding - Class in org.jmol.viewer.binding
- RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
- rawBondCount - Variable in class org.jmol.minimize.Minimizer
- rawIndex - Variable in class org.jmol.minimize.MinBond
- rawLine - Variable in class jspecview.source.JDXSourceStreamTokenizer
- RBOND - Static variable in class jme.JMEmol
- rButton - Variable in class jme.JME
- rd - Variable in class org.jmol.viewer.Viewer
- rd() - Method in class jspecview.source.JDXReader
- rd() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- rd() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- rd() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- rd() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
filter out unnecessary lines
- rd() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- rd() - Method in interface org.jmol.api.JmolJDXMOLReader
- rd() - Method in class org.jmol.jvxl.readers.JvxlReader
- rd() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- rd() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- rdline() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- Rdr - Class in javajs.util
-
A general helper class for a variety of stream and reader functionality including: stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams various stream/reader methods, including UTF-encoded stream reading reflection-protected access to a CIF parser and ZIP tools
- Rdr(BufferedReader) - Constructor for class javajs.util.Rdr
- Rdr.StreamReader - Class in javajs.util
- rdSiesta() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- reaction - Variable in class jme.JME
- reactionPart() - Method in class jme.JMEmol
- read() - Method in class org.apache.tools.bzip2.CBZip2InputStream
- read(byte[], int, int) - Method in class com.jcraft.jzlib.InflaterInputStream
- read(byte[], int, int) - Method in class org.apache.tools.bzip2.CBZip2InputStream
- read(char[], int, int) - Method in class javajs.util.ArrayDataReader
- read(char[], int, int) - Method in class javajs.util.ListDataReader
- read(char[], int, int) - Method in class jspecview.common.JSVZipFileSequentialReader
- read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
- readACDAssignments(int, boolean) - Method in interface org.jmol.api.JmolJDXMOLParser
- readACDAssignments(int, boolean) - Method in class org.jmol.jsv.JDXMOLParser
- readACDMolFile() - Method in interface org.jmol.api.JmolJDXMOLParser
- readACDMolFile() - Method in class org.jmol.jsv.JDXMOLParser
-
MOL file embedded in JDX file
- readAllAsString(BufferedReader, int, boolean, String[], int) - Static method in class javajs.util.Rdr
-
This method fills data[i] with string data from a file that may or may not be binary even though it is being read by a reader.
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readBonds() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readBrukerDir(String) - Method in class jspecview.source.BrukerReader
-
Read through a Bruker directory (Java only) looking for title, acqus, procs, 1r, 1i, 2rr.
- readBrukerZip(byte[], String) - Method in class jspecview.source.BrukerReader
-
Read through a ZIP file (Java or JavaScript) looking for title, acqus, procs, 1r, 1i, 2rr.
- readBuf(char[], int, int) - Method in class javajs.util.DataReader
- readByte() - Method in interface javajs.api.GenericBinaryDocumentReader
- readByte() - Method in class javajs.util.BinaryDocument
- readByteArray(byte[], int, int) - Method in interface javajs.api.GenericBinaryDocument
- readByteArray(byte[], int, int) - Method in class javajs.util.BinaryDocument
- readByteAsInt() - Method in class com.jcraft.jzlib.InflaterInputStream
- readByteAsInt() - Method in class org.apache.tools.bzip2.CBZip2InputStream
- readBytes(int) - Method in interface javajs.api.GenericBinaryDocumentReader
- readBytes(int) - Method in class javajs.util.BinaryDocument
- readCifData(String, Object, String) - Method in interface org.jmol.atomdata.AtomDataServer
- readCifData(String, Object, String) - Method in class org.jmol.viewer.Viewer
- readCifData(String, String) - Method in class org.jmol.viewer.Viewer
- readCifData(GenericCifDataParser, BufferedReader) - Static method in class javajs.util.Rdr
- readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
- readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Reads a set of coordinates
- readCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- readDataObject(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readDouble() - Method in interface javajs.api.GenericBinaryDocumentReader
- readDouble() - Method in class javajs.util.BinaryDocument
- readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readEnergy() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- READER_NOT_FOUND - Static variable in class org.jmol.viewer.JC
- readerClosed - Variable in class org.jmol.jvxl.readers.JvxlReader
- readerClosed - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- readerClosed - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in interface javajs.api.GenericZipTools
- readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in class javajs.util.ZipTools
- readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in class org.jmol.viewer.Viewer
- readFloat() - Method in interface javajs.api.GenericBinaryDocumentReader
- readFloat() - Method in class javajs.util.BinaryDocument
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Reads a set of vibrations.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readFrequencies(String, boolean) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interprets the Harmonic frequencies section.
- readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readHeader() - Method in class com.jcraft.jzlib.InflaterInputStream
- readInf(byte[], int, int) - Method in class com.jcraft.jzlib.InflaterInputStream
- readInputRecords() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readInt() - Method in interface javajs.api.GenericBinaryDocumentReader
- readInt() - Method in class javajs.util.BinaryDocument
- readIntLE() - Method in interface javajs.api.GenericBinaryDocument
- readIntLE() - Method in class javajs.util.BinaryDocument
- readLine() - Method in interface javajs.api.GenericCifDataParser
- readLine() - Method in class javajs.util.ArrayDataReader
- readLine() - Method in class javajs.util.CifDataParser
- readLine() - Method in class javajs.util.ListDataReader
- readLine() - Method in class jspecview.common.JSVZipFileSequentialReader
- readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readLineTrimmed() - Method in class jspecview.source.JDXSourceStreamTokenizer
- readLineWithNewline() - Method in class javajs.util.LimitedLineReader
- readList() - Method in class javajs.util.CifDataParser
-
Read a CIF 2.0 list structure, converting it to either a JSON string or to a Java data structure
- readLong() - Method in interface javajs.api.GenericBinaryDocumentReader
- readLong() - Method in class javajs.util.BinaryDocument
- readMap() - Method in class javajs.util.MessagePackReader
- readModels() - Method in interface org.jmol.api.JmolJDXMOLParser
- readModels() - Method in class org.jmol.jsv.JDXMOLParser
- readMolecularFormula() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
-
try various ways to read the optional atom labels.
- readMolecularObitals() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- readMolecule(String) - Method in class jme.JME
- readMolFile(String) - Method in class jme.JME
- ReadNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
- readNBOCoefficients(Map<String, Object>, String, Viewer) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
Called by setNBOType in IsoExt when use issues NBO TYPE xxx
- readNextLine() - Method in interface javajs.api.GenericLineReader
- readNextLine() - Method in class javajs.util.Rdr
- readNextLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ReadNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
- readNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- readNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- readOldFrequency() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
- readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readParameters() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readPeaks(boolean, int) - Method in interface org.jmol.api.JmolJDXMOLParser
- readPeaks(boolean, int) - Method in class org.jmol.jsv.JDXMOLParser
- readShort() - Method in interface javajs.api.GenericBinaryDocumentReader
- readShort() - Method in class javajs.util.BinaryDocument
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- READSPT - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
- readString(int) - Method in interface javajs.api.GenericBinaryDocumentReader
- readString(int) - Method in class javajs.util.BinaryDocument
- readStructure(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readSurfaceDataJXR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readSurfaceDataXML() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- readTable() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Read a CIF 2.0 table into either a JSON string or a java data structure
- readUInt8() - Method in interface javajs.api.GenericBinaryDocumentReader
- readUInt8() - Method in class javajs.util.BinaryDocument
- readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- readUnsignedShort() - Method in interface javajs.api.GenericBinaryDocumentReader
- readUnsignedShort() - Method in class javajs.util.BinaryDocument
- readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JvxlReader
- readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVoxelVector(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- ReattachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
- rebond() - Method in class org.jmol.api.JmolViewer
- rebond() - Method in class org.jmol.viewer.Viewer
- rebondState(boolean) - Method in class org.jmol.viewer.Viewer
- recachePngjBytes(String, byte[]) - Method in class org.jmol.viewer.FileManager
- recalcAltVertices - Variable in class org.jmol.shape.Mesh
- reCalculate(BS, M3) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
- recalculateAllPolymers(BS, Group[]) - Method in class org.jmol.modelsetbio.BioModelSet
- recalculateEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
- recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
- recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelSet
- recalculatePoints(int) - Method in class org.jmol.modelsetbio.BioModelSet
- recalculatePolymers(BS) - Method in class org.jmol.modelset.ModelSet
- recalculatePositionDependentQuantities(BS, M4) - Method in class org.jmol.modelset.ModelSet
- recallCommand(boolean, boolean) - Method in class org.jmol.console.GenericConsole
- recallCommand(boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
-
Recall command history.
- recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
- recordData(float) - Method in class org.jmol.jvxl.readers.JvxlReader
- recordData(float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- recordData(float) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- Rectangle - Class in org.jmol.util
- Rectangle() - Constructor for class org.jmol.util.Rectangle
- rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- RED - Static variable in class jspecview.common.ColorParameters
- RED - Static variable in class org.jmol.util.C
- REDBLUE - Enum constant in enum class org.jmol.c.STER
- REDCYAN - Enum constant in enum class org.jmol.c.STER
- REDGREEN - Enum constant in enum class org.jmol.c.STER
- redo - Static variable in class org.jmol.script.T
- redomove - Static variable in class org.jmol.script.T
- reducedAnisotropy() - Method in class org.jmol.util.Tensor
-
reduced anisotropy = largest difference from isotropy (may be negative)
- reEnable() - Method in class jspecview.dialog.JSVDialog
- REF_TYPE_BRUKER - Static variable in class jspecview.source.JDXDataObject
- REF_TYPE_STANDARD - Static variable in class jspecview.source.JDXDataObject
- REF_TYPE_UNSPECIFIED - Static variable in class jspecview.source.JDXDataObject
- REF_TYPE_VARIAN - Static variable in class jspecview.source.JDXDataObject
- reference - Variable in class org.jmol.modelset.TickInfo
- reference - Static variable in class org.jmol.script.T
- referenceCenter - Variable in class org.jmol.export.___Exporter
- referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
- reformatDistanceIfSelected(boolean) - Method in class org.jmol.modelset.Measurement
- refPoint - Variable in class jspecview.source.AnIMLReader
- refresh - Static variable in class org.jmol.script.T
- refresh() - Method in class jspecview.common.PanelData
- refresh() - Method in class jspecview.common.RepaintManager
- refresh(boolean) - Method in class org.jmol.script.ScriptEval
-
Refresh the display NOW
- refresh(int, String) - Method in class org.jmol.api.JmolViewer
- refresh(int, String) - Method in class org.jmol.viewer.Viewer
-
initiate a repaint/update sequence if it has not already been requested.
- refresh(Point3fi[]) - Method in class org.jmol.modelset.Measurement
- REFRESH_REPAINT - Static variable in class org.jmol.viewer.Viewer
- REFRESH_REPAINT_NO_MOTION_ONLY - Static variable in class org.jmol.viewer.Viewer
- REFRESH_SEND_WEBGL_NEW_ORIENTATION - Static variable in class org.jmol.viewer.Viewer
- REFRESH_SYNC - Static variable in class org.jmol.viewer.Viewer
- REFRESH_SYNC_MASK - Static variable in class org.jmol.viewer.Viewer
- refreshing - Static variable in class org.jmol.script.T
- refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
- regainFocus() - Method in interface org.jmol.api.JmolAppConsoleInterface
- regainFocus() - Method in class org.jmol.console.AppletConsole
- regainFocus() - Method in class org.jmol.consolejs.AppletConsole
- regainFocus() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- register(String, JmolSyncInterface) - Method in class jspecview.application.MainFrame
-
called by Jmol's StatusListener to register itself, indicating to JSpecView that it needs to synchronize with it
- register(String, JmolSyncInterface) - Method in interface org.jmol.api.JmolSyncInterface
- register(String, JmolSyncInterface) - Method in class org.jmol.util.GenericApplet
- register(String, JmolSyncInterface) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- register(Component, String) - Method in interface org.jmol.awtjs.swing.SwingController
-
Set c's id to a unique identifier and add it to an associative array that will associate that id with c.
- registerAudio(String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
- registerDialog(JSVDialog) - Method in class jspecview.dialog.DialogManager
-
register the JSV dialog with a unique key to be used as an ID in callbacks optionKeys ending with "!" are one-of-a-kind, such as "views"
- registerSelector(String, Object) - Method in class jspecview.dialog.DialogManager
- registryKey - Variable in class jspecview.java.AwtDialog
- registryKey - Variable in class jspecview.js2d.JsDialog
- reinitializeLightingAndColor(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- reinitShape() - Method in class org.jmol.shape.Axes
- reinstateMenu(JMenuItem, MenuElement[]) - Method in class org.jmol.awt.AwtPopupHelper
-
Cause the menu to persist in its open state.
- rejectAtomName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- Related Documentation - Search tag in package org.jmol.g3d
- Section
- RELATIVE_DRAG_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- RELATIVE_DRAG_EVENT - Static variable in class com.sparshui.GestureType
- RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- RELATIVE_DRAG_GESTURE - Static variable in class com.sparshui.GestureType
- RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- RelativeDragEvent - Class in com.sparshui.common.messages.events
- RelativeDragEvent() - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
- RelativeDragEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
-
Constructs a dragEvent from a complete serialized version of the drag event.
- RelativeDragEvent(float, float) - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
- relativeStereo - Variable in class jme.JME
- release() - Method in interface org.jmol.api.AtomIndexIterator
- release() - Method in class org.jmol.bspt.CubeIterator
-
nulls internal references
- release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- release() - Method in class org.jmol.symmetry.UnitCellIterator
- released(long, int, int, int) - Method in class jspecview.app.GenericMouse
- RELEASED - Static variable in class org.jmol.awtjs.Event
- releaseModelSet() - Method in class org.jmol.modelset.ModelSet
- releaseModelSetAC() - Method in class org.jmol.modelset.AtomCollection
- releaseModelSetBC() - Method in class org.jmol.modelset.BondCollection
- releaseScreenImage() - Method in class org.jmol.api.JmolViewer
- releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
- releaseScreenImage() - Method in class org.jmol.util.GData
- releaseScreenImage() - Method in class org.jmol.viewer.Viewer
- releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
- remove - Static variable in class org.jmol.script.T
- remove() - Method in class jspecview.source.JDXDecompressor
- remove(int) - Method in class javajs.util.Lst
- remove(int) - Method in class jspecview.common.IntegralData
- remove(int) - Method in interface org.jmol.api.SC
- remove(int) - Method in class org.jmol.awt.AwtSwingComponent
- remove(int) - Method in class org.jmol.awtjs.swing.Container
- remove(Object) - Method in class javajs.util.Lst
-
Deprecated.
- removeAll() - Method in interface org.jmol.api.SC
- removeAll() - Method in class org.jmol.awt.AwtSwingComponent
- removeAll() - Method in class org.jmol.awtjs.swing.Container
- removeAllHighlights() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that removes all highlights from the plot area of a
JSVPanel
- removeAllHighlights() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that removes all highlights from the plot area of a
JSVPanel
- removeAllHighlights() - Method in class jspecview.appletjs.JSVApplet
- removeAllHighlights() - Method in class jspecview.application.MainFrame
- removeAllHighlights() - Method in class jspecview.common.PanelData
-
Removes all highlights from the display
- removeAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells
- removeCommand() - Method in class org.jmol.util.CommandHistory
- removeCommand() - Method in class org.jmol.viewer.Viewer
-
Removes one command from the command history
- removeCommand(int) - Method in class org.jmol.util.CommandHistory
- removeCurrentAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- removeDialog(JSVDialog) - Method in class jspecview.common.PanelData
- removeDuplicates(ModelSet, BS, boolean) - Method in interface org.jmol.api.SymmetryInterface
- removeDuplicates(ModelSet, BS, boolean) - Method in class org.jmol.symmetry.Symmetry
- removeFunction(String) - Method in class org.jmol.viewer.Viewer
- removeHighlight(double, double) - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that removes a highlight from the plot area of a
JSVPanel
- removeHighlight(double, double) - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that removes a highlight from the plot area of a
JSVPanel
- removeHighlight(double, double) - Method in class jspecview.appletjs.JSVApplet
- removeHighlight(double, double) - Method in class jspecview.application.MainFrame
- removeHighlight(double, double) - Method in class jspecview.common.PanelData
-
Remove the highlight specified by the starting and ending x value
- removeItemAt(int) - Method in class javajs.util.Lst
- removeLastUnselectedAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- removeMapKeys(Map<String, ?>, String) - Static method in class javajs.util.AU
-
remove all keys from a map that start with given root
- removeNodeFromParent(JSVTreeNode) - Method in class jspecview.tree.SimpleTreeModel
- removeObj(Object) - Method in class javajs.util.Lst
- removePacking(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- removeParam(String) - Method in class org.jmol.viewer.GlobalSettings
- removePropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
- removeScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
-
Removes the scale factor from the coordinates
- removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
- removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
- removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
- removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
- render() - Method in class org.jmol.render.AxesRenderer
- render() - Method in class org.jmol.render.BallsRenderer
- render() - Method in class org.jmol.render.BbcageRenderer
- render() - Method in class org.jmol.render.EchoRenderer
- render() - Method in class org.jmol.render.FrankRenderer
- render() - Method in class org.jmol.render.HalosRenderer
- render() - Method in class org.jmol.render.HoverRenderer
- render() - Method in class org.jmol.render.LabelsRenderer
- render() - Method in class org.jmol.render.MeasuresRenderer
- render() - Method in class org.jmol.render.ShapeRenderer
- render() - Method in class org.jmol.render.StarsRenderer
- render() - Method in class org.jmol.render.SticksRenderer
- render() - Method in class org.jmol.render.UccageRenderer
- render() - Method in class org.jmol.renderbio.BioMeshRenderer
- render() - Method in class org.jmol.renderbio.BackboneRenderer
- render() - Method in class org.jmol.renderbio.CartoonRenderer
- render() - Method in class org.jmol.renderbio.MeshRibbonRenderer
- render() - Method in class org.jmol.renderbio.RibbonsRenderer
- render() - Method in class org.jmol.renderbio.RocketsRenderer
- render() - Method in class org.jmol.renderbio.StrandsRenderer
- render() - Method in class org.jmol.renderbio.TraceRenderer
- render() - Method in class org.jmol.rendercgo.CGORenderer
- render() - Method in class org.jmol.renderspecial.DipolesRenderer
- render() - Method in class org.jmol.renderspecial.DotsRenderer
- render() - Method in class org.jmol.renderspecial.DrawRenderer
- render() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- render() - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
- render() - Method in class org.jmol.renderspecial.PolyhedraRenderer
- render() - Method in class org.jmol.renderspecial.VectorsRenderer
- render() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- render() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
- render() - Method in class org.jmol.rendersurface.PmeshRenderer
- render(GData, ModelSet, boolean, int[]) - Method in interface org.jmol.api.JmolRepaintManager
- render(GData, ModelSet, boolean, int[]) - Method in class org.jmol.render.RepaintManager
- render1(Dots) - Method in class org.jmol.renderspecial.DotsRenderer
- render2(boolean) - Method in class org.jmol.render.MeshRenderer
-
Overridden in DrawRenderer and IsosurfaceRenderer
- render2(boolean) - Method in class org.jmol.renderspecial.DrawRenderer
- render2(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- render2b(boolean) - Method in class org.jmol.render.MeshRenderer
- render2Strand(boolean, float, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderAllStrings(Object) - Method in interface org.jmol.api.JmolGraphicsInterface
- renderAllStrings(Object) - Method in class org.jmol.export.Export3D
- renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
- renderAllStrings(Object) - Method in class org.jmol.util.GData
- renderArc - Variable in class org.jmol.modelset.Measurement
- renderArrowHeads - Variable in class org.jmol.renderbio.RocketsRenderer
- renderAxis - Variable in class org.jmol.modelset.Measurement
- renderBackground(JmolRendererInterface) - Method in interface org.jmol.api.JmolRendererInterface
- renderBackground(JmolRendererInterface) - Method in class org.jmol.export.Export3D
- renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
- renderBackground(JmolRendererInterface) - Method in class org.jmol.util.GData
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.BackboneRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.CartoonRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.RibbonsRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.RocketsRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.StrandsRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.TraceRenderer
- renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.AxesRenderer
- renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.BbcageRenderer
- renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.UccageRenderer
- renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.DotsRenderer
-
generic renderer -- dots and geosurface
- renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
- renderCrossHairs(int[], int, int, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
- renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.export.Export3D
- renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.g3d.Graphics3D
- renderDots(int) - Method in class org.jmol.renderspecial.DotsRenderer
-
also called by GeoSurface when in motion
- renderExport(GData, ModelSet, Map<String, Object>) - Method in interface org.jmol.api.JmolRepaintManager
- renderExport(GData, ModelSet, Map<String, Object>) - Method in class org.jmol.render.RepaintManager
- renderHeight - Variable in class org.jmol.awtjs.swing.Component
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.BackboneRenderer
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.CartoonRenderer
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.RibbonsRenderer
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.RocketsRenderer
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.StrandsRenderer
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.TraceRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.BackboneRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.CartoonRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.RibbonsRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.RocketsRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.StrandsRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.TraceRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.BackboneRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.CartoonRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.RibbonsRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.RocketsRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.StrandsRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.TraceRenderer
- renderHermiteRibbon(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, int) - Method in class org.jmol.g3d.HermiteRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.BackboneRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.CartoonRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.RibbonsRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.StrandsRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.TraceRenderer
- renderHermiteRope(boolean, int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
- renderInfo() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderInfo() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
- rendering - Variable in class org.jmol.jvxl.data.JvxlData
- renderIso() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderLabelOrMeasure(Text, String) - Method in class org.jmol.render.LabelsRenderer
- renderLine(P3, P3, int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
- renderLow - Variable in class org.jmol.render.MeshRenderer
- renderMesh2(Mesh) - Method in class org.jmol.render.MeshRenderer
-
overridden in BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
- renderMeshes() - Method in class org.jmol.renderbio.BioMeshRenderer
- renderMeshRibbon() - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderPass2(short) - Static method in class org.jmol.util.C
- renderPoints() - Method in class org.jmol.render.MeshRenderer
- renderPoints() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderRockets() - Method in class org.jmol.renderbio.RocketsRenderer
- renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolViewer
- renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
-
JmolViewer interface uses this, but that is all
- renderScreenImage(Object, Object) - Method in class jspecview.java.AwtPlatform
-
legacy apps will use this
- renderScreenImage(Object, Object) - Method in class jspecview.js2d.JsPlatform
-
legacy apps will use this
- renderScreenImage(Object, Object) - Method in interface org.jmol.api.GenericPlatform
-
Deprecated.
- renderScreenImage(Object, Object) - Method in class org.jmol.awt.Platform
-
legacy apps will use this
- renderScreenImage(Object, Object) - Method in class org.jmol.awtjs2d.Platform
-
legacy apps will use this
- renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
-
Deprecated.
- renderScreenImageStereo(Object, boolean, int, int) - Method in class org.jmol.viewer.Viewer
- renderShape(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
- renderStrands() - Method in class org.jmol.renderbio.StrandsRenderer
- renderStrandShape() - Method in class org.jmol.renderbio.StrandsRenderer
- renderTrace() - Method in class org.jmol.renderbio.TraceRenderer
- renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.render.MeshRenderer
- renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderWidth - Variable in class org.jmol.awtjs.swing.Component
- rep(String, String, String) - Static method in class javajs.util.PT
-
Does a clean ITERATIVE replace of strFrom in str with strTo.
- repaint() - Method in interface jspecview.api.AppletFrame
- repaint() - Method in interface jspecview.api.JSVPanel
- repaint() - Method in interface jspecview.api.PlatformDialog
- repaint() - Method in interface jspecview.api.ScriptInterface
- repaint() - Method in class jspecview.app.JSVApp
- repaint() - Method in class jspecview.appletjs.JSVApplet
- repaint() - Method in class jspecview.application.JSpecView
- repaint() - Method in class jspecview.common.PanelData
- repaint() - Method in class jspecview.dialog.JSVDialog
- repaint() - Method in class jspecview.js2d.JsPanel
- repaint() - Method in class org.jmol.awtjs.swing.Component
- repaint() - Method in class org.jmol.awtjs.swing.JDialog
- repaint(Object) - Method in class jspecview.java.AwtPlatform
- repaint(Object) - Method in class jspecview.js2d.JsPlatform
- repaint(Object) - Method in interface org.jmol.api.GenericPlatform
- repaint(Object) - Method in class org.jmol.awt.Platform
- repaint(Object) - Method in class org.jmol.awtjs2d.Platform
- repaint(JSAppletObject, boolean) - Method in interface javajs.api.js.J2SObjectInterface
- REPAINT_IGNORE - Static variable in class org.jmol.viewer.JC
- repaintDone() - Method in class jspecview.common.JSViewer
- repaintDone() - Method in class jspecview.common.RepaintManager
- repaintDone() - Method in interface org.jmol.api.JmolRepaintManager
- repaintDone() - Method in class org.jmol.render.RepaintManager
- repaintIfReady(String) - Method in interface org.jmol.api.JmolRepaintManager
- repaintIfReady(String) - Method in class org.jmol.render.RepaintManager
- repaintManager - Variable in class jspecview.common.JSViewer
- RepaintManager - Class in jspecview.common
- RepaintManager - Class in org.jmol.render
- RepaintManager() - Constructor for class org.jmol.render.RepaintManager
- RepaintManager(JSViewer) - Constructor for class jspecview.common.RepaintManager
- repaintwaitms - Static variable in class org.jmol.script.T
- repaintWaitMs - Variable in class org.jmol.viewer.GlobalSettings
- replace - Static variable in class org.jmol.script.T
- replace(int, int, String) - Method in class javajs.util.SB
- replaceAllCharacters(String, String, String) - Static method in class javajs.util.PT
-
Does a clean replace of any of the characters in str with strTo If strTo contains strFrom, then only a single pass is done.
- replaceGroup(Group, Group) - Method in class org.jmol.shape.Shape
- replaceGroup(Group, Group) - Method in class org.jmol.shapebio.BioShapeCollection
- replaceGroup(Group, Group) - Method in class org.jmol.viewer.ShapeManager
- replaceQuotedStrings(String, Lst<String>, Lst<String>) - Static method in class javajs.util.PT
- replaceStrings(String, Lst<String>, Lst<String>) - Static method in class javajs.util.PT
- replaceTransformMatrix(M4) - Method in interface org.jmol.api.SymmetryInterface
- replaceTransformMatrix(M4) - Method in class org.jmol.symmetry.Symmetry
- replaceWithCharacter(String, String, char) - Static method in class javajs.util.PT
-
Does a clean replace of any of the characters in str with chrTo If strTo contains strFrom, then only a single pass is done.
- reply(int, Object) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- reply(int, Object) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- report(String, boolean) - Method in class org.jmol.minimize.Minimizer
- report(String, boolean) - Method in class org.jmol.script.ScriptEval
- reportAll - Variable in class org.jmol.shape.Sticks
- reportSelection(int) - Method in class org.jmol.viewer.ChimeMessenger
-
report atom selection in Chime format
- reportSelection(int) - Method in interface org.jmol.viewer.JmolChimeMessenger
- repositionWindow(String, Component) - Method in class org.openscience.jmol.app.HistoryFile
-
Uses the informations in the history to reposition the window.
- repositionWindow(String, Component, int, int, boolean) - Method in class org.openscience.jmol.app.HistoryFile
-
Uses the informations in the history to reposition the window.
- requestFocusInWindow(Object) - Method in class jspecview.java.AwtPlatform
- requestFocusInWindow(Object) - Method in class jspecview.js2d.JsPlatform
- requestFocusInWindow(Object) - Method in interface org.jmol.api.GenericPlatform
- requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
- requestFocusInWindow(Object) - Method in class org.jmol.awtjs2d.Platform
- requestRepaint() - Method in class jspecview.common.JSViewer
- requestRepaintAndWait(String) - Method in interface org.jmol.api.JmolRepaintManager
- requestRepaintAndWait(String) - Method in class org.jmol.render.RepaintManager
- requestRepaintAndWait(String) - Method in class org.jmol.viewer.Viewer
- RequestThread() - Constructor for class jspecview.java.AwtPanel.RequestThread
- requiresBSFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- requiresEndTag() - Method in class jspecview.source.XMLParser
- reset - Static variable in class org.jmol.script.T
- reset() - Method in class com.jcraft.jzlib.Adler32
- reset() - Method in interface com.jcraft.jzlib.Checksum
- reset() - Method in class com.jcraft.jzlib.CRC32
- reset() - Method in class com.jcraft.jzlib.Inflater
- reset() - Method in class com.jcraft.jzlib.InflaterInputStream
- reset() - Method in interface javajs.api.GenericOutputChannel
- reset() - Method in class javajs.util.ArrayDataReader
- reset() - Method in class javajs.util.ListDataReader
- reset() - Method in class javajs.util.OC
- reset() - Method in class jme.JME
- reset() - Method in class jspecview.common.JSVZipFileSequentialReader
- reset() - Method in class org.jmol.thread.JmolThread
- reset() - Method in class org.jmol.util.BoxInfo
- reset(boolean) - Method in class org.jmol.viewer.Viewer
- reset(int) - Method in class org.jmol.util.CommandHistory
-
Resets instance.
- RESET_NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
- resetAromatic() - Method in class org.jmol.modelset.BondCollection
- resetAtomPickType() - Method in class org.jmol.modelkit.ModelKit
- resetBioshapes(BS) - Method in class org.jmol.viewer.ShapeManager
- resetBoundCount() - Method in class org.jmol.modelset.Model
- resetChanged() - Method in class com.sparshui.server.TouchPoint
-
Reset the changed flag.
- resetDSSR(boolean) - Method in class org.jmol.modelset.Model
-
Something has changed; clear the DSSR cache and possibly remove DSSR entirely.
- resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
-
reset some parameters at the "MAP" keyword or initially
- resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
- resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
- resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
- resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
- resetLighting() - Method in class org.jmol.viewer.StateManager
-
Reset lighting to Jmol defaults
- resetLong(long) - Method in class com.jcraft.jzlib.Adler32
- resetLong(long) - Method in interface com.jcraft.jzlib.Checksum
- resetLong(long) - Method in class com.jcraft.jzlib.CRC32
- resetMolecules() - Method in class org.jmol.modelset.ModelSet
- resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
-
something has arisen that requires resetting of the navigation point.
- resetObjects() - Method in class org.jmol.shape.MeshCollection
- resetRasmolBonds(BS, int) - Method in class org.jmol.modelsetbio.BioModel
-
from Trajectory.setAtomPositions base models only; not trajectories
- resetRotation() - Method in class org.jmol.viewer.TransformManager
- resetRotation() - Method in class org.jmol.viewer.TransformManager4D
- resetScaleFactors() - Method in class jspecview.common.ViewData
- resetShapes(boolean) - Method in class org.jmol.viewer.ShapeManager
- resetShapes(boolean) - Method in class org.jmol.viewer.Viewer
- resetSlab() - Method in class org.jmol.util.MeshSurface
- resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- resetView() - Method in class jspecview.common.PanelData
-
Resets the spectrum to it's original view
- residue - Static variable in class org.jmol.script.T
- RESIZE - Enum constant in enum class org.jmol.c.CBK
- resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
- resizeApplet(Object, int[]) - Method in interface javajs.api.js.J2SObjectInterface
- resizeInnerPanel(int, int) - Method in class org.jmol.api.JmolViewer
- resizeInnerPanel(int, int) - Method in class org.jmol.viewer.StatusManager
- resizeInnerPanel(int, int) - Method in class org.jmol.viewer.Viewer
- resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
- resizeInnerPanel(String) - Method in class org.jmol.util.GenericApplet
- resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- resizeInnerPanelString(String) - Method in class org.jmol.viewer.StatusManager
-
called by file droppers
- resLabel - Variable in class jspecview.source.AnIMLReader
- resno - Static variable in class org.jmol.script.T
- resolution - Variable in class jspecview.export.AMLExporter
- resolution - Variable in class jspecview.export.CMLExporter
- resolution - Variable in class jspecview.source.AnIMLReader
- resolution - Variable in class org.jmol.jvxl.readers.Parameters
- resolution - Static variable in class org.jmol.script.T
- resolveDataBase(String, String, String) - Static method in class org.jmol.viewer.JC
- resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- Resolver - Class in org.jmol.adapter.smarter
- Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
- resourceName - Variable in class org.jmol.quantum.MepCalculation
- restorativeForceAndAngleRadians(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restorativeForceAndDistance(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restorativeForceAndOutOfPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restorativeForceAndTorsionAngleRadians(V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restore - Static variable in class org.jmol.script.T
- restore(float, boolean) - Method in class org.jmol.modelset.Orientation
- restoreAtomPositions(P3[]) - Method in class org.jmol.modelset.ModelSet
- restoreBonds(String) - Method in class org.jmol.viewer.StateManager
- restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
- restoreScene(String, float) - Method in class org.jmol.viewer.StateManager
- restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- restoreSelection(String) - Method in class org.jmol.viewer.StateManager
- restoreUnitCell(String) - Method in class org.jmol.viewer.StateManager
- restoreXY(double[][]) - Method in class jme.JMEmol
- restrict - Static variable in class org.jmol.script.T
- restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEval
- restrictSelected(boolean, boolean) - Method in class org.jmol.viewer.ShapeManager
- restrictToModel(BS, int) - Method in class org.jmol.viewer.Viewer
-
Restrict this bitset to the current model or its initial atom's model.
- RESU - Static variable in class org.jmol.util.ColorEncoder
- resume - Static variable in class org.jmol.script.T
- resumeEval() - Method in class org.jmol.thread.JmolThread
- resumeEval(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
- resumeEval(Object) - Method in class org.jmol.script.ScriptEval
-
From dispatchCommands and JmolThread resumeEval.
- resumePausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
- resumePausedExecution() - Method in class org.jmol.script.ScriptEval
- returncmd - Static variable in class org.jmol.script.T
- reverse - Static variable in class org.jmol.script.T
- reverse(Coordinate[]) - Static method in class jspecview.common.Coordinate
- reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
-
Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE.
- reversecolor - Static variable in class org.jmol.script.T
- reverseColor - Variable in class org.jmol.shape.Mesh
- reversed - Variable in class org.jmol.modelsetbio.BioPolymer
- reverseModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- reversePlot() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that toggles reversing the plot on a
JSVPanel
- reversePlot() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that toggles reversing the plot on a
JSVPanel
- reversePlot() - Method in class jspecview.appletjs.JSVApplet
- reversePlot() - Method in class jspecview.application.MainFrame
- REVERSEPLOT - Enum constant in enum class jspecview.common.ScriptToken
- revertStereo - Variable in class jme.JME
- rewind - Static variable in class org.jmol.script.T
- rgb(int, int, int) - Static method in class javajs.util.CU
- Rgb16 - Class in org.jmol.util
- Rgb16() - Constructor for class org.jmol.util.Rgb16
- rgbFractionalFromArgb(int) - Method in class org.jmol.export.___Exporter
- rgbFractionalFromColix(short) - Method in class org.jmol.export.___Exporter
- rgbToHSL(P3, boolean) - Static method in class javajs.util.CU
-
Convert RGB values to HSL (hue/saturation/lightness)
- rgbToXyz(P3, P3) - Method in class javajs.img.GifEncoder
- RHOMB_TO_HEX - Static variable in class org.jmol.util.SimpleUnitCell
- ribbon - Static variable in class org.jmol.script.T
- ribbonaspectratio - Static variable in class org.jmol.script.T
- ribbonborder - Static variable in class org.jmol.script.T
- ribbonBottomScreens - Variable in class org.jmol.renderbio.BackboneRenderer
- ribbonBottomScreens - Variable in class org.jmol.renderbio.CartoonRenderer
- ribbonBottomScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- ribbonBottomScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
- ribbonBottomScreens - Variable in class org.jmol.renderbio.RocketsRenderer
- ribbonBottomScreens - Variable in class org.jmol.renderbio.StrandsRenderer
- ribbonBottomScreens - Variable in class org.jmol.renderbio.TraceRenderer
- Ribbons - Class in org.jmol.shapebio
- Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
- RibbonsRenderer - Class in org.jmol.renderbio
- RibbonsRenderer() - Constructor for class org.jmol.renderbio.RibbonsRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.BackboneRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.CartoonRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.RocketsRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.StrandsRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.TraceRenderer
- right - Variable in class jspecview.common.PanelData
- right - Static variable in class org.jmol.script.T
- RIGHT - Static variable in class org.jmol.awtjs.swing.SwingConstants
- RIGHT - Static variable in class org.jmol.viewer.binding.Binding
- rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- rightbrace - Static variable in class org.jmol.script.T
- rightDifference(Quat) - Method in class javajs.util.Quat
- rightJustify(String, String) - Static method in class jme.JMEUtil
- rightJustify(SB, String, String) - Static method in class javajs.util.PT
- rightMargin - Static variable in class jspecview.common.PanelData
- rightparen - Static variable in class org.jmol.script.T
- rightsquare - Static variable in class org.jmol.script.T
- RL() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- rldecode32(byte[], int) - Static method in class javajs.util.MessagePackReader
-
mmtf type 7 Decode an array of int32 using run-length decoding.
- rldecode32Delta(byte[], int) - Static method in class javajs.util.MessagePackReader
-
mmtf type 8 Decode an array of int32 using run-length decoding of a difference array.
- rldecode32ToChar(byte[], int) - Static method in class javajs.util.MessagePackReader
-
mmtf type 6 Decode an array of int32 using run-length decoding to one char per int.
- rldecode32ToStr(byte[]) - Static method in class javajs.util.MessagePackReader
-
mmtf type 5 Decode each four bytes as a 1- to 4-character string label where a 0 byte indicates end-of-string.
- rldecodef(byte[], int, float) - Static method in class javajs.util.MessagePackReader
-
mmtf type 9 Decode an array of int32 using run-length decoding and divide by a divisor to give a float32.
- rmsd - Static variable in class org.jmol.script.T
- rna - Static variable in class org.jmol.script.T
- RNA - Enum constant in enum class org.jmol.c.STR
- RNA_MASK - Static variable in class org.jmol.viewer.JC
- rna3d - Static variable in class org.jmol.script.T
- rNums - Static variable in interface org.apache.tools.bzip2.BZip2Constants
-
This array really shouldn't be here.
- rock - Static variable in class org.jmol.script.T
- rocket - Static variable in class org.jmol.script.T
- rocketbarrels - Static variable in class org.jmol.script.T
- RocketRenderer - Class in org.jmol.renderbio
- RocketRenderer() - Constructor for class org.jmol.renderbio.RocketRenderer
- Rockets - Class in org.jmol.shapebio
- Rockets() - Constructor for class org.jmol.shapebio.Rockets
- RocketsRenderer - Class in org.jmol.renderbio
- RocketsRenderer() - Constructor for class org.jmol.renderbio.RocketsRenderer
- ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
- rotate - Static variable in class org.jmol.script.T
- rotate(T3) - Method in class javajs.util.M34
- ROTATE_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- ROTATE_EVENT - Static variable in class com.sparshui.GestureType
- ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- ROTATE_GESTURE - Static variable in class com.sparshui.GestureType
- ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- rotate2(T3, T3) - Method in class javajs.util.M34
-
Transform the vector vec using this Matrix3f and place the result into vecOut.
- rotate3DBall(float, float, BS) - Method in class org.jmol.viewer.TransformManager
- rotate45 - Static variable in class org.jmol.script.T
- rotate4DBall(float, float, float) - Method in class org.jmol.viewer.TransformManager4D
- rotateAboutPointsInternal(JmolScriptEvaluator, P3, P3, float, float, boolean, BS, V3, Lst<P3>, float[], M4, boolean) - Method in class org.jmol.viewer.Viewer
- rotateAxes(int, V3[], P3, M3) - Method in interface org.jmol.api.SymmetryInterface
- rotateAxes(int, V3[], P3, M3) - Method in class org.jmol.symmetry.Symmetry
- rotateAxisAngle(V3, float) - Method in class org.jmol.viewer.TransformManager
- rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.Viewer
- rotateAxisAngleRadiansFixed(float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateAxisAngleRadiansInternal(float, BS, M4, boolean) - Method in class org.jmol.viewer.TransformManager
- RotateEvent - Class in com.sparshui.common.messages.events
- RotateEvent() - Constructor for class com.sparshui.common.messages.events.RotateEvent
- RotateEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.RotateEvent
-
Constructs a new Rotate Event based on a serial representation of a rotate event.
- RotateEvent(float, Location, long) - Constructor for class com.sparshui.common.messages.events.RotateEvent
- rotateFront() - Method in class org.jmol.api.JmolViewer
- rotateFront() - Method in class org.jmol.viewer.Viewer
- rotateHexCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- rotatePoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
- rotateSelected - Static variable in class org.jmol.script.T
- rotateTranslate(Quat, T3, boolean) - Method in class org.jmol.shape.Mesh
- rotateXRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager4D
- rotateYRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
- rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
- rotation - Static variable in class org.jmol.script.T
- rotationradius - Static variable in class org.jmol.script.T
- rotTrans(T3) - Method in class javajs.util.M4
-
Transforms the point parameter with this Matrix4f and places the result back into point.
- rotTrans2(T3, T3) - Method in class javajs.util.M4
-
Transforms the point parameter with this Matrix4f and places the result into pointOut.
- round() - Method in class org.openscience.jmol.app.janocchio.Measure
- round(double) - Static method in class org.jmol.export.___Exporter
- round(float) - Method in class javajs.util.M4
- round(T3) - Static method in class org.jmol.export.___Exporter
- roundInt(int) - Static method in class org.jmol.util.GData
-
JavaScript won't really have an integer here after integer division.
- row - Static variable in class org.jmol.script.T
- ROYGB - Static variable in class org.jmol.util.ColorEncoder
- rubberband - Static variable in class org.jmol.script.T
- run() - Method in class com.sparshui.client.ClientServerConnection
-
Begin processing requests.
- run() - Method in class com.sparshui.server.GestureServer
-
Start accepting connections.
- run() - Method in class com.sparshui.server.InputDeviceConnection
-
Begin receiving data from the input device.
- run() - Method in class jspecview.java.AwtPanel.RequestThread
- run() - Method in class org.jmol.io.FileReader
- run() - Method in class org.jmol.io.FilesReader
- run() - Method in class org.jmol.script.CommandWatcherThread
- run() - Method in class org.jmol.script.ScriptProcessRunnable
- run() - Method in class org.jmol.thread.JmolThread
- run() - Method in class org.openscience.jmol.app.InputScannerThread
- run() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
- run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
- run1(int) - Method in class org.jmol.minimize.MinimizationThread
- run1(int) - Method in class org.jmol.navigate.Navigator
- run1(int) - Method in class org.jmol.script.CommandWatcherThread
- run1(int) - Method in class org.jmol.script.ScriptQueueThread
- run1(int) - Method in class org.jmol.thread.AnimationThread
- run1(int) - Method in class org.jmol.thread.HoverWatcherThread
- run1(int) - Method in class org.jmol.thread.JmolThread
- run1(int) - Method in class org.jmol.thread.MoveToThread
- run1(int) - Method in class org.jmol.thread.SpinThread
-
Java: run1(INIT) while(!interrupted()) { run1(MAIN) } run1(FINISH) JavaScript: run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or run1(FINISH) and return
- run1(int) - Method in class org.jmol.thread.TimeoutThread
- run1(int) - Method in class org.jmol.thread.VibrationThread
- RUNA - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- runAllProcesses(Viewer) - Method in interface org.jmol.api.JmolParallelProcessor
- runAllProcesses(Viewer) - Method in class org.jmol.script.ScriptParallelProcessor
- runAsync(JMEUtil.RunAsyncCallback) - Static method in class jme.JMEUtil
- RUNB - Static variable in interface org.apache.tools.bzip2.BZip2Constants
- runBufferedSafely(String, SB) - Method in class org.jmol.script.ScriptEval
- runButton - Variable in class org.jmol.console.GenericConsole
- runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- runScript(String) - Method in interface jspecview.api.JSVAppletInterface
-
runs a script in proper order as listed
- runScript(String) - Method in interface jspecview.api.ScriptInterface
- runScript(String) - Method in class jspecview.app.JSVApp
- runScript(String) - Method in class jspecview.appletjs.JSVApplet
- runScript(String) - Method in class jspecview.application.JSpecView
-
for the applet, this is queued
- runScript(String) - Method in class jspecview.application.MainFrame
-
ScriptInterface requires this.
- runScript(String) - Method in class jspecview.common.JSViewer
- runScript(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- runScript(String) - Method in class org.jmol.api.JmolViewer
-
starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older version
- runScript(String) - Method in interface org.jmol.api.JSVInterface
- runScript(String) - Method in class org.jmol.script.ScriptEval
- runScript(String) - Method in class org.jmol.viewer.Viewer
-
Run a script immediately using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )
- runScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
no queuing here -- called by MainFrame
- runScriptBuffer(String, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- runScriptBuffer(String, SB, boolean) - Method in class org.jmol.script.ScriptEval
-
runs a script immediately and sends selected output to a provided SB
- runScriptCautiously(String) - Method in class org.jmol.api.JmolViewer
-
Formerly runScript(script).
- runScriptCautiously(String) - Method in class org.jmol.viewer.Viewer
-
formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script.
- runScriptFromThread(Lst<Object>) - Method in class org.jmol.script.ScriptManager
- runScriptNow() - Method in class org.jmol.script.ScriptManager
- runScriptNow(String) - Method in interface jspecview.api.JSVAppletInterface
- runScriptNow(String) - Method in interface jspecview.api.ScriptInterface
- runScriptNow(String) - Method in class jspecview.app.JSVApp
- runScriptNow(String) - Method in class jspecview.appletjs.JSVApplet
- runScriptNow(String) - Method in class jspecview.application.JSpecView
- runScriptNow(String) - Method in class jspecview.application.MainFrame
- runScriptNow(String) - Method in class jspecview.common.JSViewer
- runSleep(int, int) - Method in class org.jmol.thread.JmolThread
- runsmi - Variable in class jme.JME
- runUserAction(String, Object[], Viewer) - Static method in class org.jmol.script.ScriptEval
- RWB - Static variable in class org.jmol.util.ColorEncoder
- rxyz - Static variable in class org.jmol.script.T
S
- S - Static variable in class org.jmol.quantum.QS
- s1 - Variable in class org.jmol.render.FontLineShapeRenderer
- s2 - Variable in class org.jmol.render.FontLineShapeRenderer
- safeJSON(String, Object) - Static method in class org.jmol.script.SV
-
Safely create a JSON key - object pair, allowing for already-named arrays
- safeTruncate(float, int) - Static method in class javajs.util.PT
- sameAs(int, int) - Method in class org.jmol.modelset.Measurement
- sameAsPoints(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
- sampleID - Variable in class jspecview.source.AnIMLReader
- samplenum - Variable in class jspecview.source.AnIMLReader
- sampleowner - Variable in class jspecview.source.AnIMLReader
- sampleRefNum - Variable in class jspecview.source.AnIMLReader
- sasurface - Static variable in class org.jmol.script.T
- SAUSAGE - Static variable in class org.jmol.shapecgo.CGOMesh
- save - Static variable in class org.jmol.script.T
- save() - Method in class org.openscience.jmol.app.HistoryFile
-
Saves properties to the history file.
- saveAtomPositions() - Method in class org.jmol.modelset.ModelSet
- saveBonds(String) - Method in class org.jmol.viewer.StateManager
- saveContext(String, Object) - Method in class org.jmol.viewer.StateManager
- saveCoordinates(String, BS) - Method in class org.jmol.viewer.StateManager
- saved - Static variable in class org.jmol.script.T
- saved - Variable in class org.jmol.viewer.StateManager
- saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
- saveImage(String, GenericFileInterface, OC) - Method in interface jspecview.api.JSVPanel
- saveImage(String, GenericFileInterface, OC) - Method in class jspecview.java.AwtPanel
- saveImage(String, GenericFileInterface, OC) - Method in class jspecview.js2d.JsPanel
- saveImage(JSAppletObject, String, String) - Method in interface javajs.api.js.J2SObjectInterface
- saveModelOrientation(int, Orientation) - Method in class org.jmol.modelset.ModelSet
- saveName - Variable in class org.jmol.modelset.Orientation
- saveOrientation(String, float[]) - Method in class org.jmol.viewer.StateManager
- savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- saveProperties(Properties) - Method in class jspecview.app.JSVAppPro
- saveProperties(Properties) - Method in class jspecview.application.JSpecView
- saveProperties(Properties) - Method in interface org.jmol.api.JSVInterface
- saveProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- saveproteinstructurestate - Static variable in class org.jmol.script.T
- saveScene(String, Map<String, Object>) - Method in class org.jmol.viewer.StateManager
- saveSelection(String, BS) - Method in class org.jmol.viewer.StateManager
- saveState(String) - Method in class org.jmol.viewer.StateManager
- saveStructure(String) - Method in class org.jmol.viewer.StateManager
- saveUnitCell(String) - Method in class org.jmol.viewer.StateManager
- saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
- saveWindowSizes() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- saveWindowSizes() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- saveXY() - Method in class jme.JMEmol
- saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Saves the currently active collection as a multistep XYZ file.
- say(String) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SB - Class in javajs.util
-
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
- SB() - Constructor for class javajs.util.SB
- sbKey - Variable in class org.jmol.minimize.MinAngle
- sbOut - Variable in class org.jmol.jvxl.data.JvxlData
- sbOut - Variable in class org.jmol.jvxl.readers.Parameters
- sbType - Variable in class org.jmol.minimize.MinAngle
- sc - Variable in class org.jmol.thread.JmolThread
- SC - Interface in org.jmol.api
-
SwingComponent interface common to javax.swing and org.jmol.awtjs.swing Can be augmented as needed, provided classes of org.jmol.awtjs.swing are also updated.
- scale - Variable in class org.jmol.modelset.TickInfo
- scale - Static variable in class org.jmol.script.T
- scale - Variable in class org.jmol.shape.Axes
- scale - Variable in class org.jmol.shapespecial.DrawMesh
- scale - Variable in class org.jmol.shapespecial.Polyhedron
- scale(double) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the scalar multiplication of itself.
- scale(float) - Method in class javajs.util.M3
-
Multiplies each element of this matrix by a scalar.
- scale(float) - Method in class javajs.util.M4
-
Multiplies each element of this matrix by a scalar.
- scale(float) - Method in class javajs.util.T3
-
Sets the value of this tuple to the scalar multiplication of itself.
- scale3d - Variable in class org.jmol.jvxl.data.JvxlData
- scale3d - Variable in class org.jmol.jvxl.readers.Parameters
- scale3d - Static variable in class org.jmol.script.T
- scale3d - Variable in class org.jmol.shape.Mesh
- scale3D - Variable in class org.jmol.viewer.TransformManager
- scale4(float) - Method in class javajs.util.T4
-
Sets the value of this tuple to the scalar multiplication of itself.
- scaleAdd(double, T3d, T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
- scaleAdd(int, T3i, T3i) - Method in class javajs.util.T3i
-
Sets the value of this tuple to the scalar multiplication of tuple t1 plus tuple t2 (this = s*t1 + t2).
- scaleAdd(Matrix, double) - Method in class javajs.util.Matrix
-
X = A + B*scale
- scaleAdd2(double, T3d, T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
- scaleAdd2(float, T3, T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
- scaleangstromsperinch - Static variable in class org.jmol.script.T
- scaleAxes(float[]) - Method in class org.jmol.shapespecial.Ellipsoid
- scaleBox(P3[], float) - Static method in class org.jmol.util.BoxInfo
- SCALEBY - Enum constant in enum class jspecview.common.ScriptToken
- scaleColor - Variable in class jspecview.common.PanelData
- SCALECOLOR - Enum constant in enum class jspecview.common.ScriptToken
- ScaleData - Class in jspecview.common
-
Stores information about scale and range that
JSVPanel
needs to to display a graph with a single plot. - ScaleData(Coordinate[], int, int, boolean, boolean) - Constructor for class jspecview.common.ScaleData
-
Calculates values that
JSVPanel
needs in order to render a graph, (eg. - scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
- scaleFractionalVibs() - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes.
- scaleObject - Variable in class org.jmol.shape.Echo
- scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
- scalePixelsPerMicron - Variable in class org.jmol.modelset.Text
- scalePixelsPerMicron - Variable in class org.jmol.render.MeshRenderer
- scaleSelectedBy(double) - Method in class jspecview.common.PanelData
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Perform implementation-specific scaling.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
-
Perform implementation-specific scaling.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
Perform implementation-specific scaling.
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.AmsReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.DgridReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
- scaleSpectrum(int, double) - Method in class jspecview.common.ViewData
- scaleT(T3) - Method in class javajs.util.T3
-
{x*p.x, y*p.y, z*p.z) used for three-way scaling
- scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
- scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
- scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
- scaleVectorsToMax(float) - Method in class org.jmol.modelset.AtomCollection
-
Scales vibrations and associated vectors such that the maximum length is the given value
- scaleVibration(float) - Method in interface org.jmol.api.JmolModulationSet
- scaleVibration(float) - Method in class org.jmol.util.ModulationSet
- scaleYBy(double) - Method in class jspecview.common.PanelData
- scalingFactor - Variable in class jspecview.common.PanelData
- scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
- scene - Static variable in class org.jmol.script.T
- SCENE_TAG - Static variable in class org.jmol.viewer.OutputManagerAwt
- SCENE_TAG - Static variable in class org.jmol.viewer.OutputManagerJS
- schemes - Variable in class org.jmol.util.ColorEncoder
- scm - Variable in class org.jmol.viewer.Viewer
- score - Variable in class org.jmol.util.ContactPair
- scrCoords - Variable in class org.jmol.renderspecial.DotsRenderer
- SCREEN - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
- screenDotCount - Variable in class org.jmol.renderspecial.DotsRenderer
- screenHeight - Variable in class org.jmol.export.___Exporter
- screenLevel - Variable in class org.jmol.renderspecial.DotsRenderer
- screenLocation(Location) - Static method in class com.sparshui.common.Location
- screenPixelCount - Variable in class org.jmol.viewer.TransformManager
- screens - Variable in class org.jmol.render.MeshRenderer
- screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- screenWidth - Variable in class org.jmol.export.___Exporter
- screenx - Static variable in class org.jmol.script.T
- screenxyz - Static variable in class org.jmol.script.T
- screeny - Static variable in class org.jmol.script.T
- screenz - Static variable in class org.jmol.script.T
- script - Variable in class org.jmol.jvxl.readers.Parameters
- script - Variable in class org.jmol.modelset.Text
- script - Variable in class org.jmol.script.ScriptContext
- script - Variable in class org.jmol.script.ScriptCompiler
- script - Static variable in class org.jmol.script.T
- script - Variable in class org.jmol.thread.TimeoutThread
- script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- script(String) - Method in class jspecview.appletjs.JSVApplet
-
Deprecated.
- script(String) - Method in class jspecview.appletjs.JSVAppletPro
-
JSVAppletPro uses "script()" for executing a real script, not a parameter initialization.
- script(String) - Method in interface org.jmol.api.JmolAppletInterface
- script(String) - Method in class org.jmol.api.JmolViewer
- script(String) - Method in class org.jmol.util.GenericApplet
- script(String) - Method in class org.jmol.viewer.Viewer
- SCRIPT - Enum constant in enum class jspecview.common.ScriptToken
- SCRIPT - Enum constant in enum class org.jmol.c.CBK
- SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.JC
- SCRIPT_CONSOLE - Static variable in class org.jmol.viewer.JC
- SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JC
- SCRIPT_EXT - Static variable in class org.jmol.viewer.JC
- SCRIPT_GUI - Static variable in class org.jmol.viewer.JC
- SCRIPT_ISEDITOR - Static variable in class org.jmol.viewer.JC
- SCRIPT_NOENDCHECK - Static variable in class org.jmol.viewer.JC
- SCRIPT_ONLY - Static variable in interface org.jmol.api.JmolScriptManager
- SCRIPT_QUIET - Static variable in class org.jmol.viewer.JC
- SCRIPT_START - Static variable in class org.jmol.viewer.JC
- SCRIPT_STEP - Static variable in class org.jmol.viewer.JC
- SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- scriptCallback(String) - Method in class org.molecularplayground.MPJmolApp
- scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptCheck(String) - Method in class org.jmol.api.JmolViewer
- scriptCheck(String) - Method in class org.jmol.util.GenericApplet
- scriptCheck(String) - Method in class org.jmol.viewer.Viewer
- scriptCheckRet(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
- scriptCheckRet(String, boolean) - Method in class org.jmol.script.ScriptManager
- scriptCommand - Static variable in class org.jmol.script.T
- scriptCommand - Variable in class org.jmol.shape.Mesh
- ScriptCompiler - Class in org.jmol.script
- ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
- scriptCompleted(StatusManager, String, String) - Method in class org.jmol.viewer.ChimeMessenger
-
called when a script exits.
- scriptCompleted(StatusManager, String, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
- ScriptContext - Class in org.jmol.script
- scriptEcho(String) - Method in class org.jmol.viewer.Viewer
- scriptEditor - Variable in class org.jmol.console.JmolConsole
- ScriptEditor - Class in org.jmol.console
- ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
- ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
- scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
- ScriptError - Class in org.jmol.script
-
Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
- ScriptError() - Constructor for class org.jmol.script.ScriptError
- ScriptEval - Class in org.jmol.script
- ScriptEval() - Constructor for class org.jmol.script.ScriptEval
- ScriptException - Exception Class in org.jmol.script
- ScriptExt - Class in org.jmol.scriptext
- ScriptExt() - Constructor for class org.jmol.scriptext.ScriptExt
- scriptFileName - Variable in class org.jmol.script.ScriptContext
- scriptFileName - Variable in class org.jmol.script.ScriptEval
- ScriptFunction - Class in org.jmol.script
- ScriptFunction() - Constructor for class org.jmol.script.ScriptFunction
- ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
- ScriptInterface - Interface in jspecview.api
- ScriptInterruption - Exception Class in org.jmol.script
- ScriptInterruption(ScriptEval, String, int) - Constructor for exception class org.jmol.script.ScriptInterruption
- scriptLevel - Variable in class org.jmol.script.ScriptEval
- ScriptManager - Class in org.jmol.script
- ScriptManager() - Constructor for class org.jmol.script.ScriptManager
- ScriptMathProcessor - Class in org.jmol.script
-
Reverse Polish Notation Engine for IF, SET, and @{...} Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f -- Bob Hanson 2/16/2007
- scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptNoWait(String) - Method in class org.jmol.util.GenericApplet
- ScriptParallelProcessor - Class in org.jmol.script
- ScriptParallelProcessor() - Constructor for class org.jmol.script.ScriptParallelProcessor
-
parallel operations
- ScriptParam - Class in org.jmol.script
-
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
- ScriptParam() - Constructor for class org.jmol.script.ScriptParam
- ScriptProcessRunnable - Class in org.jmol.script
- ScriptProcessRunnable(ScriptParallelProcessor, ScriptProcess, Object, ShapeManager) - Constructor for class org.jmol.script.ScriptProcessRunnable
- scriptqueue - Static variable in class org.jmol.script.T
- scriptQueue - Variable in class jspecview.common.JSViewer
- scriptQueue - Variable in class org.jmol.script.ScriptManager
- ScriptQueueThread - Class in org.jmol.script
- ScriptQueueThread(ScriptManager, Viewer, boolean, int) - Constructor for class org.jmol.script.ScriptQueueThread
- scriptreportinglevel - Static variable in class org.jmol.script.T
- scriptStatus(String) - Method in class org.jmol.viewer.Viewer
-
scriptCallback is the primary way to monitor script status.
- scriptStatusMsg(String, String) - Method in class org.jmol.viewer.Viewer
- ScriptToken - Enum Class in jspecview.common
-
ScriptToken takes care of script command processing
- ScriptTokenizer - Class in jspecview.common
- ScriptTokenizer(String, boolean) - Constructor for class jspecview.common.ScriptTokenizer
- scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptWait(String) - Method in class org.jmol.api.JmolViewer
- scriptWait(String) - Method in class org.jmol.util.GenericApplet
- scriptWait(String) - Method in class org.jmol.viewer.Viewer
- scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptWait(String, String) - Method in class org.jmol.util.GenericApplet
- scriptWaitOutput(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptWaitOutput(String) - Method in class org.jmol.util.GenericApplet
- scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
- scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
- ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
- sD - Variable in class org.jmol.util.Point3fi
-
screen diameter
- search - Static variable in class org.jmol.script.T
- SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
- seek(long) - Method in interface javajs.api.GenericBinaryDocument
- seek(long) - Method in class javajs.util.BinaryDocument
- SEESAW - Static variable in class org.jmol.smiles.SmilesStereo
- select - Static variable in class org.jmol.script.T
- select(BS, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
- SELECT - Enum constant in enum class jspecview.common.ScriptToken
- SELECT - Enum constant in enum class org.jmol.c.CBK
- selectAll() - Method in class org.jmol.api.JmolViewer
- selectAll() - Method in class org.jmol.viewer.Viewer
- selectAll(boolean) - Method in class jspecview.dialog.ViewsDialog
- selectallmodels - Static variable in class org.jmol.script.T
- selectBonds(BS) - Method in class org.jmol.viewer.Viewer
- selectDisplayed(BS) - Method in class org.jmol.modelset.Trajectory
-
Remove trajectories that are not currently displayed from the visible frames bitset.
- selected - Static variable in class org.jmol.script.T
- selectedfloat - Static variable in class org.jmol.script.T
- selectedGroupCount - Variable in class org.jmol.modelset.Chain
-
Calculated just prior to coloring by group so that the range is appropriate for each chain.
- selectedIndex - Variable in class org.jmol.modelset.Group
-
for coloring by group
- selectedPanel - Variable in class jspecview.common.JSViewer
- selectedPolyOnly - Variable in class org.jmol.render.MeshRenderer
- selectedRow - Variable in class jspecview.java.AwtDialog
- selectedRow - Variable in class jspecview.js2d.JsDialog
- selectedTrajectory - Variable in class org.jmol.modelset.Model
- selectedTreeNode(JSVTreeNode) - Method in class jspecview.common.JSViewer
- selectFrameNode(JSVPanel) - Method in class jspecview.common.JSViewer
- selectFromEntireSet(int) - Method in class jspecview.common.PanelData
-
sets bsSelected to the specified pointer from "select 3.1*1"
- selecthetero - Static variable in class org.jmol.script.T
- selecthydrogen - Static variable in class org.jmol.script.T
- selection - Static variable in class org.jmol.script.T
- selectionChanged(BS) - Method in interface org.jmol.api.JmolSelectionListener
-
Called when the selected atoms change
- selectionhalos - Static variable in class org.jmol.script.T
- SelectionManager - Class in org.jmol.viewer
- selectPanel(JSVPanel, Lst<PanelNode>) - Method in class jspecview.common.JSViewer
- selectPeakByFileIndex(String, String, String) - Method in class jspecview.common.PanelData
- selectPeakByFileIndex(String, String, String) - Method in class jspecview.common.Spectrum
- selectPeakByFilePathTypeModel(String, String, String) - Method in class jspecview.common.Spectrum
- selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- selectSpectrum(String, String, String, boolean) - Method in class jspecview.common.PanelData
- selectStatus(BS, boolean, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
"SELECT" starting with comma triggers the SELECT callback from a SELECT command.
- selectTableRow(int) - Method in interface jspecview.api.PlatformDialog
- selectTableRow(int) - Method in class jspecview.dialog.JSVDialog
- selectTableRow(int) - Method in class jspecview.java.AwtDialog
- selectTableRow(int) - Method in class jspecview.js2d.JsDialog
- semicolon - Static variable in class org.jmol.script.T
- sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- sendConsoleEcho(String) - Method in class org.jmol.console.GenericConsole
- sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- sendConsoleMessage(String) - Method in class org.jmol.console.GenericConsole
- sendConsoleMessage(String) - Method in class org.jmol.viewer.Viewer
- sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- sendMessage(Map<String, Object>, String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- sendPanelChange() - Method in class jspecview.common.JSViewer
- sendToJmol(int, String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
-
from JmolPanel and SYNC command
- sendToJmol(int, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
-
send the message - not for replies.
- seqcode - Variable in class org.jmol.modelset.Group
- seqcode - Static variable in class org.jmol.script.T
- seqid - Static variable in class org.jmol.script.T
- sequence - Static variable in class org.jmol.script.T
- sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
- serialize() - Method in interface com.sparshui.common.Event
-
Serializes this event for transmission over the network.
- serialize() - Method in class com.sparshui.common.messages.events.DragEvent
-
Constructs the data packet with this event data.
- serialize() - Method in class com.sparshui.common.messages.events.FlickEvent
-
Constructs the data packet with this event data.
- serialize() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
-
Constructs the data packet with this event data.
- serialize() - Method in class com.sparshui.common.messages.events.RotateEvent
-
Constructs the data packet with this event data.
- serialize() - Method in class com.sparshui.common.messages.events.SpinEvent
-
Constructs the data packet with this event data.
- serialize() - Method in class com.sparshui.common.messages.events.TouchEvent
-
Constructs the data packet with this event data.
- serialize() - Method in class com.sparshui.common.messages.events.ZoomEvent
-
Constructs the data packet with this event data.
- serializeDisplaySchemes(Writer) - Method in class jspecview.application.DisplaySchemesProcessor
-
Serializes the display schemes to the given writer
- serverCycle() - Method in class org.molecularplayground.MPJmolApp
- serverCycle() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- serverCycle() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- ServerToClientProtocol - Class in com.sparshui.server
-
Represents the server to client connection.
- ServerToClientProtocol(Socket) - Constructor for class com.sparshui.server.ServerToClientProtocol
-
Constructs a new connection to the client.
- service - Variable in class org.molecularplayground.MPJmolApp
- SERVICE - Enum constant in enum class org.jmol.c.CBK
- SERVICE_LOST - Static variable in class com.sparshui.common.messages.events.EventType
- SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
- set - Static variable in class org.jmol.script.T
- set(double, double) - Method in class jspecview.common.Coordinate
-
Constructor
- set(double, double, double) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the specified xyz coordinates.
- set(float, float, float) - Method in class javajs.util.T3
-
Sets the value of this tuple to the specified xyz coordinates.
- set(float, float, float) - Method in interface org.jmol.util.Node
- set(int) - Method in class javajs.util.BS
-
Sets the bit at the specified index to
true
. - set(int) - Method in class javajs.util.Eigen
- set(int, int) - Method in class org.jmol.awtjs.swing.Dimension
- set(int, int, char, int, int, char, int, int) - Method in class org.jmol.adapter.smarter.Structure
- set(int, int, int) - Method in class javajs.util.T3i
-
Sets the value of this tuple to to the specified x, y, and z coordinates.
- set(int, Map<String, Integer>, RadiusData, String, String, String, TickInfo, boolean, boolean, Boolean, boolean, int, short, Text, float, BS) - Method in class org.jmol.modelset.MeasurementData
- set(int, BS, int[]) - Method in class org.jmol.minimize.MMConstraint
- set(InputStream, String[], String) - Method in interface jspecview.api.JSVZipReader
- set(InputStream, String[], String) - Method in class jspecview.common.JSVZipFileSequentialReader
- set(Object, PrintLayout, boolean) - Method in interface jspecview.api.JSVPrintDialog
- set(Object, PrintLayout, boolean) - Method in class jspecview.java.AwtPrintDialog
-
Initialises a modal
PrintLayoutDialog
with a default title of "Print Layout". - set(String) - Method in class org.jmol.viewer.binding.JmolBinding
- set(String, int) - Method in interface org.jmol.api.JmolParallelProcessor
- set(String, int) - Method in class org.jmol.script.ScriptFunction
- set(GenericLineReader, BufferedReader, boolean) - Method in interface javajs.api.GenericCifDataParser
- set(GenericLineReader, BufferedReader, boolean) - Method in class javajs.util.CifDataParser
-
A Chemical Information File data parser.
- set(Quat) - Method in class javajs.util.Quat
- set(JSViewer) - Method in interface jspecview.api.JSVFileDropper
- set(JSViewer) - Method in interface jspecview.api.JSVFileHelper
- set(JSViewer) - Method in class jspecview.dialog.DialogManager
- set(JSViewer) - Method in class jspecview.java.AwtFileDropper
- set(JSViewer) - Method in class jspecview.java.AwtFileHelper
- set(JSViewer) - Method in class jspecview.js2d.JsFileHelper
- set(PanelData, ScriptToken, String) - Method in class jspecview.common.ColorParameters
- set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
- set(AtomSetCollectionReader) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- set(JmolJDXMOLReader, String, Map<String, Object>) - Method in interface org.jmol.api.JmolJDXMOLParser
- set(JmolJDXMOLReader, String, Map<String, Object>) - Method in class org.jmol.jsv.JDXMOLParser
- set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.CircleRenderer
- set(JmolRendererInterface, GData) - Method in interface org.jmol.g3d.G3DRenderer
- set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.HermiteRenderer
- set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.TriangleRenderer
- set(SymmetryInterface, Atom, Atom[], BS, float) - Method in class org.jmol.symmetry.UnitCellIterator
- set(AtomDataServer, int, short[]) - Method in interface org.jmol.api.JmolEnvCalc
- set(AtomDataServer, int, short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
- set(ModelSet) - Method in class org.jmol.modelset.MeasurementPending
- set(ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
- set(ModelSet, int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelset.Model
- set(MeshSlicer) - Method in class org.jmol.util.MeshCapper
- set(FileManager) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
- set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
- set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.io.FilesReader
- set(TransformManager, Viewer) - Method in interface org.jmol.api.JmolNavigatorInterface
- set(TransformManager, Viewer) - Method in class org.jmol.navigate.Navigator
- set(Viewer) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- set(Viewer) - Method in interface org.jmol.api.JmolDataManager
- set(Viewer) - Method in class org.jmol.quantum.MepCalculation
- set(Viewer) - Method in class org.jmol.viewer.ChimeMessenger
- set(Viewer) - Method in class org.jmol.viewer.DataManager
- set(Viewer) - Method in interface org.jmol.viewer.JmolChimeMessenger
- set(Viewer, BS) - Method in class org.jmol.symmetry.CIPData
-
Actual constructor.
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CDXMLWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CIFWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CMLWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PDBWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PWMATWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.QCJSONWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.XSFWriter
- set(Viewer, OC, Object[]) - Method in interface org.jmol.api.JmolWriter
- set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioModelSet
- set(Viewer, ShapeManager) - Method in interface org.jmol.api.JmolRepaintManager
- set(Viewer, ShapeManager) - Method in class org.jmol.render.RepaintManager
- set2(int, boolean) - Method in class org.jmol.smiles.SmilesBond
- set2(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.Monomer
- set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- set2DCrossHairsLinked(GraphSet, double, double, boolean) - Method in class jspecview.common.PanelData
- set33(int, int, float) - Method in class javajs.util.M34
- set3dContourVector(Lst<Object>, int[][], T3[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
- set4(float, float, float, float) - Method in class javajs.util.A4
-
Sets the value of this axis angle to the specified x,y,z,angle.
- set4(float, float, float, float) - Method in class javajs.util.T4
-
Sets the value of this tuple to the specified xyzw coordinates.
- setA(double[]) - Method in class javajs.util.T3d
-
Sets the value of this tuple from the 3 values specified in the array.
- setA(double, double, Spectrum, String, boolean, boolean, int, int) - Method in class jspecview.common.Annotation
- setA(float[]) - Method in class javajs.util.M3
-
Sets the values in this Matrix3f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
- setA(float[]) - Method in class javajs.util.M4
-
Sets the values in this Matrix4f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
- setA(float[]) - Method in class javajs.util.T3
-
Sets the value of this tuple from the 3 values specified in the array.
- setAA(A4) - Method in class javajs.util.A4
-
Sets the value of this axis angle to the value of axis angle t1.
- setAA(A4) - Method in class javajs.util.M3
-
Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.
- setAA(A4) - Method in class javajs.util.Quat
- setAA33(A4) - Method in class javajs.util.M34
- setAbc(String, float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
-
set cell vectors by string.
- setABC(int) - Method in class org.jmol.util.MeshSurface
- setAbcFromParams(float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
- setAbstractButtonLabels(Map<String, Object>, Map<String, String>) - Static method in class org.jmol.console.GenericConsole
- setACDAssignments(String, String, int, Lst<String[]>, String) - Method in interface org.jmol.api.JmolJDXMOLParser
- setACDAssignments(String, String, int, Lst<String[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
- setActionCommand(String) - Method in interface org.jmol.api.SC
- setActionCommand(String) - Method in class org.jmol.awt.AwtSwingComponent
- setActionCommand(String) - Method in class org.jmol.awtjs.swing.JComponent
- setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
-
Changes the activation state for a logging level.
- setActiveMenu(String) - Method in class org.jmol.modelkit.ModelKitPopup
-
Set the active menu and request a repaint.
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.P2nReader
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
adaptable via subclassing
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PqrReader
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- setAlignment(int) - Method in class org.jmol.modelset.Text
- setAlignmentLCR(String) - Method in class org.jmol.modelset.Text
- setAll(int) - Static method in class org.jmol.util.BSUtil
- setAll(P3, M3, P3, float, float, float, float, float, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
- setAllConformation(BS) - Method in class org.jmol.modelsetbio.BioModelSet
- setAllowJSThreads(boolean) - Method in class org.jmol.script.ScriptEval
- setAllProteinType(BS, STR) - Method in class org.jmol.modelsetbio.BioModelSet
-
called from state STRUCTURE command
- setAllStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.BioModelSet
- setAmbientOcclusion(int) - Method in class org.jmol.util.GData
- setAmbientPercent(int) - Method in class org.jmol.util.GData
-
fractional distance from black for ambient color
- setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
- setAnimation(int) - Method in class org.jmol.viewer.Viewer
- setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
- setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
- setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
- setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
- setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
- setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
- setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
- setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.AnimationManager
- setAnimDisplay(BS) - Method in class org.jmol.viewer.Viewer
- setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAPa(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
- setAPm(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
- setApplicationProperties(boolean) - Method in class jspecview.application.JSpecView
- setArrays(Atom[], BS, Bond[], int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- setAsBallRotation(float, float, float) - Method in class javajs.util.M3
-
3D ball rotation from dx dy in-plane mouse motion adapted from Andrew Hanson Computer Graphics beyond the Third Dimension: Geometry, Orientation Control, and Rendering for Graphics in Dimensions Greater than Three Course Notes for SIGGRAPH ’98 http://www.cse.ohio-state.edu/~hwshen/888_su02/hanson_note.pdf
- setAsBallRotation(M4, float, float, float, float) - Method in class org.jmol.viewer.TransformManager4D
-
4D ball rotation from nominal dx, dy, dz motion.
- setAsXRotation(float) - Method in class javajs.util.M3
-
Sets the value of this matrix to a rotation matrix about the x axis by the passed angle.
- setAsXYRotation(float) - Method in class javajs.util.M4
-
Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
- setAsXZRotation(float) - Method in class javajs.util.M4
-
Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
- setAsYRotation(float) - Method in class javajs.util.M3
-
Sets the value of this matrix to a rotation matrix about the y axis by the passed angle.
- setAsYZRotation(float) - Method in class javajs.util.M4
-
Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
- setAsZRotation(float) - Method in class javajs.util.M3
-
Sets the value of this matrix to a rotation matrix about the z axis by the passed angle.
- setAtom(int, int, P3, float, BS, int, short, int, boolean) - Method in class org.jmol.modelset.Atom
- setAtom(Atom, int, int, int, float, float, float) - Method in class org.jmol.adapter.readers.simple.InputReader
- setAtom(Atom, int, String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- setAtomBits(BS) - Method in class org.jmol.modelset.Chain
- setAtomBits(BS) - Method in class org.jmol.modelset.Group
-
note that we may pick up additional bits here that were added later
- setAtomBits(BS) - Method in interface org.jmol.modelset.Structure
- setAtomBits(BS) - Method in class org.jmol.modelsetbio.BioPolymer
- setAtomBits(BS) - Method in class org.jmol.modelsetbio.ProteinStructure
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Chain
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Group
-
Setting and clearing
- setAtomBitsAndClear(BS, BS) - Method in interface org.jmol.modelset.Structure
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.ProteinStructure
- setAtomChooser() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setAtomChooser() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setAtomClickability() - Method in class org.jmol.shape.AtomShape
- setAtomClickability() - Method in class org.jmol.shape.Balls
- setAtomClickability() - Method in class org.jmol.shape.Labels
- setAtomClickability() - Method in class org.jmol.shape.Shape
- setAtomClickability() - Method in class org.jmol.shape.Sticks
- setAtomClickability() - Method in class org.jmol.shapebio.Backbone
- setAtomClickability() - Method in class org.jmol.shapebio.BioShape
- setAtomClickability() - Method in class org.jmol.shapebio.BioShapeCollection
- setAtomClickability() - Method in class org.jmol.shapespecial.Dots
- setAtomClickability() - Method in class org.jmol.shapespecial.Ellipsoids
- setAtomColoring(int, int) - Method in class jme.JMEmol
- setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
- setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomCoord2(BS, int, Object) - Method in class org.jmol.modelset.AtomCollection
- setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
- setAtomCoords(BS, int, Object) - Method in class org.jmol.modelset.ModelSet
- setAtomCoords(BS, int, Object) - Method in class org.jmol.viewer.Viewer
- setAtomCoordScaled(Atom, String[], int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomCoordsRelative(T3, BS) - Method in class org.jmol.modelset.ModelSet
- setAtomCoordsRelative(T3, BS) - Method in class org.jmol.viewer.Viewer
- setAtomCoordTokens(Atom, String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
- setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
- setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
- setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the atomic mass of the atom.
- setAtomIndexes(int, int) - Method in class org.jmol.util.Tensor
- setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
- setAtomMapAnyCase() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomName(int, String, boolean) - Method in class org.jmol.modelset.AtomCollection
- setAtomNamesAndNumbers(int, int, AtomCollection, boolean) - Method in class org.jmol.modelset.ModelSet
- setAtomNumber(int, int, boolean) - Method in class org.jmol.modelset.AtomCollection
- setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptEval
- setAtomProperties(double, double, int, int) - Method in class jme.JMEmol
- setAtomProperties(String, Object, int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
- setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
- setAtoms(Node[], int, BS) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
- setAtomsCoordRelative(BS, float, float, float) - Method in class org.jmol.modelset.AtomCollection
- setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the partial atomic charges based on asc auxiliary info
- setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomSetFrequency(int, String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies
- setAtomSetModelPropertyForSet(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the a property for the an AtomSet
- setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the name for the current AtomSet
- setAtomSetNumber(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomsForSmiles(Viewer, String) - Method in class org.jmol.symmetry.CIPDataSmiles
- setAtomTensors(int, Lst<Object>) - Method in class org.jmol.modelset.AtomCollection
- setAtropisomerOptions() - Method in class org.jmol.modelset.Bond
- setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
- setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
- setAutoscrolls(boolean) - Method in interface org.jmol.api.SC
- setAutoscrolls(boolean) - Method in class org.jmol.awt.AwtSwingComponent
- setAutoscrolls(boolean) - Method in class org.jmol.awtjs.swing.JComponent
- setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
- setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
- setB(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- setBackground(GenericColor) - Method in class org.jmol.awtjs.swing.Component
- setBackgroundArgb(int) - Method in class org.jmol.util.GData
-
sets background color to the specified argb value
- setBackgroundColor(GenericColor) - Method in interface jspecview.api.JSVPanel
- setBackgroundColor(GenericColor) - Method in class jspecview.java.AwtPanel
- setBackgroundColor(GenericColor) - Method in class jspecview.js2d.JsPanel
- setBackgroundImage(Object) - Method in class org.jmol.util.GData
- setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
- setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
- setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
- setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
- setBannerLabel(String) - Method in class org.molecularplayground.MPJmolApp
- setBaseModels(BS) - Method in class org.jmol.modelset.Trajectory
-
set bits for all base models only
- setBbcage(float) - Method in class org.jmol.util.BoxInfo
- setBBox(T3, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setBFactor(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
- setBigEndian(boolean) - Method in interface javajs.api.GenericBinaryDocumentReader
- setBigEndian(boolean) - Method in class javajs.util.BinaryDocument
- setBigEndian(boolean) - Method in class javajs.util.OC
- setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
- setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
- setBioColix(short) - Method in class org.jmol.renderbio.BackboneRenderer
- setBioColix(short) - Method in class org.jmol.renderbio.CartoonRenderer
- setBioColix(short) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- setBioColix(short) - Method in class org.jmol.renderbio.RibbonsRenderer
- setBioColix(short) - Method in class org.jmol.renderbio.RocketsRenderer
- setBioColix(short) - Method in class org.jmol.renderbio.StrandsRenderer
- setBioColix(short) - Method in class org.jmol.renderbio.TraceRenderer
- setBits(int, int) - Method in class javajs.util.BS
-
Sets the bits from the specified
fromIndex
(inclusive) to the specifiedtoIndex
(exclusive) totrue
. - setBitTo(int, boolean) - Method in class javajs.util.BS
-
Sets the bit at the specified index to the specified value.
- setBlockID(double) - Method in class jspecview.source.JDXDataObject
- setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
- setBondArray() - Method in class org.jmol.smiles.SmilesAtom
- setBondingRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
- setBondMeasure(int, MeasurementPending) - Method in class org.jmol.modelkit.ModelKit
- setBondProperties(int, int, int, int) - Method in class jme.JMEmol
- setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
- setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
- setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
- setBoolean(ScriptToken, boolean) - Method in class jspecview.common.PanelData
- setBoolean(ScriptToken, boolean) - Method in class jspecview.common.Parameters
- setBoolean(ScriptToken, ItemEvent) - Method in class jspecview.application.ApplicationMenu
- setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
- setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptParam
- setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
- setBooleanPropertyTok(String, int, boolean) - Method in class org.jmol.viewer.Viewer
- setBooleans(Parameters, ScriptToken) - Method in class jspecview.common.PanelData
- setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.modelset.ModelSet
- setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.util.BoxInfo
- setBoundBoxFromOABC(T3[]) - Method in class org.jmol.util.BoxInfo
- setBoundingBox(P3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setBoundingBox(P3[]) - Method in class org.jmol.util.MeshSurface
- setBox(float, float, P3, V3, V3, P3, float) - Method in class org.jmol.modelsetbio.Sheet
- setBox(P3, P3) - Method in class org.jmol.util.MeshSurface
- setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.modelset.Text
- setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.modelset.Text
- setBSAtomsForSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Add a full set of atoms to BSAtoms if they are not already indicated there.
- setBsHidden(BS) - Method in class org.jmol.modelset.AtomCollection
- setButton(String) - Method in class org.jmol.console.GenericConsole
- setButton(String) - Method in class org.jmol.console.JmolConsole
- setButton(String) - Method in class org.jmol.consolejs.AppletConsole
- setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setBytes(byte[]) - Method in class javajs.util.OC
- setC(short) - Method in interface org.jmol.api.JmolRendererInterface
-
sets current color from colix color index
- setC(short) - Method in class org.jmol.export.Export3D
-
sets current color from colix color index
- setC(short) - Method in class org.jmol.g3d.Graphics3D
-
sets current color from colix color index
- setC(short) - Method in class org.jmol.util.GData
- setCA(double, double, Spectrum, String, GenericColor, boolean, boolean, int, int) - Method in class jspecview.common.ColoredAnnotation
- setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.ModulationSet
-
get updated value for offset vector and for occupancy
- setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.Vibration
- setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- setCallback(String, Object) - Method in interface org.jmol.api.JmolAppletInterface
- setCallback(String, Object) - Method in class org.jmol.util.GenericApplet
-
set a callback either as a function or a function name from JavaScript
- setCallback(ScriptToken, String) - Method in class jspecview.application.MainFrame
- setCallbackFunction(String, Object) - Method in class org.jmol.viewer.StatusManager
-
Set a JmolScript or JavaScript or Java callback.
- setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
- setCallbackFunction(String, String) - Method in class org.jmol.console.GenericConsole
- setCallbackFunction(String, String) - Method in class org.jmol.util.GenericApplet
-
From StatusManager
- setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setCamera(float, float) - Method in class org.jmol.viewer.TransformManager
- setCameraDepthPercent(float, boolean) - Method in class org.jmol.viewer.TransformManager
-
either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
- setCanvasImage(Object, int, int) - Method in interface javajs.api.js.J2SObjectInterface
- setCel(boolean) - Method in class org.jmol.util.GData
- setCellSelectionEnabled(boolean) - Method in interface jspecview.api.PlatformDialog
- setCellSelectionEnabled(boolean) - Method in class jspecview.java.AwtDialog
- setCellSelectionEnabled(boolean) - Method in class jspecview.js2d.JsDialog
- setCellSelectionEnabled(boolean) - Method in class org.jmol.awtjs.swing.JTable
- setCelPower(int) - Method in class org.jmol.util.GData
- setCenter(Location) - Method in class com.sparshui.common.messages.events.RotateEvent
- setCenter(Location) - Method in class com.sparshui.common.messages.events.ZoomEvent
- setCenter(P3) - Method in class org.jmol.shapespecial.Ellipsoid
- setCenter(T3, float) - Method in interface org.jmol.api.AtomIndexIterator
- setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
- setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
- setCenter(T3, float) - Method in class org.jmol.symmetry.UnitCellIterator
- setCenter2(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
- setCenterAt(int, P3) - Method in class org.jmol.viewer.TransformManager
- setCenterBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
- setCenterSelected() - Method in class org.jmol.api.JmolViewer
- setCenterSelected() - Method in class org.jmol.viewer.Viewer
- setCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
-
deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell
- setCGO(Lst<Object>) - Method in class org.jmol.viewer.Viewer
- setChainID(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the charge of the atom.
- setChemicalShiftReference(String, float) - Method in interface org.jmol.api.JmolNMRInterface
- setChemicalShiftReference(String, float) - Method in class org.jmol.quantum.NMRCalculation
- setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setCIPChirality(int) - Method in class org.jmol.modelset.Atom
- setCIPChirality(int) - Method in class org.jmol.modelset.Bond
-
Not implemented.
- setCIPChirality(int) - Method in class org.jmol.smiles.SmilesAtom
- setCIPChirality(int) - Method in class org.jmol.util.Edge
- setCIPChirality(int) - Method in interface org.jmol.util.Node
- setCIPChirality(int) - Method in interface org.jmol.util.SimpleNode
- setCIR(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- setClickable(int) - Method in class org.jmol.modelset.Atom
- setClipboard(Object) - Static method in class jspecview.java.AwtClipboard
-
Transfers text or image into the clipboard.
- setClipboard(Object) - Static method in class org.jmol.awt.AwtClipboard
-
Transfers text or image into the clipboard.
- setColix(short) - Method in class org.jmol.render.MeshRenderer
- setColix(short) - Method in class org.jmol.renderbio.BackboneRenderer
- setColix(short) - Method in class org.jmol.renderbio.CartoonRenderer
- setColix(short) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- setColix(short) - Method in class org.jmol.renderbio.RibbonsRenderer
- setColix(short) - Method in class org.jmol.renderbio.RocketsRenderer
- setColix(short) - Method in class org.jmol.renderbio.StrandsRenderer
- setColix(short) - Method in class org.jmol.renderbio.TraceRenderer
- setColix(short) - Method in class org.jmol.util.MeshSurface
- setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
- setColixBack(short) - Method in class org.jmol.util.MeshSurface
- setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setColor(float[], boolean) - Method in class javajs.export.PDFCreator
- setColor(int) - Method in class org.jmol.util.GData
- setColor(ScriptToken, GenericColor) - Method in class jspecview.common.ColorParameters
-
Sets the color of an element
- setColor(ScriptToken, GenericColor) - Method in class jspecview.common.PanelData
- setColorBackground(String) - Method in class org.jmol.api.JmolViewer
- setColorBackground(String) - Method in class org.jmol.viewer.Viewer
- setColorFromString(ScriptToken, String) - Method in class jspecview.common.ColorParameters
- setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.common.PanelData
- setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.java.AwtPanel
- setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.js2d.JsPanel
- setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
- setColumn3(int, float, float, float) - Method in class javajs.util.M3
-
Sets the specified column of this matrix3d to the three values provided.
- setColumn33(int, float[]) - Method in class javajs.util.M34
- setColumn4(int, float, float, float, float) - Method in class javajs.util.M4
-
Sets the specified column of this matrix4f to the four values provided.
- setColumnA(int, float[]) - Method in class javajs.util.M3
-
Sets the specified column of this matrix3d to the four values provided.
- setColumnA(int, float[]) - Method in class javajs.util.M4
-
Sets the specified column of this matrix4f to the four values provided.
- setColumnComparator(Class, Comparator) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setColumnV(int, T3) - Method in class javajs.util.M3
-
Sets the specified column of this matrix3d to the vector provided.
- setComboSelected(int) - Method in class jspecview.dialog.JSVDialog
- setCommandHooks() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setComment(String) - Method in class com.jcraft.jzlib.GZIPHeader
- setCompiler() - Method in interface org.jmol.api.JmolScriptEvaluator
- setCompiler() - Method in class org.jmol.script.ScriptEval
- setConformation(BS) - Method in class org.jmol.modelset.ModelSet
- setConformation(BS) - Method in class org.jmol.modelsetbio.BioPolymer
- setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
- setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
-
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
- setConsoleFontScale(int) - Method in class org.jmol.viewer.Viewer
- setConstraint(SymmetryInterface, int, int) - Method in class org.jmol.modelkit.ModelKit
-
This constraint will be set for the site only.
- setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
- setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in class org.jmol.scriptext.MathExt
- setContext() - Method in class jspecview.export.AMLExporter
- setContext() - Method in class jspecview.export.CMLExporter
- setContinuous(boolean) - Method in class jspecview.source.JDXDataObject
-
Sets value to true if spectrum is continuous
- setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- setContourVector(Lst<Object>, int, BS, float, short, int, SB) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- setConvertedSpectrum(Spectrum) - Method in class jspecview.common.Spectrum
- setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setCorrelationTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
set the correlation time to be used in the NOE calculation
- setCorrelationTimeTauPS(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
set the correlation time to be used in the NOE calculation
- setCorrelationTimeTauPS(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setCount(int) - Method in class org.jmol.modelset.Measurement
- setCount(int) - Method in class org.jmol.modelset.MeasurementPending
- setCountM(int) - Method in class org.jmol.modelset.Measurement
- setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setCRC(long) - Method in class com.jcraft.jzlib.GZIPHeader
- setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelSet
- setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
- setCurrentAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the number for the current AtomSet
- setCurrentCage(String) - Method in class org.jmol.viewer.Viewer
- setCurrentColor(String, Color) - Method in class jspecview.application.PreferencesDialog
- setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
- setCurrentModelID(String) - Method in class org.jmol.viewer.Viewer
- setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
- setCurrentModelIndexClear(int, boolean) - Method in class org.jmol.viewer.Viewer
- setCurrentModelInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets auxiliary information for the AtomSet
- setCurrentSubSpectrum(int) - Method in class jspecview.common.Spectrum
- setCursor(int) - Method in interface jspecview.api.ScriptInterface
- setCursor(int) - Method in class jspecview.app.JSVApp
- setCursor(int) - Method in class jspecview.application.JSpecView
- setCursor(int) - Method in class org.jmol.viewer.Viewer
- setCursor(int, Object) - Method in class jspecview.java.AwtPlatform
- setCursor(int, Object) - Method in class jspecview.js2d.JsPlatform
- setCursor(int, Object) - Method in interface org.jmol.api.GenericPlatform
- setCursor(int, Object) - Method in class org.jmol.awt.Platform
- setCursor(int, Object) - Method in class org.jmol.awtjs2d.Platform
- setCursor(JSmolAppletObject, int) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- setCursorObject(Object) - Method in class jspecview.application.MainFrame
- setCursorWait(boolean) - Method in class org.jmol.script.ScriptError
- setCutoff(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
sets the cutoff distance beyond which atom interactions are not considered
- setCutoffAng(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
sets the cutoff distance beyond which atom interactions are not considered
- setCutoffAng(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
sets the cutoff distance beyond which atom interactions are not considered
- setData(byte[], int) - Method in class javajs.img.PngEncoder
- setData(Object) - Method in class javajs.util.ArrayDataReader
- setData(Object) - Method in class javajs.util.DataReader
- setData(Object) - Method in class javajs.util.ListDataReader
- setData(Object) - Method in class javajs.util.StringDataReader
- setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
-
A general-purpose data storage method.
- setData(String, Object[], int, int, int, int, int, int) - Method in interface org.jmol.api.JmolDataManager
- setData(String, Object[], int, int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
-
This method needs to be redone using a class instead of Object[]
- setData(AnnotationData) - Method in class jspecview.dialog.JSVDialog
- setDataClass(String) - Method in class jspecview.source.JDXHeader
-
Sets the data class
- setDataDistanceToPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
- setDataType(String) - Method in class jspecview.source.JDXHeader
-
Sets the data type
- setDate(String) - Method in class jspecview.source.JDXHeader
-
Sets the date the file was created
- setDebugging() - Method in interface org.jmol.api.JmolScriptEvaluator
- setDebugging() - Method in class org.jmol.script.ScriptEval
- setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
- setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
- setDefaultLattice(P3) - Method in class org.jmol.viewer.Viewer
- setDefaultPrintOptions(PrintLayout) - Method in class jspecview.common.PanelData
- setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
- setDepth(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setDescription(String) - Method in class jspecview.java.AwtDialogFileFilter
-
Sets the description for the JSpecViewFileFilter
- setDialog(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
The HTML for this dialog has been generated.
- setDialogLocation(Point) - Method in class org.jmol.dialog.FileChooser
- setDialogSize(Dimension) - Method in class org.jmol.dialog.FileChooser
- setDictionary(byte[], int) - Method in class com.jcraft.jzlib.Deflater
- setDictionary(byte[], int) - Method in class com.jcraft.jzlib.Inflater
- setDiffusePercent(int) - Method in class org.jmol.util.GData
-
df in I = df * (N dot L) + sf * (R dot V)^p
- setDihedrals(float[], BS[], float) - Method in class org.jmol.modelset.ModelSet
- setDihedrals(float[], BS[], float) - Method in class org.jmol.viewer.Viewer
- setDirLastExported(String) - Method in interface jspecview.api.JSVFileHelper
- setDirLastExported(String) - Method in class jspecview.java.AwtFileHelper
- setDirLastExported(String) - Method in class jspecview.js2d.JsFileHelper
- setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setDisplay(Object) - Method in interface javajs.api.JSInterface
- setDisplay(Object) - Method in class jspecview.appletjs.JSVApplet
- setDisplay(Object) - Method in class jspecview.common.JSViewer
- setDisplay(Object) - Method in class org.jmol.util.GenericApplet
- setDisplay(Object) - Method in class org.jmol.viewer.Viewer
- setDocStream(GenericZipTools, BufferedInputStream) - Method in class javajs.util.CompoundDocument
- setDocumentBase(JSViewer, URL) - Static method in class jspecview.common.JSVFileManager
- setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
- setDragAtomIndex(int) - Method in class org.jmol.viewer.ActionManager
- setDropTargetListener(boolean, JSViewer) - Method in interface jspecview.api.AppletFrame
- setDropTargetListener(boolean, JSViewer) - Method in class jspecview.appletjs.JSVApplet
- setDx(float) - Method in class com.sparshui.common.messages.events.DragEvent
- setDy(float) - Method in class com.sparshui.common.messages.events.DragEvent
- setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
- setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
- setElement(int, int, float) - Method in class javajs.util.M3
-
Sets the specified element of this matrix3d to the value provided.
- setElement(int, int, float) - Method in class javajs.util.M4
-
Sets the specified element of this matrix4f to the value provided.
- setElement(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
- setElementAndIsotope(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
allow 13C, 15N, 2H, etc.
- setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
- setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
- setElementColors(ColorParameters) - Method in class jspecview.common.ColorParameters
- setEllipsoidAF(float[]) - Method in class org.jmol.jvxl.readers.Parameters
- setEnabled(boolean) - Method in interface jspecview.api.JSVViewPanel
- setEnabled(boolean) - Method in class jspecview.js2d.JsMainPanel
- setEnabled(boolean) - Method in class jspecview.js2d.JsPanel
- setEnabled(boolean) - Method in interface org.jmol.api.JmolAbstractButton
- setEnabled(boolean) - Method in interface org.jmol.api.SC
- setEnabled(boolean) - Method in class org.jmol.awt.AwtSwingComponent
- setEnabled(boolean) - Method in class org.jmol.awtjs.swing.Component
- setEnabled(boolean, boolean) - Method in class jspecview.popup.JSVGenericPopup
- setEnabled(Object, boolean) - Method in interface jspecview.api.PlatformDialog
- setEnabled(Object, boolean) - Method in class jspecview.java.AwtDialog
- setEnabled(Object, boolean) - Method in class jspecview.js2d.JsDialog
- setEnabled(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- setEnergy(float) - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- setErrorLog(String) - Method in class jspecview.source.JDXSource
-
Sets the error log for this source
- setErrorMessage(String) - Method in class org.jmol.script.ScriptError
- setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
- setEval(JmolScriptEvaluator) - Method in class org.jmol.thread.JmolThread
-
JavaScript only -- -- scriptDelay, moveTo, spin -- save context for restoration later -- move program counter forward one command
- setException(ScriptException, String, String) - Method in class org.jmol.script.ScriptEval
- setExpCouple(String, int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setExpDist(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of explicit hydrogen atoms bonded with this atom.
- setExpNoe(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setExportXAxisDirection(boolean) - Method in class jspecview.common.Spectrum
- setF(String, float) - Method in class org.jmol.viewer.GlobalSettings
- setFancyArrowHead(int) - Method in class org.jmol.renderbio.BioMeshRenderer
- setFancyConic(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
- setFancyRibbon(int) - Method in class org.jmol.renderbio.BioMeshRenderer
- setFields() - Method in class jspecview.dialog.JSVDialog
- setFileChooser(ExportType) - Method in interface jspecview.api.JSVFileHelper
- setFileChooser(ExportType) - Method in class jspecview.java.AwtFileHelper
- setFileChooser(ExportType) - Method in class jspecview.js2d.JsFileHelper
- setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
-
Set fullPathName, fileName, and nameAsGiven
- setFilename(String) - Method in class org.jmol.console.ScriptEditor
- setFilePath(String) - Method in interface jspecview.api.JSVAppletInterface
- setFilePath(String) - Method in class jspecview.app.JSVApp
- setFilePath(String) - Method in class jspecview.appletjs.JSVApplet
- setFilePath(String) - Method in class jspecview.application.MainFrame
- setFilePath(String) - Method in class jspecview.source.JDXDataObject
- setFilePath(String) - Method in class jspecview.source.JDXSource
- setFileType(String) - Method in class org.jmol.viewer.FileManager
- setFillColor(GenericColor) - Method in class jspecview.common.Spectrum
- setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setFilterAtomTypeStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in interface org.jmol.api.SymmetryInterface
- setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in class org.jmol.symmetry.Symmetry
- setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
- setFloatProperty(String, float) - Method in class org.jmol.script.ScriptParam
- setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
- setFocus() - Method in class org.jmol.viewer.Viewer
- setFocus(boolean) - Method in interface jspecview.api.PlatformDialog
- setFocus(boolean) - Method in class jspecview.dialog.JSVDialog
- setFocus(boolean) - Method in class jspecview.java.AwtDialog
- setFocus(boolean) - Method in class jspecview.js2d.JsDialog
- setFocusable(boolean) - Method in interface jspecview.api.JSVViewPanel
- setFocusable(boolean) - Method in class jspecview.js2d.JsMainPanel
- setFocusable(boolean) - Method in class jspecview.js2d.JsPanel
- setFont(Object, int, int, float, boolean) - Method in class jspecview.common.PanelData
- setFont(Object, Font) - Method in class jspecview.common.PDFWriter
- setFont(Object, Font) - Method in class jspecview.java.AwtG2D
- setFont(Object, Font) - Method in class jspecview.js2d.JsG2D
- setFont(Object, Font) - Method in interface org.jmol.api.GenericGraphics
- setFont(Object, Font) - Method in class org.jmol.awt.AwtG2D
- setFont(Object, Font) - Method in class org.jmol.awtjs2d.JsG2D
- setFont(String, float) - Method in class javajs.export.PDFCreator
- setFont(Font) - Method in class org.jmol.g3d.Graphics3D
- setFont(Font) - Method in class org.jmol.util.GData
- setFont(Font, boolean) - Method in class org.jmol.modelset.Text
- setFontBold(String, float) - Method in class org.jmol.util.GData
- setFontFromFid(int) - Method in class org.jmol.modelset.Text
- setFontName(ScriptToken, String) - Method in class jspecview.common.PanelData
- setFontScale(float) - Method in class org.jmol.modelset.Text
- setFontScale(int) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- setFor(JSVPanel, ColorParameters, boolean) - Method in class jspecview.common.ColorParameters
- setFormalCharge(int) - Method in class org.jmol.modelset.Atom
- setFormalCharges(BS, int) - Method in class org.jmol.modelset.AtomCollection
- setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
- setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setFractionalCoordPt(P3, P3, boolean) - Method in class org.jmol.modelset.Atom
- setFrame(int) - Method in class org.jmol.viewer.AnimationManager
- setFrame(JFrame) - Method in class jme.JME
- setFrameAndTreeNode(int) - Method in class jspecview.common.JSViewer
- setFrameCount(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- setFrameDelayMs(long) - Method in class org.jmol.viewer.Viewer
- setFrameDelayMs(long, BS) - Method in class org.jmol.modelset.ModelSet
- setFrameDeltaCouple(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setFrameDeltaNoe(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setFrameModelInfo(String, Object) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- setFrameNumberChangeViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- setFrameOffsets(BS, boolean) - Method in class org.jmol.viewer.Viewer
- setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
- setFrameTitle(String) - Method in class jspecview.common.PanelNode
- setFrameTitle(BS, Object) - Method in class org.jmol.modelset.ModelSet
- setFrameTitleObj(Object) - Method in class org.jmol.viewer.Viewer
- setFrameVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
- setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
- setFromAsymmetricTensor(double[][], String, String) - Method in class org.jmol.util.Tensor
-
Standard constructor for QM tensors
- setFromAxes(V3[]) - Method in class org.jmol.util.Tensor
-
Standard constructor for ellipsoids based on axes
- setFromBits(int, BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
- setFromEigenVectors(T3[], float[], String, String, Tensor) - Method in class org.jmol.util.Tensor
-
Standard constructor for charge and iso.
- setFromMD(MeasurementData, boolean) - Method in class org.jmol.modelset.Measurement
- setFromThermalEquation(double[], String) - Method in class org.jmol.util.Tensor
-
standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
- setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setGraphicsColor(Object, GenericColor) - Method in class jspecview.common.PDFWriter
- setGraphicsColor(Object, GenericColor) - Method in class jspecview.java.AwtG2D
- setGraphicsColor(Object, GenericColor) - Method in class jspecview.js2d.JsG2D
- setGraphicsColor(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
- setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
- setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
- setGraphSetKey(String) - Method in interface jspecview.api.AnnotationData
- setGraphSetKey(String) - Method in class jspecview.common.MeasurementData
- setGraphSetKey(String) - Method in class jspecview.dialog.JSVDialog
- setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
-
controls greyscale rendering
- setGroup(Group) - Method in class com.sparshui.server.TouchPoint
-
Set the group for this touch point.
- setGroup(Chain, String, int, int, int) - Method in class org.jmol.modelset.Group
- setGroup1(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
- setGroup1(ModelSet, int) - Method in interface org.jmol.api.JmolAnnotationParser
- setGroup1(ModelSet, int) - Method in class org.jmol.dssx.AnnotationParser
- setGroup1(ModelSet, int) - Method in class org.jmol.dssx.DSSR1
- setGroupID(String) - Method in class org.jmol.modelset.Group
- setGroupID(String) - Method in class org.jmol.modelsetbio.Monomer
- setGroupLists(int) - Method in class org.jmol.modelsetbio.BioResolver
- setHasUnitCell() - Method in class org.jmol.modelkit.ModelKit
- setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.BioResolver
- setHeaderTable(Lst<String[]>) - Method in class jspecview.source.JDXHeader
-
Sets the headerTable for this Source or spectrum
- setHighlightColor(GenericColor) - Method in class jspecview.common.PanelData
- setHighlightedPeak(PeakInfo) - Method in class jspecview.common.Spectrum
- setHistory(String) - Method in class org.jmol.viewer.Viewer
- setHorizAlignment(int, int) - Static method in class org.jmol.viewer.JC
- setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
- setHoverLabel(String, String) - Method in class org.jmol.modelkit.ModelKit
- setHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
-
Finalizes the hydrogen count hydrogens in a
SmilesMolecule
. - setHydrogenCount(int) - Method in class jspecview.source.JDXDataObject
- setHZtoPPM(boolean) - Method in class jspecview.source.JDXDataObject
-
Sets the value to true if the spectrum should be displayed with abscissa unit of Part Per Million (PPM) instead of Hertz (HZ)
- setIcon(Object) - Method in interface org.jmol.api.SC
- setIcon(Object) - Method in class org.jmol.awt.AwtSwingComponent
- setIcon(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
- setId(String) - Method in class jspecview.common.Spectrum
- setID(String) - Method in class jspecview.source.JDXSource
- setIdentity() - Method in class javajs.util.M4
-
Sets this Matrix4f to identity.
- setImage(Object) - Method in interface org.jmol.api.GenericImageDialog
- setImage(Object) - Method in class org.jmol.console.ImageDialog
- setImage(Object) - Method in class org.jmol.modelset.Text
- setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Sets the output image dimensions.
- setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
- setImageInfo(int, int, String) - Method in class org.jmol.dialog.Dialog
- setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of implicit hydrogen atoms bonded with this atom.
- setIncreasing(boolean) - Method in class jspecview.source.JDXDataObject
-
Sets value to true if spectrum is increasing
- setIndex(int) - Method in interface jspecview.api.JSVTreeNode
- setIndex(int) - Method in class jspecview.application.AwtTreeNode
- setIndex(int) - Method in class jspecview.tree.SimpleTreeNode
- setIndex(int) - Method in class org.jmol.smiles.SmilesAtom
-
Constructs a
SmilesAtom
. - setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Sets the indexes to the atomSetIndex values of each leaf of the node.
- setInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelSet
- setInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setInlineData(String) - Method in class jspecview.source.JDXDataObject
- setInlineData(String) - Method in class jspecview.source.JDXSource
- setInMotion(boolean) - Method in class org.jmol.api.JmolViewer
- setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
- setInsertedCommand(String) - Method in class org.jmol.viewer.Viewer
- setInt(double, double, Spectrum, double, double, double) - Method in class jspecview.common.Integral
- setInt(int) - Method in class org.jmol.util.Rgb16
- setIntegrationRatios(String) - Method in class jspecview.common.PanelData
-
DEPRECATED Sets the integration ratios that will be displayed
- setIntLocation(int[]) - Method in interface jspecview.api.PlatformDialog
- setIntLocation(int[]) - Method in class jspecview.java.AwtDialog
- setIntLocation(int[]) - Method in class jspecview.js2d.JsDialog
- setIntoFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setIntoFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
- setIntProperty(String, int) - Method in class org.jmol.script.ScriptParam
- setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
- setIntPropertyTok(String, int, int) - Method in class org.jmol.viewer.Viewer
- setInverseNormixes() - Static method in class org.jmol.util.Normix
- setInvoker(Object) - Method in class org.jmol.awtjs.swing.JPopupMenu
- setIRmode(String) - Method in class jspecview.common.JSViewer
- setIRMode(Spectrum.IRMode, String) - Method in class jspecview.common.PanelData
- setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
- setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
- setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelSet
- setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in interface org.jmol.atomdata.AtomDataServer
- setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.modelset.ModelSet
- setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.viewer.Viewer
- setJcampdx(String) - Method in class jspecview.source.JDXHeader
-
Sets the JCAMP-DX version number
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
- setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelSet
- setJmolDefaults() - Method in class org.jmol.api.JmolViewer
- setJmolDefaults() - Method in class org.jmol.viewer.Viewer
- setJmolSize(Dimension) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
- setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
- setJSOptions(Map<String, Object>) - Method in class org.jmol.util.GenericApplet
- setJSpecView(String, boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
- setLabel(int, String) - Method in class jme.JMEmol
- setLabel(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- setLabel(Object, BS) - Method in class org.jmol.viewer.ShapeManager
- setLabel(String) - Method in class org.openscience.jmol.app.jsonkiosk.BannerFrame
- setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setLabels() - Method in class org.jmol.console.GenericConsole
- setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setLabelString(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- setLastColix(int, boolean) - Method in class org.jmol.util.Shader
- setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
-
set symmetry lattice type using Hall rotations
- setLattice(int) - Method in class org.jmol.symmetry.Symmetry
- setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
Shelx and Wien2k readers
- setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setLeadAtomIndex() - Method in class org.jmol.modelsetbio.Monomer
- setLeftComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
- setLegend(JSVDialog) - Method in class jspecview.common.PanelNode
- setLength(int) - Method in class javajs.util.SB
- setLengths() - Method in class org.jmol.shapespecial.Ellipsoid
- setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
- setLighting(int) - Method in class org.jmol.shape.Mesh
- setLine(String) - Method in interface org.jmol.api.JmolJDXMOLParser
- setLine(String) - Method in class org.jmol.jsv.JDXMOLParser
- setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
- setLineWidth(float) - Method in class javajs.export.PDFCreator
- setlinkedXMove(GraphSet, double, boolean) - Method in class jspecview.common.PanelData
- setLoader(ModelLoader) - Method in class org.jmol.modelsetbio.BioResolver
- setLoadFormat(boolean, String, char, boolean) - Method in class org.jmol.viewer.Viewer
-
Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
- setLoading(String, String) - Method in class jspecview.application.MainFrame
- setLoadNote() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
- setLocalPath(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
-
called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
- setLocation(int[]) - Method in class org.jmol.awtjs.swing.JDialog
- setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
-
Replaces the current logger implementation by a new one.
- setLogLevel(int) - Static method in class org.jmol.util.Logger
-
Activates all logging levels up through a given level.
- setLongDate(String) - Method in class jspecview.source.JDXHeader
-
Sets the long date of when the file was created
- setlrefSingle(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setM(double[][]) - Method in interface javajs.api.EigenInterface
- setM(double[][]) - Method in class javajs.util.Eigen
- setM(M3) - Method in class javajs.util.A4
-
Sets the value of this axis-angle to the rotational component of the passed matrix.
- setM(ModelSet, Measurement, float, short, String, int) - Method in class org.jmol.modelset.Measurement
- setM1(double, double, Spectrum) - Method in class jspecview.common.Measurement
- setM3(M34) - Method in class javajs.util.M3
-
Sets the value of this matrix to the double value of the Matrix3f argument.
- setM33(M34) - Method in class javajs.util.M34
-
Sets the value of this matrix to the double value of the Matrix3f argument.
- setM4(M4) - Method in class javajs.util.M4
-
Sets the value of this matrix to a copy of the passed matrix m1.
- setMad(short) - Method in class org.jmol.modelset.Bond
- setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
- setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
- setMainFrame(MainFrame) - Method in class jspecview.application.JSpecView
- setManager(Object, Viewer, Object) - Method in class org.jmol.minimize.MinimizationThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.script.CommandWatcherThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.AnimationThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.JmolThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.MoveToThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.SpinThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.VibrationThread
- setMapBitSet(Map<String, BS>, int, int, String) - Static method in class org.jmol.util.BSUtil
- setMappingPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
- setMarBond(short) - Method in class org.jmol.api.JmolViewer
- setMarBond(short) - Method in class org.jmol.viewer.Viewer
- setMargin(float) - Method in class org.jmol.util.BoxInfo
- setMatchingAtom(Node, int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of a matching atom in a molecule.
- setMaxSize(int) - Method in class org.jmol.util.CommandHistory
-
Resets maximum size of command queue.
- setMeasurementText(Measurement) - Method in class jspecview.source.JDXDataObject
- setMenu(String, boolean) - Method in class org.jmol.api.JmolViewer
- setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
- setMenu(ModelKitPopup) - Method in class org.jmol.modelkit.ModelKit
- setMenuEnables(PanelNode) - Method in class jspecview.application.ApplicationMenu
- setMenuEnables(PanelNode, boolean) - Method in class jspecview.application.MainFrame
- setMenuItem(JMenuItem, char, String, int, int, EventListener) - Static method in class jspecview.application.ApplicationMenu
- setMenuKeys(String, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setMenuKeys(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
opportunity to adjust menus for a custom application
- setMenus(JMenu, JMenu, JMenu, ActionListener) - Static method in class jspecview.application.ApplicationMenu
- setMenuState() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setMeshColor() - Method in class org.jmol.shape.MeshCollection
- setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
-
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
- setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEval
- setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
- setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
- setMinimumIntegral(double) - Method in class jspecview.common.IntegralData
- setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
- setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.JScrollPane
- setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
- setMinMax0(P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
- setMinMax0(P3, P3) - Method in interface org.jmol.adapter.smarter.MSInterface
- setMinMaxLatticeParameters(int, P3i, P3i, int) - Static method in class org.jmol.util.SimpleUnitCell
- setMixingTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
sets the mixing time for the NOE experiment
- setMixingTimeSec(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
sets the mixing time for the NOE experiment
- setMixingTimeSec(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
sets the mixing time for the NOE experiment
- setMKState(int) - Method in class org.jmol.modelkit.ModelKit
- setMnemonic(char) - Method in interface org.jmol.api.JmolAbstractButton
- setMnemonic(char) - Method in class org.jmol.console.JmolLabel
- setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- setMod(String, P3, P3, int, Lst<Modulation>, M3, Matrix[], SymmetryInterface, int, int, Vibration, boolean) - Method in class org.jmol.util.ModulationSet
-
A collection of modulations for a specific atom.
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
- setModDim(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
- setModel(int) - Method in interface org.jmol.api.JmolJSpecView
- setModel(int) - Method in class org.jmol.jsv.JSpecView
- setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceField
- setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
- setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
- setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.symmetry.UnitCellIterator
- setModelCage(int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
-
This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command.
- setModelCagePts(int, T3[], String) - Method in class org.jmol.modelset.ModelSet
- setModelFields() - Method in class org.jmol.minimize.forcefield.ForceField
- setModelIndex(int) - Method in class org.jmol.modelset.StateScript
- setModelIndex(short) - Method in class org.jmol.modelset.Measurement
- setModelInfoForSet(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets auxiliary information for an AtomSet
- setModelkitPropertySafely(String, Object) - Method in class org.jmol.viewer.Viewer
- setModelPDB(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setModelSet(ModelSet) - Method in class org.jmol.modelset.MeasurementData
- setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
- setModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
- setModelSet(ModelSet) - Method in class org.jmol.viewer.Viewer
- setModelVisibility() - Method in class org.jmol.viewer.Viewer
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Bbcage
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Halos
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.MeshCollection
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Shape
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.TextShape
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapecgo.CGO
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Dipoles
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Draw
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Polyhedra
- setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
-
only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the vwr references are all removed
- setModifiedTime(long) - Method in class com.jcraft.jzlib.GZIPHeader
- setModifyKeys(Map<String, String>) - Method in class org.jmol.util.JSONWriter
- setModTQ(T3, boolean, T3, boolean, float) - Method in interface org.jmol.api.JmolModulationSet
- setModTQ(T3, boolean, T3, boolean, float) - Method in class org.jmol.util.ModulationSet
-
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
- setModulation(boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Both the Jana reader and the CIF reader will call this to set the modulation for a given model.
- setModulation(boolean, XtalSymmetry.FileSymmetry) - Method in interface org.jmol.adapter.smarter.MSInterface
- setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.modelset.ModelSet
-
Sets the modulation for all atoms in bs.
- setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.viewer.Viewer
- setMol(boolean) - Method in class jme.JME
- setMol(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setMoment() - Method in interface org.jmol.api.JmolModulationSet
- setMoment() - Method in class org.jmol.util.ModulationSet
- setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setMorphCount(int) - Method in class org.jmol.viewer.AnimationManager
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.AmsReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- setMotion(int, boolean) - Method in class org.jmol.viewer.ActionManager
- setMotionFixed(BS) - Method in class org.jmol.viewer.Viewer
- setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.Viewer
- setMouseMode() - Method in class org.jmol.viewer.ActionManager
- setMovableX(int) - Method in class org.jmol.modelset.Text
- setMovableXPercent(int) - Method in class org.jmol.modelset.Text
- setMovableY(int) - Method in class org.jmol.modelset.Text
- setMovableYPercent(int) - Method in class org.jmol.modelset.Text
- setMovableZPercent(int) - Method in class org.jmol.modelset.Text
- setMovie(Map<String, Object>) - Method in class org.jmol.viewer.AnimationManager
-
support for PyMOL movies and anim FRAMES [....] currently no support for scripted movies
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- setMustResume() - Method in class org.jmol.script.ScriptContext
- setMV(M3, T3) - Method in class javajs.util.M4
-
Initializes a Matrix4f from the rotation matrix and translation.
- setName(String) - Method in class com.jcraft.jzlib.GZIPHeader
- setName(String) - Method in class jspecview.common.Parameters
- setName(String) - Method in interface org.jmol.api.SC
- setName(String) - Method in class org.jmol.awt.AwtSwingComponent
- setName(String) - Method in class org.jmol.awtjs.swing.Component
- setName(String) - Method in class org.jmol.script.SV
- setNavFps(int) - Method in class org.jmol.viewer.TransformManager
- setNavigatePt(P3) - Method in class org.jmol.viewer.TransformManager
-
scripted entry point for navigation
- setNavigationDepthPercent(float) - Method in interface org.jmol.api.JmolNavigatorInterface
- setNavigationDepthPercent(float) - Method in class org.jmol.navigate.Navigator
- setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
-
sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be invalid input: '<'0 or >100)
- setNavigationDepthPercent(float) - Method in class org.jmol.viewer.Viewer
- setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
- setNavigationOffsetRelative() - Method in interface org.jmol.api.JmolNavigatorInterface
- setNavigationOffsetRelative() - Method in class org.jmol.navigate.Navigator
- setNavigationOffsetRelative() - Method in class org.jmol.viewer.TransformManager
- setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
- setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
- setNboLabels(String[], int, Lst<Map<String, Object>>, int, String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
- setNewRotationCenter(P3) - Method in class org.jmol.viewer.Viewer
- setNewWindowParametersForExport() - Method in class org.jmol.util.GData
- setNextPeak(Coordinate, int) - Method in class jspecview.common.Spectrum
- setNMRfreq(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
set the NMR frequency for the NOE simulation
- setNMRfreqMHz(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
set the NMR frequency for the NOE simulation
- setNMRfreqMHz(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
set the NMR frequency for the NOE simulation
- setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setNode(PanelNode) - Method in class jspecview.common.JSViewer
- setNoeExprefValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setNoeNPrefIndices(int[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setNoesy(boolean) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
sets the experiemnt type to NOESY or ROESY
- setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
- setNormixes(V3[]) - Method in class org.jmol.shape.Mesh
- setNth(int) - Method in class org.jmol.minimize.forcefield.ForceField
- setNucleusAndFreq(String, boolean) - Method in class jspecview.source.JDXDataObject
- setNullValue(String) - Method in class javajs.util.CifDataParser
-
Set the string value of what is returned for "." and "?"
- setNumDim(int) - Method in class jspecview.source.JDXDataObject
- setO(String, Object) - Method in class org.jmol.viewer.GlobalSettings
- setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
- setObjectMad10(int, String, int) - Method in class org.jmol.script.ScriptEval
- setObjectMad10(int, String, int) - Method in class org.jmol.viewer.Viewer
-
input here is a JC.SHAPE_xxxx identifier
- setObjectProp(String, int) - Method in class org.jmol.viewer.Viewer
- setObjectProperty() - Method in class org.jmol.script.ScriptEval
- setObjectPropSafe(String, int) - Method in interface org.jmol.api.JmolScriptEvaluator
- setObjectPropSafe(String, int) - Method in class org.jmol.script.ScriptEval
-
called by Viewer in setting up a PyMOL scene.
- setObjectVisibility(String, boolean) - Method in class org.jmol.viewer.Viewer
- setObservedFreq(double) - Method in class jspecview.source.JDXDataObject
-
Sets the Observed Frequency (for NMR Spectra)
- setObservedNucleus(String) - Method in class jspecview.source.JDXDataObject
- setOccupancy(double[], double, double) - Method in class org.jmol.util.ModulationSet
-
get the occupancy, first from the reader, then from renderer
- setOccupancy(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
- setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
- setOffset(int) - Method in class org.jmol.modelset.Text
- setOffset(int) - Method in class org.jmol.symmetry.Symmetry
- setOffsetPt(P3) - Method in class org.jmol.shapespecial.Dipole
- setOffsetPt(T3) - Method in interface org.jmol.api.SymmetryInterface
- setOffsetPt(T3) - Method in class org.jmol.symmetry.Symmetry
- setOpacity255(int) - Method in interface javajs.api.GenericColor
- setOpacity255(int) - Method in class jspecview.java.AwtColor
- setOpacity255(int) - Method in class org.jmol.awt.AwtColor
- setOpacity255(int) - Method in class org.jmol.awtjs.swing.Color
- setOptions(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- setOrder(int) - Method in class org.jmol.modelset.Bond
- setOrigin(String) - Method in class jspecview.source.JDXHeader
-
Sets the origin of the JCAMP-DX spectrum
- setOS(int) - Method in class com.jcraft.jzlib.GZIPHeader
- setOutputChannel(GenericBinaryDocument, OC) - Method in interface org.jmol.jvxl.api.MeshDataServer
- setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.shapesurface.Isosurface
- setOutputChannel(GenericOutputChannel) - Method in interface javajs.api.GenericBinaryDocument
- setOutputChannel(GenericOutputChannel) - Method in class javajs.util.BinaryDocument
- setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.JvxlReader
- setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setOutputStream(OutputStream) - Method in class javajs.export.PDFCreator
- setOwner(String) - Method in class jspecview.source.JDXHeader
-
Sets the owner
- setP(T3) - Method in class javajs.util.T3
- setP(PanelData, ScriptToken, String) - Method in class jspecview.common.Parameters
- setPanel(JPanel) - Method in class org.openscience.jmol.app.jsonkiosk.KioskFrame
- setPanelVisible(boolean) - Method in interface jspecview.api.AppletFrame
- setPanelVisible(boolean) - Method in class jspecview.appletjs.JSVApplet
- setParallel() - Method in class org.jmol.viewer.ShapeManager
- setParallel(boolean) - Method in class org.jmol.viewer.Viewer
- setparam - Static variable in class org.jmol.script.T
- setParameters(Spectrum) - Method in class jspecview.export.AMLExporter
- setParameters(Spectrum) - Method in class jspecview.export.CMLExporter
- setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
- setParams(Object[], int[], BS) - Method in class org.jmol.shapebio.BioShape
- setParams(String, JSViewer, Spectrum) - Method in class jspecview.dialog.JSVDialog
-
required initializer; from JSViewer
- setParams(Map<String, Object>) - Method in class javajs.img.GifEncoder
-
we allow for animated GIF by being able to re-enter the code with different parameters held in params
- setParams(Map<String, Object>) - Method in class javajs.img.ImageEncoder
- setParams(Map<String, Object>) - Method in class javajs.img.Jpg64Encoder
- setParams(Map<String, Object>) - Method in class javajs.img.JpgEncoder
- setParams(Map<String, Object>) - Method in class javajs.img.PdfEncoder
- setParams(Map<String, Object>) - Method in class javajs.img.PngEncoder
- setParams(Map<String, Object>) - Method in class javajs.img.PpmEncoder
- setParams(BytePoster, String, boolean, OutputStream) - Method in class javajs.util.OC
-
Set up an output channel.
- setParent(Object) - Method in class org.jmol.awtjs.swing.Component
- setPartialCharge(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
- setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
- setPass2(boolean) - Method in class org.jmol.util.GData
- setPath(JSVTreePath) - Method in interface jspecview.api.JSVTree
- setPath(JSVTreePath) - Method in class jspecview.application.AwtTree
- setPath(JSVTreePath) - Method in class jspecview.tree.SimpleTree
- setPdbConectBonding(int, int, BS) - Method in class org.jmol.modelset.ModelSet
- SETPEAK - Enum constant in enum class jspecview.common.ScriptToken
- setPeakList(Lst<PeakInfo>, String, String) - Method in class jspecview.common.Spectrum
- setPeakList(Parameters, int, ScaleData) - Method in class jspecview.common.PeakData
- setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
- setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
- setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
- setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
- setPhongExponent(int) - Method in class org.jmol.util.GData
-
p in I = df * (N dot L) + sf * (R dot V)^p
- setPicked(int, boolean) - Method in class org.jmol.viewer.Viewer
- setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
- setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
- setPixelRange(int, int) - Method in class jspecview.common.PeakInfo
- setPlaneParameters(P4) - Method in class org.jmol.jvxl.data.VolumeData
- setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
-
Raw file data planes are passed to us here from VolumeFileReader
- setPlanes(float[][]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Planes to use for holding raw file data.
- setPlotColors(GenericColor[]) - Method in class jspecview.common.PanelData
- setPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setPointer(int, int) - Static method in class org.jmol.viewer.JC
- setPointGroup(Viewer, SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in interface org.jmol.api.SymmetryInterface
- setPointGroup(Viewer, SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in class org.jmol.symmetry.Symmetry
- setPoints(int) - Method in class org.jmol.shape.Axes
- setPoints(ModelSet, int[], Point3fi[], TickInfo) - Method in class org.jmol.modelset.Measurement
- setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
- setPopulationDisplay(PopulationDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- setPopupMenu(boolean, boolean) - Method in class jspecview.common.JSViewer
- setPosition(float, float, boolean, float[]) - Method in class org.jmol.modelset.Text
- setPrecision() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Called by PWMAT ALWAYS and CIFReader as well if a double-precision value for alpha is found.
- setPrecision(float) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- setPrecision(float) - Method in class org.jmol.util.SimpleUnitCell
- setPreferredScrollableViewportSize(Dimension) - Method in class org.jmol.awtjs.swing.JTable
- setPreferredSize(int, int) - Method in interface jspecview.api.PlatformDialog
- setPreferredSize(int, int) - Method in class jspecview.java.AwtDialog
- setPreferredSize(int, int) - Method in class jspecview.js2d.JsDialog
- setPreferredSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
- setPreferredWidth(int) - Method in interface org.jmol.awtjs.swing.TableColumn
- setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
- setPreviewOptions(boolean) - Method in class org.jmol.dialog.FilePreview
- setPrimitive(int) - Method in class org.jmol.smiles.SmilesBond
- setPrint(PrintLayout, String) - Method in class jspecview.common.PanelData
- setProcessingMenu(JComponent) - Method in class jspecview.application.ApplicationMenu
- setProp(String, Object, BS) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setPropAS(String, Object, BS) - Method in class org.jmol.shape.AtomShape
- setPropBSC(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setProperties(Object) - Method in class org.jmol.shape.Shape
- setProperties(Properties) - Method in class jspecview.app.JSVAppPro
- setProperties(Properties) - Method in class jspecview.application.JSpecView
- setProperties(Properties) - Method in interface org.jmol.api.JSVInterface
- setProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
- setProperty(String, Object) - Method in class org.jmol.modelkit.ModelKit
-
Modify the state by setting a property.
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Axes
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Balls
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Bbcage
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Echo
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Frank
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Halos
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Hover
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Labels
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Measures
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Shape
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Stars
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Sticks
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Uccage
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Backbone
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShape
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Trace
- setProperty(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dipoles
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dots
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Polyhedra
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Vectors
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Contact
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.LcaoCartoon
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.MolecularOrbital
- setProperty(String, String) - Method in class jspecview.common.JSViewer
- setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
- setPropertyColorRangeData(float[], BS) - Method in class org.jmol.viewer.ColorManager
- setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- setPropFLS(String, Object) - Method in class org.jmol.shape.FontLineShape
- setPropI(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
- setPropMC(String, Object, BS) - Method in class org.jmol.shape.MeshCollection
- setPropS(String, Object, BS) - Method in class org.jmol.shape.Shape
- setPropTS(String, Object, BS) - Method in class org.jmol.shape.TextShape
- setProteinStructureType(STR, int) - Method in class org.jmol.modelset.Group
- setProteinStructureType(STR, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
- setProteinType(BS, STR) - Method in class org.jmol.modelset.ModelSet
- setProteinType(STR, BS) - Method in class org.jmol.viewer.Viewer
- setPt2(double, double) - Method in class jspecview.common.Measurement
- setPt2(Spectrum, boolean) - Method in class jspecview.common.Measurement
- setRadius(float) - Method in class org.jmol.modelset.Atom
- setRandom(boolean) - Method in class javajs.util.BinaryDocument
- setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
- setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
- setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
- setRastAB(int, int, int, int) - Method in class org.jmol.g3d.PrecisionRenderer
- setRastABFloat(float, float, float, float) - Method in class org.jmol.g3d.PrecisionRenderer
- setReader(CifReader) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb
- setRecentMenu(Lst<String>) - Method in class jspecview.application.ApplicationMenu
- setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setRef(Quat) - Method in class javajs.util.Quat
- setRequiredFile(String, String) - Method in interface org.jmol.jvxl.api.MeshDataServer
- setRequiredFile(String, String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setRequiredFile(String, String) - Method in class org.jmol.shapesurface.Isosurface
- setResno(int) - Method in class org.jmol.modelset.Group
- setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
- setRhoStar(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setRightComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
- setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
- setRingData(int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
- setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
- setRingsClickable() - Method in class org.jmol.modelsetbio.NucleicMonomer
- setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
- setRingsVisible(boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
- setRotation(M3) - Method in class org.jmol.viewer.TransformManager
- setRotationMatrix(M3) - Method in class org.jmol.g3d.Graphics3D
- setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
- setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
- setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelSet
- setRotationScale(M3) - Method in class javajs.util.M4
-
Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.
- setRotationX(float) - Method in class com.sparshui.common.messages.events.SpinEvent
- setRotationY(float) - Method in class com.sparshui.common.messages.events.SpinEvent
- setRotationZ(float) - Method in class com.sparshui.common.messages.events.SpinEvent
- setRow(int, float, float, float) - Method in class javajs.util.M3
-
Sets the specified row of this matrix3d to the three values provided.
- setRow33(int, float[]) - Method in class javajs.util.M34
- setRowA(int, float[]) - Method in class javajs.util.M3
-
Sets the specified row of this matrix3d to the four values provided.
- setRowA(int, float[]) - Method in class javajs.util.M4
-
Sets the specified row of this matrix4f to the four values provided.
- setRowSelectionAllowed(boolean) - Method in class org.jmol.awtjs.swing.JTable
- setRowSelectionInterval(int, int) - Method in class org.jmol.awtjs.swing.JTable
- setRowV(int, T3) - Method in class javajs.util.M3
-
Sets the specified row of this matrix3d to the Vector provided.
- setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
- setRule6Full(boolean) - Method in class org.jmol.symmetry.CIPData
- setScale() - Method in class org.jmol.viewer.ShapeManager
- setScale(float) - Method in class javajs.util.M3
-
Sets this Matrix3f to a scalar * Identity.
- setScale(float) - Method in class org.jmol.modelset.Text
- setScale(float, boolean) - Method in class org.jmol.shapespecial.Ellipsoid
- setScale(int, int, int, boolean) - Method in class jspecview.common.ViewData
- setScalePixelsPerMicron(float) - Method in class org.jmol.modelset.Text
- setScreenDimension(int, int) - Method in interface javajs.api.JSInterface
- setScreenDimension(int, int) - Method in class jspecview.appletjs.JSVApplet
- setScreenDimension(int, int) - Method in class jspecview.common.JSViewer
- setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
- setScreenDimension(int, int) - Method in class org.jmol.util.GenericApplet
- setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
- setScript(String) - Method in class org.jmol.modelset.Text
- setScriptArguments(Object, boolean) - Method in class org.jmol.script.ScriptParam
- setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
- setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
- setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
- setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
- setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
- setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
- setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
- setSelected(boolean) - Method in interface org.jmol.api.SC
- setSelected(boolean) - Method in class org.jmol.awt.AwtSwingComponent
- setSelected(boolean) - Method in class org.jmol.awtjs.swing.AbstractButton
- setSelected(Object, boolean) - Method in interface jspecview.api.PlatformDialog
- setSelected(Object, boolean) - Method in class jspecview.java.AwtDialog
- setSelected(Object, boolean) - Method in class jspecview.js2d.JsDialog
- setSelected(String, boolean) - Method in class jspecview.popup.JSVGenericPopup
- setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- setSelected(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this check box's selection has been changed.
- setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
- setSelectedAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- setSelectedIndex(int) - Method in class org.jmol.awtjs.swing.JComboBox
- setSelectedIndex(Object, int) - Method in interface jspecview.api.PlatformDialog
- setSelectedIndex(Object, int) - Method in class jspecview.java.AwtDialog
- setSelectedIndex(Object, int) - Method in class jspecview.js2d.JsDialog
- setSelectedIndex(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this combo box's selected item has been changed.
- setSelectedIntegral(double) - Method in class jspecview.common.PanelData
- setSelectedIntegral(Measurement, double) - Method in class jspecview.common.IntegralData
- setSelectedPanel(JSVPanel) - Method in class jspecview.application.MainFrame
- setSelectedPanel(ScriptInterface, JSVPanel) - Method in interface jspecview.api.JSVTree
- setSelectedPanel(ScriptInterface, JSVPanel) - Method in class jspecview.application.AwtTree
- setSelectedPanel(ScriptInterface, JSVPanel) - Method in class jspecview.tree.SimpleTree
- setSelectedPanel(JSViewer, JSVPanel, Lst<PanelNode>) - Method in interface jspecview.api.JSVMainPanel
- setSelectedPanel(JSViewer, JSVPanel, Lst<PanelNode>) - Method in class jspecview.java.AwtMainPanel
- setSelectedPanel(JSViewer, JSVPanel, Lst<PanelNode>) - Method in class jspecview.js2d.JsMainPanel
- setSelectedPeak(PeakInfo) - Method in class jspecview.common.Spectrum
- setSelectionHalos(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- setSelectionHalosEnabled(boolean) - Method in class org.jmol.viewer.Viewer
- setSelections(boolean, boolean, boolean, JSVPanel) - Method in class jspecview.application.ApplicationMenu
- setSelectionSet(BS) - Method in class org.jmol.api.JmolViewer
- setSelectionSet(BS) - Method in class org.jmol.viewer.Viewer
- setSelectionSubset(BS) - Method in class org.jmol.viewer.SelectionManager
- setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
- setShapeId(int, int, boolean) - Method in class org.jmol.scriptext.ScriptExt
- setShapeNameParameter(int) - Method in class org.jmol.script.ScriptEval
- setShapeProperties(int, Object[]...) - Method in class org.jmol.viewer.ShapeManager
- setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEval
- setShapeProperty(int, String, Object) - Method in class org.jmol.scriptext.ScriptExt
- setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
- setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.script.ScriptEval
- setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.viewer.ShapeManager
- setShapeSize(int, int, BS) - Method in class org.jmol.viewer.Viewer
- setShapeSizeBs(int, int, BS) - Method in class org.jmol.script.ScriptEval
- setShapeSizeBs(int, int, RadiusData, BS) - Method in class org.jmol.viewer.ShapeManager
- setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shape.Shape
- setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.Backbone
- setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setShapeTranslucency(int, String, String, float, BS) - Method in class org.jmol.script.ScriptEval
- setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
- setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
- setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
- setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
- setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
- setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
- setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
- setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
- setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
- setShowWithin(Lst<P3>, float, boolean) - Method in class org.jmol.shape.Mesh
- setSigma(String, Matrix) - Method in class org.jmol.symmetry.SymmetryOperation
- setSimpleCage(SymmetryInterface) - Method in class org.jmol.modelset.Model
- setSimulated(String) - Method in class jspecview.common.Spectrum
- setSite(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
- setSize(int, BS) - Method in class org.jmol.shape.AtomShape
- setSize(int, BS) - Method in class org.jmol.shape.Balls
- setSize(int, BS) - Method in class org.jmol.shape.Measures
- setSize(int, BS) - Method in class org.jmol.shape.Shape
- setSize(int, BS) - Method in class org.jmol.shape.Sticks
-
sets the size of a bond, or sets the selectedBonds set
- setSize(int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setSize2(int, BS) - Method in class org.jmol.shape.AtomShape
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.AtomShape
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Balls
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Shape
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shapespecial.Dots
- setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shape.AtomShape
- setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shapespecial.Vectors
- setSlab(int) - Method in interface org.jmol.api.JmolGraphicsInterface
- setSlab(int) - Method in class org.jmol.export.Export3D
- setSlab(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setSlabAndZShade(int, int, int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.export.Export3D
- setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.util.GData
- setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
-
set internal slab or depth from screen-based slab or depth
- setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.AmsReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
after the vectors intinfo and floatinfo are completed, we
- setSmilesString(String) - Method in class org.jmol.viewer.Viewer
- setSolutionColor(String) - Method in class jspecview.common.PanelData
- setSortingStatus(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setSourceEnabled(boolean) - Method in class jspecview.application.ApplicationMenu
- setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
- setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
- setSpaceGroup(int, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
-
Set up all the model-related fields in association with a new space group.
- setSpaceGroupName(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setSpaceGroupName(String) - Method in interface org.jmol.api.SymmetryInterface
- setSpaceGroupName(String) - Method in class org.jmol.symmetry.Symmetry
- setSpaceGroupTo(Object) - Method in interface org.jmol.api.SymmetryInterface
- setSpaceGroupTo(Object) - Method in class org.jmol.symmetry.Symmetry
- setSpecForIRMode(Spectrum) - Method in class jspecview.common.PanelData
- setSpecShift(double) - Method in interface jspecview.api.AnnotationData
- setSpecShift(double) - Method in class jspecview.common.IntegralData
- setSpecShift(double) - Method in class jspecview.common.MeasurementData
- setSpecShift(double) - Method in class jspecview.dialog.JSVDialog
- setSpectrum(int, boolean) - Method in class jspecview.common.PanelData
- setSpectrumNumber(int) - Method in interface jspecview.api.JSVAppletInterface
-
Sets the spectrum to the specified block number
- setSpectrumNumber(int) - Method in class jspecview.app.JSVApp
-
Sets the spectrum to the specified block number
- setSpectrumNumber(int) - Method in class jspecview.appletjs.JSVApplet
- setSpectrumNumber(int) - Method in class jspecview.application.MainFrame
- setSpectrumPeaks(int, String, String) - Method in class jspecview.source.JDXReader
- setSpectrumPeaks(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- setSpectrumPeaks(int, String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
- setSpecular(boolean) - Method in class org.jmol.util.GData
- setSpecularExponent(int) - Method in class org.jmol.util.GData
-
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
- setSpecularPercent(int) - Method in class org.jmol.util.GData
-
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
- setSpecularPower(int) - Method in class org.jmol.util.GData
-
fractional distance to white for specular dot
- setSphereMatrix(T3, float, float, float, A4, M4) - Method in class org.jmol.export.__CartesianExporter
- setSpin(String, int) - Method in class org.jmol.viewer.Viewer
- setSpinOff() - Method in class org.jmol.viewer.TransformManager
- setSpinOn() - Method in class org.jmol.viewer.TransformManager
- setSpinVectors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSplitPane(boolean) - Method in class jspecview.application.MainFrame
- setState(boolean) - Method in interface jspecview.api.AnnotationData
- setState(boolean) - Method in class jspecview.common.MeasurementData
- setState(boolean) - Method in class jspecview.dialog.JSVDialog
- setState(int) - Method in class com.sparshui.server.TouchPoint
- setStatement(T[], int) - Method in class org.jmol.script.ScriptEval
-
provides support for @x and @{....} in statements.
- setStateScriptVersion(Viewer, String) - Static method in class org.jmol.script.ScriptManager
- setStatic(int, int) - Method in interface org.jmol.api.JmolScriptEvaluator
- setStatic(int, int) - Method in class org.jmol.script.ScriptEval
-
set a static variable, with checking for range
- setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
- SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
- setStatusAtomMoved(boolean, BS) - Method in class org.jmol.viewer.Viewer
- setStatusAtomPicked(int, String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
- setStatusDragDropped(int, int, int, String, String[]) - Method in interface javajs.api.JSInterface
- setStatusDragDropped(int, int, int, String, String[]) - Method in class jspecview.appletjs.JSVApplet
- setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.util.GenericApplet
- setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.viewer.Viewer
-
Allows a handler to set Jmol variable doDrop=false to cancel and also set the file type directly (Java) via the Jmol variable dropFileType (Java or JavaScript) if desired.
- setStatusListener(JmolStatusListener) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
- setStatusPicked(int, T3, Map<String, Object>) - Method in class org.jmol.shape.MeshCollection
- setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
-
resizeCallback is called whenever the applet gets a resize notification from the browser jmolSetCallback("resizeCallback", "myResizeCallback") function myResizeCallback(width, height) {}
- setStatusSelect(BS) - Method in class org.jmol.viewer.Viewer
-
Make the SelectCallback call and reset the hasSelected value to false.
- setStatusStructureModified(int, int, int, String, int, BS) - Method in class org.jmol.viewer.StatusManager
- setStereo(boolean, Object) - Method in class org.jmol.viewer.Viewer
- setStereoGraphics(boolean) - Method in interface org.jmol.api.JmolAppletInterface
- setStereoGraphics(boolean) - Method in class org.jmol.util.GenericApplet
- setStereoMode(int[], STER, float) - Method in class org.jmol.viewer.Viewer
- setStrandCount() - Method in class org.jmol.renderbio.StrandsRenderer
- setStream(BufferedInputStream, boolean) - Method in interface javajs.api.GenericBinaryDocument
- setStream(BufferedInputStream, boolean) - Method in class javajs.util.BinaryDocument
- setStream(OutputStream) - Method in class org.jmol.util.JSONWriter
- setStream(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- setStream(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- setStream(String, boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- setStreamData(DataInputStream, boolean) - Method in interface javajs.api.GenericBinaryDocument
- setStreamData(DataInputStream, boolean) - Method in class javajs.util.BinaryDocument
- setString(String) - Method in class javajs.util.CifDataParser
-
sets global str and line to be parsed from the beginning \1 ....
- setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
- setStringProperty(String, String) - Method in class org.jmol.script.ScriptParam
- setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
- setStrokeBold(Object, boolean) - Method in class jspecview.common.PDFWriter
- setStrokeBold(Object, boolean) - Method in class jspecview.java.AwtG2D
- setStrokeBold(Object, boolean) - Method in class jspecview.js2d.JsG2D
- setStrokeBold(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
- setStrokeBold(Object, boolean) - Method in class org.jmol.awt.AwtG2D
- setStrokeBold(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
- setStrucNo(int) - Method in class org.jmol.modelset.Group
- setStrucNo(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
- setStrucNo(int) - Method in class org.jmol.modelsetbio.Monomer
- setStructure(String, Translator) - Method in class org.jmol.popup.PopupResource
- setStructureBS(int, int, STR, BS, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
bits in the bitset determines the type
- setStructureIndexes() - Method in class org.jmol.modelset.ModelSet
- setStructureList(float[], STR) - Method in class org.jmol.viewer.GlobalSettings
- setStructureList(float[], STR) - Method in class org.jmol.viewer.Viewer
- setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelset.ModelSet
- setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
- setSubstituent(String) - Method in class jme.JME
- setSurfaceInfo(P4, P3, int, String) - Method in class org.jmol.jvxl.data.JvxlData
- setSurfaceInfoFromBitSet(BS, P4) - Method in class org.jmol.jvxl.data.JvxlData
- setSurfaceInfoFromBitSetPts(BS, P4, P3) - Method in class org.jmol.jvxl.data.JvxlData
- setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the symbol of the atm.
- setSymmetry(XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setSymmetryInfoFromFile(ModelSet, int, float[]) - Method in class org.jmol.symmetry.Symmetry
-
Set space group and unit cell from the auxiliary info generated by XtalSymmetry specific to a given model.
- setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setSymop(int, boolean) - Method in class org.jmol.modelset.Atom
- setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
- setSyncFlush(boolean) - Method in class com.jcraft.jzlib.DeflaterOutputStream
- setT(T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the value of the Tuple3f argument.
- setT(T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the value of the Tuple3d argument.
- setT(T3i) - Method in class javajs.util.T3i
-
Sets the value of this tuple to the value of tuple t1.
- setTA(T3, float) - Method in class javajs.util.Quat
-
q = (cos(theta/2), sin(theta/2) * n)
- settable - Static variable in class org.jmol.script.T
- setTableHeader(JTableHeader) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setTableModel(TableModel) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setTableSelectionEnabled(boolean) - Method in class jspecview.dialog.JSVDialog
- setTainted(boolean) - Method in class org.jmol.viewer.Viewer
- setTaintedAll() - Method in class jspecview.common.PanelData
- setTaintedAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
- setTemplate(String, String) - Method in class jme.JME
- setTempVertex(T3, T3, T3) - Static method in class org.jmol.export.___Exporter
- setTensor(Tensor) - Method in class org.jmol.shapespecial.Ellipsoid
- setTensors() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setText(Object, String) - Method in interface jspecview.api.PlatformDialog
- setText(Object, String) - Method in class jspecview.java.AwtDialog
- setText(Object, String) - Method in class jspecview.js2d.JsDialog
- setText(String) - Method in class jme.JME
- setText(String) - Method in interface org.jmol.api.JmolAbstractButton
- setText(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
- setText(String) - Method in interface org.jmol.api.SC
- setText(String) - Method in class org.jmol.awt.AwtSwingComponent
- setText(String) - Method in class org.jmol.awtjs.swing.Component
- setText(String) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this component's text has been changed.
- setText(String) - Method in interface org.jmol.console.GenericTextArea
- setText(String) - Method in class org.jmol.modelset.Text
- setText(String, String) - Method in class org.jmol.popup.GenericPopup
- setTextPosition(int) - Method in class org.jmol.util.GData
- setThreshold(double) - Method in class jspecview.dialog.JSVDialog
- setTime(String) - Method in class jspecview.source.JDXHeader
-
Sets the time the file was created
- setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
- setTimeout(Viewer, Map<String, Object>, String, int, String) - Static method in class org.jmol.thread.TimeoutThread
- setTitle() - Method in class org.jmol.console.GenericConsole
- setTitle() - Method in class org.jmol.console.JmolConsole
- setTitle() - Method in class org.jmol.consolejs.AppletConsole
- setTitle(Object) - Method in class org.jmol.shape.MeshCollection
- setTitle(Object) - Method in class org.jmol.shapespecial.Draw
- setTitle(String) - Method in interface jspecview.api.JSVViewPanel
- setTitle(String) - Method in interface jspecview.api.PlatformDialog
- setTitle(String) - Method in class jspecview.java.AwtMainPanel
- setTitle(String) - Method in class jspecview.java.AwtPanel
- setTitle(String) - Method in class jspecview.js2d.JsMainPanel
- setTitle(String) - Method in class jspecview.js2d.JsPanel
- setTitle(String) - Method in class jspecview.source.JDXHeader
-
Sets the title of the spectrum
- setTitle(String) - Method in interface org.jmol.api.js.JSConsole
- setTitle(String) - Method in class org.jmol.awtjs.swing.JDialog
- setToAA(A4) - Method in class javajs.util.M4
-
Sets the rotational component (upper 3x3) of this matrix to a rotation given by an axis angle
- setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
- setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
- setToM3(M34) - Method in class javajs.util.M4
-
Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are initialized as if this were an identity matrix (ie, affine matrix with no translational component).
- setToolTipText(String) - Method in interface jspecview.api.JSVPanel
- setToolTipText(String) - Method in class jspecview.common.PanelData
- setToolTipText(String) - Method in class jspecview.js2d.JsPanel
- setToolTipText(String) - Method in interface org.jmol.api.JmolAbstractButton
- setTopoAtom(int, int, String, int, int) - Method in class org.jmol.smiles.SmilesAtom
- setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, Node[], boolean) - Method in class org.jmol.smiles.SmilesStereo
- setTorsionData(T3, T3, T3, T3, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
-
calculate temporary points
- setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
- setTrajectoryBs(BS) - Method in class org.jmol.modelset.ModelSet
- setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setTranslation(T3) - Method in class javajs.util.M4
-
Modifies the translational components of this matrix to the values of the Vector3f argument; the other values of this matrix are not modified.
- setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
- setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
- setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
- setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setTranslucent(float, boolean) - Method in class org.jmol.modelset.Text
- setTranslucentVertices(BS) - Method in class org.jmol.util.MeshSurface
-
Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygons
- setTransparentCursor(Object) - Method in class jspecview.java.AwtPlatform
- setTransparentCursor(Object) - Method in class jspecview.js2d.JsPlatform
- setTransparentCursor(Object) - Method in interface org.jmol.api.GenericPlatform
- setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
- setTransparentCursor(Object) - Method in class org.jmol.awtjs2d.Platform
- setTreeNode(JSVTreeNode) - Method in class jspecview.common.PanelNode
- setTurn() - Method in class org.jmol.shapebio.Rockets
- setType(int) - Method in class org.jmol.util.Vibration
- setType(String) - Method in class javajs.util.OC
- setType(String) - Method in class org.jmol.util.Tensor
-
Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.
- setType(Annotation.AType) - Method in class jspecview.dialog.JSVDialog
- setU(Atom, int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setUndoMax(int) - Method in class org.jmol.viewer.StateManager
- setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setUnitCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
- setUnitCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
- setUnitCellAtomIndex(int) - Method in class org.jmol.viewer.AnimationManager
- setUnitCellFromParams(float[], boolean, float) - Method in interface org.jmol.api.SymmetryInterface
- setUnitCellFromParams(float[], boolean, float) - Method in class org.jmol.symmetry.Symmetry
- setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setUnits(String, boolean) - Method in class org.jmol.viewer.Viewer
- setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
- setup(int, float[], P3[], BS) - Method in class org.jmol.quantum.MepCalculation
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.cif.BCIFReader
-
binary must set up initially
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
standard set up
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.MdCrdReader
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setup(JSViewer, Spectrum, OC, int, int) - Method in class jspecview.export.AMLExporter
- setup(JSViewer, Spectrum, OC, int, int) - Method in class jspecview.export.CMLExporter
- setup(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
- setupAC() - Method in class org.jmol.modelset.AtomCollection
- setupArrays() - Method in class org.jmol.modelset.Model
- setupASCR(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setupBC() - Method in class org.jmol.modelset.BondCollection
- setupCalculation(Map<String, Object>, boolean, VolumeData, BS, T3[], Atom[], int, int[][], float[], float[], boolean, float[][], T3[]) - Method in class org.jmol.quantum.MOCalculation
- setupCalculation(VolumeData, BS, BS, BS[], T3[], int, boolean, T3[], float[], int) - Method in class org.jmol.quantum.NciCalculation
- setupConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupCoordinates(float[], float[], BS, T3[], Atom[], T3[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
- setupDisplay() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupDisplay() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupDnD() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupDnD() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupLabels(Map<String, String>) - Method in class org.jmol.console.GenericConsole
- setupLabels0(Map<String, String>) - Method in class org.jmol.console.GenericConsole
- setupLabels0(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupPS(AlphaPolymer, STR, int, int) - Method in class org.jmol.modelsetbio.ProteinStructure
- setupRR(BioShape, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
- setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
- setupUI(boolean) - Method in class org.jmol.dialog.Dialog
- setupUIManager() - Static method in class org.jmol.dialog.Dialog
-
Setup the UIManager (for i18n)
- setUseNumberLocalization(boolean) - Static method in class javajs.util.DF
- setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
- setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
- setUserVariable(String, SV) - Method in class org.jmol.viewer.GlobalSettings
- setUserYFactor(double) - Method in class jspecview.common.Spectrum
-
Set by JSViewer
- setVA(V3, float) - Method in class javajs.util.A4
-
Sets the value of this AxisAngle4f to the specified axis and angle.
- setValence(int) - Method in class org.jmol.modelset.Atom
- setValence(int) - Method in class org.jmol.smiles.SmilesAtom
- setValue(double) - Method in class jspecview.common.Measurement
- setValueAt(Object, int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
- setVariable(int, int, String, boolean) - Method in class org.jmol.script.ScriptEval
- setVarName(String) - Method in class jspecview.source.JDXDataObject
-
From ##VARNAME
- setVectorAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVectorScale(float) - Method in class org.jmol.api.JmolViewer
- setVectorScale(float) - Method in class org.jmol.viewer.Viewer
- setVertexAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
- setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
- setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
-
sets the period of vibration -- period > 0: sets the period and turns vibration on -- period invalid input: '<' 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
- setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
- setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
- setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
- setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
- setVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
- setViewer(JFrame, Viewer, Container) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- setViewer(PlatformViewer, Object) - Method in class jspecview.java.AwtPlatform
- setViewer(PlatformViewer, Object) - Method in class jspecview.js2d.JsPlatform
- setViewer(PlatformViewer, Object) - Method in interface org.jmol.api.GenericPlatform
- setViewer(PlatformViewer, Object) - Method in class org.jmol.awt.Platform
- setViewer(PlatformViewer, Object) - Method in class org.jmol.awtjs2d.Platform
- setViewer(Viewer) - Method in class org.jmol.adapter.writers.MOLWriter
- setViewer(Viewer) - Method in interface org.jmol.api.JmolJSpecView
- setViewer(Viewer) - Method in interface org.jmol.api.JmolNMRInterface
- setViewer(Viewer) - Method in interface org.jmol.api.JmolPropertyManager
- setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptEvaluator
- setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptManager
- setViewer(Viewer) - Method in class org.jmol.console.GenericConsole
- setViewer(Viewer) - Method in class org.jmol.jsv.JSpecView
- setViewer(Viewer) - Method in class org.jmol.modelsetbio.BioResolver
- setViewer(Viewer) - Method in class org.jmol.quantum.NMRCalculation
- setViewer(Viewer) - Method in class org.jmol.script.ScriptEval
- setViewer(Viewer) - Method in class org.jmol.script.ScriptManager
- setViewer(Viewer) - Method in class org.jmol.viewer.PropertyManager
- setViewer(Viewer) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
- setViewer(Viewer, String) - Method in class org.jmol.thread.JmolThread
- setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
- setViewerG3dShapeID(Viewer, int) - Method in class org.jmol.render.ShapeRenderer
- setViewTitle(String) - Method in class jspecview.common.PanelData
- setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
- setVisibilityInfo() - Method in class org.jmol.shape.Measures
- setVisible(boolean) - Method in interface jspecview.api.JSVAppletInterface
- setVisible(boolean) - Method in interface jspecview.api.PlatformDialog
- setVisible(boolean) - Method in class jspecview.app.JSVApp
- setVisible(boolean) - Method in class jspecview.appletjs.JSVApplet
- setVisible(boolean) - Method in class jspecview.dialog.JSVDialog
- setVisible(boolean) - Method in class jspecview.java.AwtDialog
- setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
- setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
- setVisible(boolean) - Method in interface org.jmol.api.js.JSConsole
- setVisible(boolean) - Method in class org.jmol.awtjs.swing.Component
- setVisible(boolean) - Method in class org.jmol.awtjs.swing.JDialog
- setVisible(boolean) - Method in class org.jmol.console.AppletConsole
- setVisible(boolean) - Method in class org.jmol.console.GenericConsole
- setVisible(boolean) - Method in class org.jmol.console.JmolConsole
- setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
- setVisible(boolean) - Method in class org.jmol.consolejs.AppletConsole
- setVisible(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- setVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- setVisible(boolean) - Method in interface org.openscience.jmol.app.JmolPlugin
- setVisible(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this component's text has been changed.
- setVolumeDataV(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
- setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
- setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelDataAsArray(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
-
for sparse data mapping, as for a plane
- setWhiteSpace(boolean) - Method in class org.jmol.util.JSONWriter
- setWidthHeight(boolean) - Method in class org.jmol.util.GData
- setWidthHeightVar() - Method in class org.jmol.viewer.Viewer
- setWindow(int, int, float) - Method in class org.jmol.modelset.Text
- setWindowDimensions(float[]) - Method in class org.jmol.viewer.Viewer
- setWindowParameters(int, int) - Method in class jspecview.common.PDFWriter
- setWindowParameters(int, int) - Method in class jspecview.java.AwtG2D
- setWindowParameters(int, int) - Method in class jspecview.js2d.JsG2D
- setWindowParameters(int, int) - Method in interface org.jmol.api.GenericGraphics
- setWindowParameters(int, int) - Method in class org.jmol.awt.AwtG2D
- setWindowParameters(int, int) - Method in class org.jmol.awtjs2d.JsG2D
- setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
- setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
- setWinParams(int, int, boolean) - Method in class org.jmol.util.GData
- setWriteNullAsString(boolean) - Method in class org.jmol.util.JSONWriter
-
Set option to write a null as the string "null" or just null itself.
- setX(float) - Method in class com.sparshui.common.messages.events.TouchEvent
- SETX - Enum constant in enum class jspecview.common.ScriptToken
- setXFactor(double) - Method in class jspecview.source.JDXDataObject
-
Sets the original xfactor, from JDXReader and XMLReader
- setXLabel(String) - Method in class jspecview.source.JDXDataObject
- setXPointers(Spectrum, double, Spectrum, double) - Method in class jspecview.common.PanelData
- setXRangeForSubSpectrum(Coordinate[]) - Method in class jspecview.common.ViewData
- setXRot(float) - Method in class javajs.util.M34
- setXUnits(String) - Method in class jspecview.source.JDXDataObject
-
Sets the units for the x axis
- setXVal(double) - Method in class jspecview.common.Coordinate
-
Sets the x value of the coordinate
- setXYA(float[], int) - Method in class org.jmol.modelset.Text
- setXYCoords(Coordinate[]) - Method in class jspecview.source.JDXDataObject
-
Sets the array of coordinates
- setXYZ(P3, boolean) - Method in class org.jmol.modelset.Text
- setXYZ(T3) - Method in class org.jmol.util.ModulationSet
- setXYZ(T3) - Method in class org.jmol.util.Vibration
- setXYZBohr(T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- setXYZs(int, int, int, int) - Method in class org.jmol.modelset.Text
- setY(float) - Method in class com.sparshui.common.messages.events.TouchEvent
- setY2D(double) - Method in class jspecview.source.JDXDataObject
- setY2DUnits(String) - Method in class jspecview.source.JDXDataObject
- setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setYFactor(double) - Method in class jspecview.source.JDXDataObject
-
Sets the original y factor, from JDXReader and XMLReader
- setYLabel(String) - Method in class jspecview.source.JDXDataObject
- setYRot(float) - Method in class javajs.util.M34
- setYStackOffsetPercent(int) - Method in class jspecview.common.PanelData
- setYUnits(String) - Method in class jspecview.source.JDXDataObject
-
Sets the units for the y axis
- setYVal(double) - Method in class jspecview.common.Coordinate
-
Sets the y value of the coordinate
- setYVal2(double) - Method in class jspecview.common.Measurement
- setZero() - Method in class javajs.util.M3
-
Sets this matrix to all zeros.
- setZero() - Method in class javajs.util.M4
-
Sets this matrix to all zeros.
- setZeroOffset(float) - Method in class org.jmol.shapespecial.Polyhedron
- setZIndex(int) - Method in class org.jmol.awtjs.swing.JDialog
- setZoom(double, double, double, double) - Method in class jspecview.common.PanelData
- setZoomHeight(boolean, boolean) - Method in class org.jmol.viewer.TransformManager
- setZPosition(int, int) - Static method in class org.jmol.viewer.JC
- setZRot(float) - Method in class javajs.util.M34
- setZs(int, int) - Method in class org.jmol.modelset.Text
- sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
- sg - Variable in class org.jmol.shapesurface.Isosurface
- SG_AS_STRING - Static variable in class org.jmol.viewer.JC
- SG_CHECK_SUPERCELL - Static variable in class org.jmol.viewer.JC
- SG_FROM_SCRATCH - Static variable in class org.jmol.viewer.JC
- SG_IS_ASSIGN - Static variable in class org.jmol.viewer.JC
- sgName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- SHADE_INDEX_LAST - Static variable in class org.jmol.util.Shader
- SHADE_INDEX_NOISY_LIMIT - Static variable in class org.jmol.util.Shader
- SHADE_INDEX_NORMAL - Static variable in class org.jmol.util.Shader
- shader - Variable in class org.jmol.util.GData
- Shader - Class in org.jmol.util
-
All functions.
- Shader() - Constructor for class org.jmol.util.Shader
- shape - Variable in class org.jmol.render.ShapeRenderer
- shape - Static variable in class org.jmol.script.T
- Shape - Class in org.jmol.shape
-
Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
- Shape() - Constructor for class org.jmol.shape.Shape
- SHAPE_AXES - Static variable in class org.jmol.viewer.JC
- SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JC
- SHAPE_BALLS - Static variable in class org.jmol.viewer.JC
- SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JC
- SHAPE_CARTOON - Static variable in class org.jmol.viewer.JC
- SHAPE_CGO - Static variable in class org.jmol.viewer.JC
- SHAPE_CONTACT - Static variable in class org.jmol.viewer.JC
- SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JC
- SHAPE_DOTS - Static variable in class org.jmol.viewer.JC
- SHAPE_DRAW - Static variable in class org.jmol.viewer.JC
- SHAPE_ECHO - Static variable in class org.jmol.viewer.JC
- SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JC
- SHAPE_FRANK - Static variable in class org.jmol.viewer.JC
- SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_HALOS - Static variable in class org.jmol.viewer.JC
- SHAPE_HOVER - Static variable in class org.jmol.viewer.JC
- SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JC
- SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_LABELS - Static variable in class org.jmol.viewer.JC
- SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_MEASURES - Static variable in class org.jmol.viewer.JC
- SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_MO - Static variable in class org.jmol.viewer.JC
- SHAPE_NBO - Static variable in class org.jmol.viewer.JC
- SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JC
- SHAPE_PMESH - Static variable in class org.jmol.viewer.JC
- SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JC
- SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JC
- SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JC
- SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JC
- SHAPE_STARS - Static variable in class org.jmol.viewer.JC
- SHAPE_STICKS - Static variable in class org.jmol.viewer.JC
- SHAPE_STRANDS - Static variable in class org.jmol.viewer.JC
- SHAPE_STRUTS - Static variable in class org.jmol.viewer.JC
- SHAPE_TRACE - Static variable in class org.jmol.viewer.JC
- SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JC
- SHAPE_VECTORS - Static variable in class org.jmol.viewer.JC
- shapeClassBases - Static variable in class org.jmol.viewer.JC
- shapeCommand - Static variable in class org.jmol.script.T
- shapeID - Variable in class org.jmol.render.ShapeRenderer
- shapeID - Variable in class org.jmol.shape.Shape
- shapely - Static variable in class org.jmol.script.T
- SHAPELY - Enum constant in enum class org.jmol.c.PAL
- SHAPELY - Static variable in class org.jmol.util.ColorEncoder
- ShapeManager - Class in org.jmol.viewer
- ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
- ShapeRenderer - Class in org.jmol.render
- ShapeRenderer() - Constructor for class org.jmol.render.ShapeRenderer
- shapes - Variable in class org.jmol.viewer.ShapeManager
- shapeTokenIndex(int) - Static method in class org.jmol.viewer.JC
- shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
- shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
- shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
- sheet - Static variable in class org.jmol.script.T
- Sheet - Class in org.jmol.modelsetbio
- SHEET - Enum constant in enum class org.jmol.c.STR
- sheetsmoothing - Static variable in class org.jmol.script.T
- sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
- shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
- shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- ShelxReader - Class in org.jmol.adapter.readers.xtal
-
A reader for SHELX output (RES) files.
- ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
- SHIFT - Static variable in class org.jmol.viewer.binding.Binding
- SHIFT_MASK - Static variable in class org.jmol.awtjs.Event
- shiftBits(BS, BS, boolean, int) - Static method in class org.jmol.util.BSUtil
-
this one slides bits to higher positions based on a pattern.
- shiftPressed - Variable in class jspecview.common.PanelData
- shiftSpectrum(int, double, double) - Method in class jspecview.common.PanelData
-
shifts xyCoords for a spectrum by the specified amount
- shiftToXY(double, double) - Method in class jme.JMEmol
-
shift to an origin and return a dimension
- shiftX(Coordinate[], double) - Static method in class jspecview.common.Coordinate
- SHIFTX - Enum constant in enum class jspecview.common.ScriptToken
- shiftY(int, int, int, int) - Method in class jspecview.common.IntegralData
- shm - Variable in class org.jmol.viewer.Viewer
- shouldApplySpectrumDisplaySettingsNow() - Method in class jspecview.application.PreferencesDialog
- shouldDisplayXAxisIncreasing() - Method in class jspecview.source.JDXDataObject
-
Determines if the plot should be displayed decreasing by default
- show - Static variable in class org.jmol.script.T
- show(int, int, boolean) - Method in class org.jmol.popup.GenericPopup
- show(String[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
- show(String[]) - Method in class org.jmol.console.ScriptEditor
- show(Component, int, int) - Method in class org.jmol.awtjs.swing.JPopupMenu
- showAnnotation(Annotation.AType, Boolean) - Method in class jspecview.common.PanelData
- showAtomNumbers - Variable in class jme.JME
- showAtomNumbers() - Method in class jme.JME
- showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Show an atom set from the indexes array
- showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
- showaxes - Static variable in class org.jmol.script.T
- showboundbox - Static variable in class org.jmol.script.T
- showConsole(boolean) - Method in class org.jmol.viewer.Viewer
- showContourLines - Variable in class org.jmol.shape.Mesh
- showDialog(Annotation.AType) - Method in class jspecview.common.PanelData
- showEditor(String[]) - Method in class org.jmol.viewer.Viewer
- SHOWERRORS - Enum constant in enum class jspecview.common.ScriptToken
- showFileOpenDialog(Object, Object[]) - Method in interface jspecview.api.JSVFileHelper
- showFileOpenDialog(Object, Object[]) - Method in class jspecview.java.AwtFileHelper
- showFileOpenDialog(Object, Object[]) - Method in class jspecview.js2d.JsFileHelper
- showfrank - Static variable in class org.jmol.script.T
- showFrankMenu() - Method in class org.jmol.popup.JmolGenericPopup
- showFrankMenu() - Method in class org.jmol.popup.JmolPopup
- showGrid - Variable in class jspecview.common.PrintLayout
-
whether or not the grid should be printed
- showHash(SB, String) - Method in class org.jmol.viewer.ChimeMessenger
-
#xxxx command output
- showHash(SB, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
- showhiddenselectionhalos - Static variable in class org.jmol.script.T
- showhydrogens - Static variable in class org.jmol.script.T
- showHydrogens - Variable in class jme.JME
- showInfo(JSAppletObject, boolean) - Method in interface javajs.api.js.J2SObjectInterface
- SHOWINTEGRATION - Enum constant in enum class jspecview.common.ScriptToken
- SHOWKEY - Enum constant in enum class jspecview.common.ScriptToken
- showkeystrokes - Static variable in class org.jmol.script.T
- showmeasurements - Static variable in class org.jmol.script.T
- SHOWMEASUREMENTS - Enum constant in enum class jspecview.common.ScriptToken
- showMenu(int, int) - Method in interface jspecview.api.JSVPanel
- showMenu(int, int) - Method in class jspecview.common.JSViewer
- showMenu(int, int) - Method in class jspecview.java.AwtPanel
- showMenu(int, int) - Method in class jspecview.js2d.JsPanel
- showMenu(int, int) - Method in class org.jmol.modelkit.ModelKit
- SHOWMENU - Enum constant in enum class jspecview.common.ScriptToken
- showMessage(Object, String, String) - Method in class jspecview.dialog.DialogManager
- showMessage(Object, String, String) - Method in class jspecview.java.AwtDialogManager
- showMessage(Object, String, String) - Method in class jspecview.js2d.JsDialogManager
- showMessage(String) - Method in class jspecview.common.JSViewer
- showMessage(String, String) - Method in interface jspecview.api.JSVPanel
- showMessage(String, String) - Method in class jspecview.java.AwtPanel
- showMessage(String, String) - Method in class jspecview.js2d.JsPanel
- showMessage(String, String, int) - Method in class jspecview.dialog.JSVDialog
- showMessageDialog(Object, String, String, int) - Method in class jspecview.dialog.DialogManager
- showMessageDialog(Object, String, String, int) - Method in class jspecview.java.AwtDialogManager
- showMessageDialog(Object, String, String, int) - Method in class jspecview.js2d.JsDialogManager
- showmodvecs - Static variable in class org.jmol.script.T
- showmultiplebonds - Static variable in class org.jmol.script.T
- shownavigationpointalways - Static variable in class org.jmol.script.T
- showNotImplementedOptionPane() - Method in class jspecview.application.MainFrame
-
Shows a dialog with the message "Not Yet Implemented"
- showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
- SHOWPEAKLIST - Enum constant in enum class jspecview.common.ScriptToken
- showPoints - Variable in class org.jmol.shape.Mesh
- showPreferences() - Method in class jspecview.application.MainFrame
- showProperties(Object, Spectrum) - Method in class jspecview.dialog.DialogManager
- showProperties(Object, Spectrum) - Method in class jspecview.java.AwtDialogManager
- showProperties(Object, Spectrum) - Method in class jspecview.js2d.JsDialogManager
-
Looks a lot like Swing, right? :)
- showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Shows the properties in the propertiesPane of the AtomSetChooser window
- SHOWPROPERTIES - Enum constant in enum class jspecview.common.ScriptToken
- showscript - Static variable in class org.jmol.script.T
- showSource(Object, Spectrum) - Method in class jspecview.dialog.DialogManager
- SHOWSOURCE - Enum constant in enum class jspecview.common.ScriptToken
- showSourceErrors(Object, JDXSource) - Method in class jspecview.dialog.DialogManager
- showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
- showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
- showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
- showString(String) - Method in class org.jmol.script.ScriptEval
- showString(String) - Method in class org.jmol.scriptext.ScriptExt
- showString(String, boolean) - Method in class org.jmol.viewer.Viewer
- showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptError
- showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptEval
- showTimeout(String) - Method in class org.jmol.viewer.Viewer
- showTimeout(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
- showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- showtiming - Static variable in class org.jmol.script.T
- showTiming - Variable in class org.jmol.jvxl.readers.Parameters
- showTiming - Variable in class org.jmol.viewer.GlobalSettings
- showTitle - Variable in class jspecview.common.PrintLayout
-
whether or not the title should be printed
- showTrace - Variable in class org.jmol.util.Vibration
- showTriangles - Variable in class org.jmol.shape.Mesh
- showunitcell - Static variable in class org.jmol.script.T
- showunitcelldetails - Static variable in class org.jmol.script.T
- showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
- showUrl(String) - Method in class org.jmol.api.JmolViewer
- showUrl(String) - Method in class org.jmol.util.GenericApplet
- showUrl(String) - Method in class org.jmol.viewer.Viewer
-
syncCallback traps script synchronization messages and allows for cancellation (by returning "") or modification jmolSetCallback("syncCallback", "mySyncCallback") function mySyncCallback(app, script, appletName) { ...[modify script here]...
- showUrl(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- showXScale - Variable in class jspecview.common.PrintLayout
-
whether or not the X-scale should be printed
- showYScale - Variable in class jspecview.common.PrintLayout
-
whether or not the Y-scale should be printed
- si - Variable in class jspecview.application.AwtTree
- si - Variable in class jspecview.common.JSViewer
- si - Variable in class jspecview.tree.SimpleTree
- siCheckCallbacks(String) - Method in interface jspecview.api.ScriptInterface
- siCheckCallbacks(String) - Method in class jspecview.app.JSVApp
- siCheckCallbacks(String) - Method in class jspecview.application.JSpecView
- sidechain - Static variable in class org.jmol.script.T
- SiestaReader - Class in org.jmol.adapter.readers.xtal
-
BH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/
- SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
- siExecHidden(boolean) - Method in interface jspecview.api.ScriptInterface
- siExecHidden(boolean) - Method in class jspecview.app.JSVApp
- siExecHidden(boolean) - Method in class jspecview.application.JSpecView
- siExecScriptComplete(String, boolean) - Method in interface jspecview.api.ScriptInterface
- siExecScriptComplete(String, boolean) - Method in class jspecview.app.JSVApp
- siExecScriptComplete(String, boolean) - Method in class jspecview.application.JSpecView
- siExecSetCallback(ScriptToken, String) - Method in interface jspecview.api.ScriptInterface
- siExecSetCallback(ScriptToken, String) - Method in class jspecview.app.JSVApp
- siExecSetCallback(ScriptToken, String) - Method in class jspecview.application.JSpecView
- siExecTest(String) - Method in interface jspecview.api.ScriptInterface
- siExecTest(String) - Method in class jspecview.app.JSVApp
- siExecTest(String) - Method in class jspecview.application.JSpecView
- siGetNewJSVPanel(Spectrum) - Method in interface jspecview.api.ScriptInterface
- siGetNewJSVPanel(Spectrum) - Method in class jspecview.app.JSVApp
- siGetNewJSVPanel(Spectrum) - Method in class jspecview.application.JSpecView
- siGetNewJSVPanel2(Lst<Spectrum>) - Method in interface jspecview.api.ScriptInterface
- siGetNewJSVPanel2(Lst<Spectrum>) - Method in class jspecview.app.JSVApp
- siGetNewJSVPanel2(Lst<Spectrum>) - Method in class jspecview.application.JSpecView
- sigma - Variable in class org.jmol.jvxl.readers.Parameters
- sigma - Static variable in class org.jmol.script.T
- sign - Static variable in class org.jmol.script.T
- signFactor - Variable in class org.jmol.modelset.TickInfo
- silent - Static variable in class org.jmol.script.T
- siLoaded(String) - Method in interface jspecview.api.ScriptInterface
- siLoaded(String) - Method in class jspecview.app.JSVApp
- siLoaded(String) - Method in class jspecview.application.JSpecView
- SILVER - Static variable in class org.jmol.util.C
- SIMPLE_LINE - Static variable in class org.jmol.shapecgo.CGOMesh
- simpleCage - Variable in class org.jmol.modelset.Model
- SimpleEdge - Interface in org.jmol.util
-
minimal bond interface for SMILES and CIP
- simpleEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
- SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
- SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, Lst<P3>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
- SimpleMarchingCubesOld() - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
- SimpleNode - Interface in org.jmol.util
-
Just the bare minimum for CIP, and non-BioSMILES
- SimpleTree - Class in jspecview.tree
- SimpleTree(JSViewer) - Constructor for class jspecview.tree.SimpleTree
- SimpleTreeEnumeration - Class in jspecview.tree
- SimpleTreeEnumeration(SimpleTreeNode) - Constructor for class jspecview.tree.SimpleTreeEnumeration
- SimpleTreeModel - Class in jspecview.tree
- SimpleTreeModel(JSVTreeNode) - Constructor for class jspecview.tree.SimpleTreeModel
- SimpleTreeNode - Class in jspecview.tree
- SimpleTreeNode(String, PanelNode) - Constructor for class jspecview.tree.SimpleTreeNode
- SimpleTreePath - Class in jspecview.tree
- SimpleTreePath(Object[]) - Constructor for class jspecview.tree.SimpleTreePath
- SimpleUnitCell - Class in org.jmol.util
-
general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
- SimpleUnitCell() - Constructor for class org.jmol.util.SimpleUnitCell
- SIMULATION_PROTOCOL - Static variable in class jspecview.common.JSVFileManager
- SIMULATION_PROTOCOL - Static variable in class org.jmol.viewer.FileManager
- sin - Static variable in class org.jmol.script.T
- sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
- sinBeta - Variable in class org.jmol.util.SimpleUnitCell
- siNewWindow(boolean, boolean) - Method in interface jspecview.api.ScriptInterface
- siNewWindow(boolean, boolean) - Method in class jspecview.app.JSVApp
-
Shows the applet in a Frame
- siNewWindow(boolean, boolean) - Method in class jspecview.application.JSpecView
- sinGamma - Variable in class org.jmol.util.SimpleUnitCell
- SINGLE - Static variable in class org.jmol.viewer.binding.Binding
- SinglePointGesture - Class in org.jmol.multitouch.sparshui
-
SINGLE_POINT_GESTURE only passes single-touch gestures.
- SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
- siNodeSet(PanelNode) - Method in interface jspecview.api.ScriptInterface
- siNodeSet(PanelNode) - Method in class jspecview.app.JSVApp
- siNodeSet(PanelNode) - Method in class jspecview.application.JSpecView
- siOpenDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String, String) - Method in interface jspecview.api.ScriptInterface
- siOpenDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String, String) - Method in class jspecview.app.JSVApp
- siOpenDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String, String) - Method in class jspecview.application.JSpecView
- siProcessCommand(String) - Method in interface jspecview.api.ScriptInterface
- siProcessCommand(String) - Method in class jspecview.app.JSVApp
-
overloaded in JSVAppletPro
- siProcessCommand(String) - Method in class jspecview.app.JSVAppPro
- siProcessCommand(String) - Method in class jspecview.application.JSpecView
- siSendPanelChange() - Method in interface jspecview.api.ScriptInterface
- siSendPanelChange() - Method in class jspecview.app.JSVApp
- siSendPanelChange() - Method in class jspecview.application.JSpecView
- siSetCurrentSource(JDXSource) - Method in interface jspecview.api.ScriptInterface
- siSetCurrentSource(JDXSource) - Method in class jspecview.app.JSVApp
- siSetCurrentSource(JDXSource) - Method in class jspecview.application.JSpecView
- siSetLoaded(String, String) - Method in interface jspecview.api.ScriptInterface
- siSetLoaded(String, String) - Method in class jspecview.app.JSVApp
- siSetLoaded(String, String) - Method in class jspecview.application.JSpecView
- siSetMenuEnables(PanelNode, boolean) - Method in interface jspecview.api.ScriptInterface
- siSetMenuEnables(PanelNode, boolean) - Method in class jspecview.app.JSVApp
- siSetMenuEnables(PanelNode, boolean) - Method in class jspecview.application.JSpecView
- siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in interface jspecview.api.ScriptInterface
- siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in class jspecview.app.JSVApp
- siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in class jspecview.application.JSpecView
-
Sets the display properties as specified from the preferences dialog or the properties file
- siSetSelectedPanel(JSVPanel) - Method in interface jspecview.api.ScriptInterface
- siSetSelectedPanel(JSVPanel) - Method in class jspecview.app.JSVApp
- siSetSelectedPanel(JSVPanel) - Method in class jspecview.application.JSpecView
- siSourceClosed(JDXSource) - Method in interface jspecview.api.ScriptInterface
- siSourceClosed(JDXSource) - Method in class jspecview.app.JSVApp
- siSourceClosed(JDXSource) - Method in class jspecview.application.JSpecView
-
Closes the
JDXSource
specified by source - siSyncLoad(String) - Method in interface jspecview.api.ScriptInterface
- siSyncLoad(String) - Method in class jspecview.app.JSVApp
-
Loads a new file into the existing applet window
- siSyncLoad(String) - Method in class jspecview.application.JSpecView
- site - Static variable in class org.jmol.script.T
- siUpdateBoolean(ScriptToken, boolean) - Method in interface jspecview.api.ScriptInterface
- siUpdateBoolean(ScriptToken, boolean) - Method in class jspecview.app.JSVApp
- siUpdateBoolean(ScriptToken, boolean) - Method in class jspecview.application.JSpecView
- siUpdateRecentMenus(String) - Method in interface jspecview.api.ScriptInterface
- siUpdateRecentMenus(String) - Method in class jspecview.app.JSVApp
- siUpdateRecentMenus(String) - Method in class jspecview.application.JSpecView
- siValidateAndRepaint(boolean) - Method in interface jspecview.api.ScriptInterface
- siValidateAndRepaint(boolean) - Method in class jspecview.app.JSVApp
- siValidateAndRepaint(boolean) - Method in class jspecview.application.JSpecView
- sixdots - Static variable in class org.jmol.render.FontLineShapeRenderer
- size - Static variable in class org.jmol.script.T
- size() - Method in class javajs.util.BS
-
Returns the number of bits of space actually in use by this
BitSet
to represent bit values. - skew() - Method in class org.jmol.util.Tensor
-
a measure of asymmetry.
- skip(long) - Method in class com.jcraft.jzlib.InflaterInputStream
- skipComments(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- skipComments(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- skipComments(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- skipData(int) - Method in class org.jmol.jvxl.readers.JvxlReader
- skipData(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- skipData(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- skipDataVFR(int) - Method in class org.jmol.jvxl.readers.JvxlReader
- skipDataVFR(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- skipDataVFR(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- skipLoop(boolean) - Method in interface javajs.api.GenericCifDataParser
- skipLoop(boolean) - Method in class javajs.util.CifDataParser
-
Skips all associated loop data.
- skipLoop(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
- skipLoopKeyword() - Method in class org.jmol.adapter.readers.cif.CifReader
- skipNextToken() - Method in interface javajs.api.GenericCifDataParser
- skipNextToken() - Method in class javajs.util.CifDataParser
- skipping - Variable in class org.jmol.adapter.readers.cif.CifReader
- skipTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
- skipTo(String, String) - Method in class org.jmol.jvxl.readers.JvxlReader
- skipTo(String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- skipTo(String, String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- slab - Static variable in class org.jmol.script.T
- slab - Variable in class org.jmol.util.GData
- slabbingObject - Variable in class org.jmol.shape.Mesh
- slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSlicer
-
"slabs" an isosurface into the first Brillouin zone moving points as necessary.
- slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSurface
- slabbyatom - Static variable in class org.jmol.script.T
- slabbymolecule - Static variable in class org.jmol.script.T
- slabColix - Variable in class org.jmol.util.MeshSurface
- slabenabled - Static variable in class org.jmol.script.T
- slabEnabled - Variable in class org.jmol.viewer.TransformManager
- slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
- slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
- slabInternal(P4, boolean) - Method in class org.jmol.viewer.TransformManager
- slabIsosurface(Lst<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
- slabMeshType - Variable in class org.jmol.util.MeshSurface
- slabOptions - Variable in class org.jmol.util.MeshSurface
- slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
- slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSlicer
- slabPolygonsList(Lst<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
- slabrange - Static variable in class org.jmol.script.T
- slabReset() - Method in class org.jmol.viewer.TransformManager
- slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
- slabValue - Variable in class org.jmol.jvxl.data.JvxlData
- slabValue - Variable in class org.jmol.viewer.TransformManager
- slabXY - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- slabZ - Variable in class org.jmol.export.___Exporter
- slaterArray - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- SlaterData - Class in org.jmol.quantum
- SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
- slaters - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- sleepTime - Variable in class org.jmol.thread.JmolThread
- slen - Variable in class org.jmol.script.ScriptParam
- slen - Variable in class org.jmol.scriptext.ScriptExt
- slm - Variable in class org.jmol.viewer.Viewer
- slop - Variable in class org.jmol.adapter.writers.XtlWriter
- slop - Variable in class org.jmol.util.SimpleUnitCell
-
initial value is set in subclass UnitCell
- SLOP_PARAMS - Static variable in class org.jmol.util.SimpleUnitCell
- SLOPDP - Static variable in class org.jmol.util.SimpleUnitCell
- SLOPSP - Static variable in class org.jmol.util.SimpleUnitCell
-
allowance for rounding in [0,1)
- sm - Variable in class org.jmol.modelset.ModelSet
- sm - Variable in class org.jmol.script.ScriptEval
- sm - Variable in class org.jmol.viewer.Viewer
- smallAtomWidthLabel - Variable in class jme.AtomDisplayLabel
- smallmoleculemaxatoms - Static variable in class org.jmol.script.T
- smartaromatic - Static variable in class org.jmol.script.T
- SmarterJmolAdapter - Class in org.jmol.adapter.smarter
- SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
- smarts - Variable in class org.jmol.shapespecial.Polyhedron
- smiles - Static variable in class org.jmol.script.T
- smiles - Variable in class org.jmol.shapespecial.Polyhedron
- smiles() - Method in class jme.JME
- smiles() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- SMILES_2D - Static variable in class org.jmol.viewer.JC
- SMILES_AROMATIC_DEFINED - Static variable in class org.jmol.viewer.JC
-
AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.
- SMILES_AROMATIC_DOUBLE - Static variable in class org.jmol.viewer.JC
-
AROMATIC_DOUBLE allows a distinction between single and double, as for example is necessary to distinguish between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing)
- SMILES_AROMATIC_MMFF94 - Static variable in class org.jmol.viewer.JC
-
AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.
- SMILES_AROMATIC_PLANAR - Static variable in class org.jmol.viewer.JC
-
AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)
- SMILES_AROMATIC_STRICT - Static variable in class org.jmol.viewer.JC
-
AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds
- SMILES_FIRST_MATCH_ONLY - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_ALL_COMPONENTS - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_ATOM_COMMENT - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_COMMENT - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_COV_CROSSLINK - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_HH_CROSSLINK - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_NOCOMMENTS - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_EXPLICIT_H_ALL - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_EXPLICIT_H2_ONLY - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_NO_BRANCHES - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_POLYHEDRAL - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_TOPOLOGY - Static variable in class org.jmol.viewer.JC
- SMILES_GROUP_BY_MODEL - Static variable in class org.jmol.viewer.JC
- SMILES_IGNORE_ATOM_CLASS - Static variable in class org.jmol.viewer.JC
- SMILES_IGNORE_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
- SMILES_INVERT_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
- SMILES_MAP_UNIQUE - Static variable in class org.jmol.viewer.JC
- SMILES_NO_AROMATIC - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_OPENSMARTS - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_OPENSMILES - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_SMARTS - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_SMILES - Static variable in class org.jmol.viewer.JC
- smiles2dimageformat - Static variable in class org.jmol.script.T
- SmilesAromatic - Class in org.jmol.smiles
- SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
- SmilesAtom - Class in org.jmol.smiles
-
This class represents an atom in a
SmilesMolecule
. - SmilesAtom() - Constructor for class org.jmol.smiles.SmilesAtom
- SmilesBond - Class in org.jmol.smiles
-
Bond in a SmilesMolecule
- SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
-
SmilesBond constructor
- SmilesExt - Class in org.jmol.scriptext
- SmilesExt() - Constructor for class org.jmol.scriptext.SmilesExt
- SmilesGenerator - Class in org.jmol.smiles
-
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
- SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
- SmilesMatcher - Class in org.jmol.smiles
-
Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
- SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
- SmilesMatcherInterface - Interface in org.jmol.api
- SmilesMeasure - Class in org.jmol.smiles
- SmilesParser - Class in org.jmol.smiles
-
Parses a SMILES string or SMARTS pattern to create a
SmilesSearch
. - SmilesSearch - Class in org.jmol.smiles
-
A class to build and carry out a SMILES or SMARTS match
- SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
- SmilesSearch.SmilesTarget - Class in org.jmol.smiles
- SmilesStereo - Class in org.jmol.smiles
-
This class relates to stereochemical issues
- SmilesTarget() - Constructor for class org.jmol.smiles.SmilesSearch.SmilesTarget
- smilesurlformat - Static variable in class org.jmol.script.T
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
- solid - Static variable in class org.jmol.script.T
- solidOnly - Variable in class org.jmol.export.___Exporter
- solvent - Static variable in class org.jmol.script.T
- solventprobe - Static variable in class org.jmol.script.T
- solventproberadius - Static variable in class org.jmol.script.T
- solvName - Variable in class jspecview.export.AMLExporter
- solvName - Variable in class jspecview.export.CMLExporter
- solvRef - Variable in class jspecview.export.AMLExporter
- solvRef - Variable in class jspecview.export.CMLExporter
- someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelSet
- someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelSet
- someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelSet
- sort - Static variable in class org.jmol.g3d.Graphics3D
- sort - Static variable in class org.jmol.script.T
- Sort(int, String) - Constructor for class org.jmol.script.SV.Sort
- sortAssemblyModels() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...
- sortedItem(Lst<String>, int) - Static method in class javajs.util.AU
- sortMapArray(String) - Method in class org.jmol.script.SV
- sortMOs() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.AmsReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
sorts coefficients by atomic number for speed later
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
sorts coefficients by atomic number for speed later
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.AmsReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrReverse(int) - Method in class org.jmol.script.SV
- SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
- source - Variable in class jspecview.common.PanelNode
- source - Variable in class jspecview.source.AnIMLReader
- SOURCE - Enum constant in enum class jspecview.common.ExportType
- sourceClosed(JDXSource) - Method in class jspecview.application.MainFrame
- sourceID - Variable in class jspecview.source.JDXDataObject
- sourceLabel - Static variable in class jspecview.common.JSViewer
- SourceReader - Interface in jspecview.api
- SOUTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
- SP - Static variable in class org.jmol.quantum.QS
- spacebeforesquare - Static variable in class org.jmol.script.T
- spacefill - Static variable in class org.jmol.script.T
- spacegroup - Static variable in class org.jmol.script.T
- spaceGroup - Variable in class org.jmol.symmetry.Symmetry
- SpaceGroup - Class in org.jmol.symmetry
-
A general class to deal with Hermann-Mauguin or Hall names Bob Hanson 9/2006 references: International Tables for Crystallography Vol.
- SpaceGroupFinder - Class in org.jmol.symmetry
-
A relatively simple space group finder given a unit cell.
- SpaceGroupFinder() - Constructor for class org.jmol.symmetry.SpaceGroupFinder
- span() - Method in class org.jmol.util.Tensor
-
width of the signal; |e2 - e0|
- spardirCache - Variable in class org.jmol.viewer.FileManager
- SparseArray(String) - Constructor for class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- SparshClient - Interface in com.sparshui.client
-
The Client interface must be implemented in all clients wishing to connect to the Sparsh-UI gesture server.
- SpartanInputReader - Class in org.jmol.adapter.readers.spartan
- SpartanInputReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanInputReader
- SpartanReader - Class in org.jmol.adapter.readers.spartan
- SpartanReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanReader
- SpartanSmolReader - Class in org.jmol.adapter.readers.spartan
- SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanSmolReader
- spartanUtil() - Method in class org.jmol.viewer.FileManager
-
An isolated class to retrieve Spartan file data from compound documents, zip files, and directories
- SpartanUtil - Class in org.jmol.adapter.readers.spartan
-
A class to isolate Spartan file reading methods from the rest of Jmol.
- SpartanUtil() - Constructor for class org.jmol.adapter.readers.spartan.SpartanUtil
- spec - Variable in class jspecview.common.MeasurementData
- spec - Variable in class jspecview.dialog.JSVDialog
- spec_alternate - Static variable in class org.jmol.script.T
- spec_atom - Static variable in class org.jmol.script.T
- spec_chain - Static variable in class org.jmol.script.T
- spec_model - Static variable in class org.jmol.script.T
- spec_model2 - Static variable in class org.jmol.script.T
- spec_name_pattern - Static variable in class org.jmol.script.T
- spec_resid - Static variable in class org.jmol.script.T
- spec_seqcode - Static variable in class org.jmol.script.T
- spec_seqcode_range - Static variable in class org.jmol.script.T
- Special - Variable in class org.jmol.popup.JmolPopup
- SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.C
- specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
- specialAtomNames - Static variable in class org.jmol.modelset.Group
- specialLabel - Variable in class org.jmol.shape.Hover
- specialposition - Static variable in class org.jmol.script.T
- spectra - Variable in class jspecview.common.PanelData
- spectraTree - Variable in class jspecview.common.JSViewer
- spectrum - Variable in class jspecview.common.PeakInfo
- Spectrum - Class in jspecview.common
-
JDXSpectrum
implements the Interface Spectrum for the display of JDX Files. - Spectrum() - Constructor for class jspecview.common.Spectrum
-
Constructor
- SPECTRUM - Enum constant in enum class jspecview.common.ScriptToken
- Spectrum.IRMode - Enum Class in jspecview.common
- SPECTRUMNUMBER - Enum constant in enum class jspecview.common.ScriptToken
- spectypeInitials - Variable in class jspecview.export.AMLExporter
- spectypeInitials - Variable in class jspecview.export.CMLExporter
- specular - Static variable in class org.jmol.script.T
- specularexponent - Static variable in class org.jmol.script.T
- specularpercent - Static variable in class org.jmol.script.T
- specularpower - Static variable in class org.jmol.script.T
- sphere - Static variable in class org.jmol.script.T
- SPHERE - Static variable in class org.jmol.shapecgo.CGOMesh
- sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
- sphereMean(Quat[], float[], float) - Static method in class javajs.util.Quat
- SphereRenderer - Class in org.jmol.g3d
-
Implements high performance rendering of shaded spheres.
- sphereShadeIndexes - Variable in class org.jmol.util.Shader
- sphereShapeCache - Variable in class org.jmol.util.Shader
- spin - Static variable in class org.jmol.script.T
- SPIN_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- SPIN_EVENT - Static variable in class com.sparshui.GestureType
- SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- SPIN_GESTURE - Static variable in class com.sparshui.GestureType
- SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- spine - Static variable in class org.jmol.script.T
- SpinEvent - Class in com.sparshui.common.messages.events
- SpinEvent() - Constructor for class com.sparshui.common.messages.events.SpinEvent
- SpinEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.SpinEvent
-
Constructs a new SpinEvent from a serialized version - 4 bytes : rotationX - 4 bytes : rotationY - 4 bytes : rotationZ - 12 bytes total
- SpinEvent(float, float, float) - Constructor for class com.sparshui.common.messages.events.SpinEvent
- spinfps - Static variable in class org.jmol.script.T
- spinFps - Variable in class org.jmol.viewer.TransformManager
- spinOn - Variable in class org.jmol.viewer.TransformManager
- spinThread - Variable in class org.jmol.viewer.TransformManager
- SpinThread - Class in org.jmol.thread
- SpinThread() - Constructor for class org.jmol.thread.SpinThread
- spinx - Static variable in class org.jmol.script.T
- spinX - Variable in class org.jmol.viewer.TransformManager
- spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
- spiny - Static variable in class org.jmol.script.T
- spinY - Variable in class org.jmol.viewer.TransformManager
- spinz - Static variable in class org.jmol.script.T
- spinZ - Variable in class org.jmol.viewer.TransformManager
- splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- Splash - Class in org.openscience.jmol.app.jmolpanel
- Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
- splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
- SplashInterface - Interface in org.openscience.jmol.app
- split - Static variable in class org.jmol.script.T
- split(String, String) - Static method in class javajs.util.PT
-
proper splitting, even for Java 1.3 -- if the text ends in the run, no new line is appended.
- splitSpectra() - Method in class jspecview.common.JSViewer
- splitStack(boolean) - Method in class jspecview.common.PanelData
- sppm - Variable in class org.jmol.render.LabelsRenderer
- sprintf(String, String, Object[]) - Static method in class javajs.util.PT
-
sprintf emulation uses (almost) c++ standard string formats 's' string 'i' or 'd' integer, 'e' double, 'f' float, 'p' point3f 'q' quaternion/plane/axisangle with added "i" (equal to the insipid "d" -- digits?)
- sprintf(String, SV) - Static method in class org.jmol.script.SV
- sqrt - Static variable in class org.jmol.script.T
- SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesStereo
- squared - Static variable in class org.jmol.script.T
- squareEuclideanDist(double, double, double, double) - Static method in class jme.JMEUtil
- SQZ - Enum constant in enum class jspecview.common.ExportType
- sr - Variable in class org.jmol.jvxl.data.VolumeData
- ssbond - Static variable in class org.jmol.script.T
- ssbondsbackbone - Static variable in class org.jmol.script.T
- st - Variable in class org.jmol.script.ScriptParam
- st - Variable in class org.jmol.scriptext.ScriptExt
- STACKOFFSETY - Enum constant in enum class jspecview.common.ScriptToken
- STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
- standardGroupList - Static variable in class org.jmol.modelset.Group
- standardLevel - Static variable in class org.jmol.util.Geodesic
-
3 levels, 0 through 3
- star - Variable in class jme.JME
- star - Static variable in class org.jmol.script.T
- Stars - Class in org.jmol.shape
- Stars() - Constructor for class org.jmol.shape.Stars
- StarsRenderer - Class in org.jmol.render
- StarsRenderer() - Constructor for class org.jmol.render.StarsRenderer
- start() - Method in class jme.JME
- start() - Method in class org.jmol.thread.JmolThread
- start() - Method in class org.jmol.util.PatternMatcher.JSPattern
- start() - Method in class org.openscience.jmol.app.InputScannerThread
- start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- start(JFrame, Viewer, Map<String, Object>) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- start(JFrame, Viewer, Map<String, Object>) - Method in interface org.openscience.jmol.app.JmolPlugin
- start(Viewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
- start(Viewer) - Method in class org.jmol.console.AppletConsole
- start(Viewer) - Method in class org.jmol.consolejs.AppletConsole
- start(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- START - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- START_ELEMENT - Static variable in class jspecview.source.XMLParser
- START_END_ELEMENT - Static variable in class jspecview.source.XMLParser
- startChainID - Variable in class org.jmol.adapter.smarter.Structure
- startCommandWatcher(boolean) - Method in interface org.jmol.api.JmolScriptManager
- startCommandWatcher(boolean) - Method in class org.jmol.script.ScriptManager
- startDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
- startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- startGestureServer() - Method in class com.sparshui.server.GestureServer
-
two independent threads -- one accepting multiple clients, one not.
- startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
- startHoverWatcher(boolean) - Method in interface javajs.api.JSInterface
- startHoverWatcher(boolean) - Method in class jspecview.appletjs.JSVApplet
- startHoverWatcher(boolean) - Method in class org.jmol.util.GenericApplet
- startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
- startHoverWatcher(boolean) - Method in class org.jmol.viewer.Viewer
- startIndex - Variable in class jspecview.export.AMLExporter
- startIndex - Variable in class jspecview.export.CMLExporter
- STARTINDEX - Enum constant in enum class jspecview.common.ScriptToken
- startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
- startJmol(JmolApp) - Static method in class org.openscience.jmol.app.Jmol
- startLayout() - Method in interface jspecview.api.PlatformDialog
- startLayout() - Method in class jspecview.java.AwtDialog
- startLayout() - Method in class jspecview.js2d.JsDialog
- startMinimization() - Method in class org.jmol.minimize.Minimizer
- startNBO(String) - Method in class org.jmol.viewer.Viewer
- startOpenTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- startPlugin(String) - Method in class org.jmol.viewer.Viewer
-
startup -U nbo option
- startPos - Variable in class javajs.img.PngEncoder
- startRecording() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
- startService(int, JsonNioClient, Viewer, String, int) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- startService(int, JsonNioClient, Viewer, String, int) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- startSimulator(Object) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- startSpinningAxis(T3, T3, boolean) - Method in class org.jmol.viewer.Viewer
- startTime - Variable in class org.jmol.thread.JmolThread
- startTimer(String) - Static method in class org.jmol.util.Logger
- startTrace(int) - Method in class org.jmol.util.Vibration
- startupDim - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- startupHeight - Variable in class org.openscience.jmol.app.JmolApp
- startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- startupPinTip - Variable in class jspecview.common.PanelData
- startupWidth - Variable in class org.openscience.jmol.app.JmolApp
- startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- startViewer(JmolViewer, SplashInterface, boolean) - Method in class org.openscience.jmol.app.JmolApp
- starwidth - Static variable in class org.jmol.script.T
- state - Variable in class jspecview.export.AMLExporter
- state - Variable in class jspecview.export.CMLExporter
- state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- state - Variable in class org.jmol.jvxl.readers.Parameters
- state - Static variable in class org.jmol.script.T
- STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.JC
- stateButton - Variable in class org.jmol.console.GenericConsole
- stateChanged(ChangeEvent) - Method in class org.jmol.dialog.Dialog.QualityListener
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- StateCreator - Class in org.jmol.viewer
-
StateCreator handles all aspects of working with the "state" as generally defined, including -- creating the state script -- general output, including logging -- handling undo/redo -- processing SYNC directives Called by reflection only; all state generation script here, for modularization in JavaScript
- StateCreator() - Constructor for class org.jmol.viewer.StateCreator
- StateManager - Class in org.jmol.viewer
- statement - Variable in class org.jmol.script.ScriptContext
- statementAsString(Viewer, T[], int, boolean) - Static method in class org.jmol.script.ScriptEval
- StateScript - Class in org.jmol.modelset
- stateScripts - Variable in class org.jmol.modelset.ModelSet
- stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
- staticCleanTransform(String) - Method in interface org.jmol.api.SymmetryInterface
- staticCleanTransform(String) - Method in class org.jmol.symmetry.Symmetry
- staticConvertOperation(String, M4) - Method in interface org.jmol.api.SymmetryInterface
- staticConvertOperation(String, M4) - Method in class org.jmol.symmetry.Symmetry
- staticGetAtomSetCollection(AtomSetCollectionReader) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- staticGetAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
The primary file or string reader -- returns just the reader now
- staticGetTransformABC(Object, boolean) - Method in interface org.jmol.api.SymmetryInterface
- staticGetTransformABC(Object, boolean) - Method in class org.jmol.symmetry.Symmetry
- staticID - Static variable in class org.jmol.minimize.Minimizer
- staticToRationalXYZ(P3, String) - Method in interface org.jmol.api.SymmetryInterface
- staticToRationalXYZ(P3, String) - Method in class org.jmol.symmetry.Symmetry
- stats() - Method in class org.jmol.bspt.Bspf
- stats() - Method in class org.jmol.bspt.Bspt
-
prints some simple stats to stdout
- status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- STATUS_COORD - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- STATUS_TEXT - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- STATUS_TIME - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- StatusBar - Class in org.openscience.jmol.app.jmolpanel
- StatusBar(int) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
- statusForm - Variable in class org.jmol.util.GenericApplet
- statusList - Variable in class org.jmol.viewer.StatusManager
- StatusListener - Class in org.openscience.jmol.app.jmolpanel
- StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
- StatusManager - Class in org.jmol.viewer
-
The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
- statusreporting - Static variable in class org.jmol.script.T
- statusText - Variable in class org.jmol.util.GenericApplet
- statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
- statusTextarea - Variable in class org.jmol.util.GenericApplet
- stddev - Static variable in class org.jmol.script.T
- stdinchi - Static variable in class org.jmol.script.T
- stdinchikey - Static variable in class org.jmol.script.T
- steepestDescentInitialize(int, double, double) - Method in class org.jmol.minimize.forcefield.ForceField
- steepestDescentTakeNSteps(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- step - Static variable in class org.jmol.script.T
- stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
- stepMinimization() - Method in class org.jmol.minimize.Minimizer
- stepPausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
- stepPausedExecution() - Method in class org.jmol.script.ScriptEval
- steps - Variable in class jspecview.common.ScaleData
-
The step values for the X and Y scales
- steps - Variable in class org.jmol.jvxl.readers.Parameters
- STER - Enum Class in org.jmol.c
- stereo - Variable in class jme.JME
- stereo - Static variable in class org.jmol.script.T
- stereo - Variable in class org.jmol.smiles.SmilesAtom
- stereodegrees - Static variable in class org.jmol.script.T
- stereoTransformation(int[], int[]) - Static method in class jme.JMEUtil
- Sticks - Class in org.jmol.shape
- Sticks() - Constructor for class org.jmol.shape.Sticks
- SticksRenderer - Class in org.jmol.render
- SticksRenderer() - Constructor for class org.jmol.render.SticksRenderer
- stm - Variable in class org.jmol.viewer.Viewer
- stop - Static variable in class org.jmol.script.T
- stop() - Method in class jme.JME
- STOP - Static variable in class org.jmol.shapecgo.CGOMesh
- stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
- stopMotion() - Method in class org.jmol.viewer.TransformManager
- stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- stopped - Variable in class org.jmol.thread.JmolThread
- stopScriptThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
- stopScriptThreads() - Method in class org.jmol.script.ScriptEval
- stopThread(boolean) - Method in class org.jmol.viewer.AnimationManager
- store() - Method in class jspecview.application.DisplaySchemesProcessor
-
Saves the display schemes to file in XML format
- str - Variable in class javajs.util.CifDataParser
-
working string (buffer)
- str - Variable in class jme.AtomDisplayLabel
- STR - Enum Class in org.jmol.c
- straightness - Static variable in class org.jmol.script.T
- STRAIGHTNESS - Enum constant in enum class org.jmol.c.PAL
- strandcount - Static variable in class org.jmol.script.T
- strandCount - Variable in class org.jmol.adapter.smarter.Structure
- strandCount - Variable in class org.jmol.renderbio.StrandsRenderer
- strandcountformeshribbon - Static variable in class org.jmol.script.T
- strandcountforstrands - Static variable in class org.jmol.script.T
- strandID - Variable in class org.jmol.adapter.smarter.Structure
- strands - Static variable in class org.jmol.script.T
- Strands - Class in org.jmol.shapebio
- Strands() - Constructor for class org.jmol.shapebio.Strands
- strandSeparation - Variable in class org.jmol.renderbio.StrandsRenderer
- StrandsRenderer - Class in org.jmol.renderbio
- StrandsRenderer() - Constructor for class org.jmol.renderbio.StrandsRenderer
- stream - Variable in class javajs.util.BinaryDocument
- StreamReader(BufferedInputStream, String) - Constructor for class javajs.util.Rdr.StreamReader
- streamToBytes(InputStream) - Static method in class javajs.util.Rdr
-
Read an InputStream in its entirety as a byte array, closing the stream.
- streamToString(InputStream) - Static method in class javajs.util.Rdr
-
Read an InputStream in its entirety as a string, closing the stream.
- streamToUTF8String(BufferedInputStream) - Static method in class javajs.util.Rdr
-
Read a UTF-8 stream fully, converting it to a String.
- strFormat - Variable in class org.jmol.modelset.Measurement
- strFormat - Variable in class org.jmol.modelset.MeasurementData
- string - Static variable in class org.jmol.script.T
- StringDataReader - Class in javajs.util
- StringDataReader() - Constructor for class javajs.util.StringDataReader
- StringDataReader(String) - Constructor for class javajs.util.StringDataReader
- stringHeight(FontMetrics) - Static method in class jme.JMEUtil
-
Provide the ideal height of a string consisting of usual upper case characters.
- stringParameter(int) - Method in class org.jmol.script.ScriptParam
- stringParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- stringParameterSet(int) - Method in class org.jmol.script.ScriptParam
- strings - Variable in class org.jmol.shape.Labels
- stringToByteArray(String) - Static method in class com.sparshui.common.utils.Converter
- stringWidth(String) - Method in class org.jmol.util.Font
- stripPath(String) - Static method in class org.jmol.viewer.FileManager
- stripTypePrefix(String) - Static method in class org.jmol.viewer.FileManager
-
Stip PDB::file://...
- strJavaVendor - Static variable in class org.jmol.viewer.Viewer
- strJavaVersion - Static variable in class org.jmol.viewer.Viewer
- strListValue(T) - Static method in class org.jmol.script.SV
- strMenuStructure - Variable in class org.jmol.popup.GenericPopup
- StrObFreq - Variable in class jspecview.source.AnIMLReader
- stroke() - Method in class javajs.export.PDFCreator
- strOSName - Static variable in class org.jmol.viewer.Viewer
- strparam - Static variable in class org.jmol.script.T
- strproperty - Static variable in class org.jmol.script.T
- strSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- strucid - Static variable in class org.jmol.script.T
- strucno - Static variable in class org.jmol.script.T
- structure - Variable in class org.jmol.popup.PopupResource
- structure - Static variable in class org.jmol.script.T
- Structure - Class in org.jmol.adapter.smarter
- Structure - Interface in org.jmol.modelset
- Structure(int, STR, STR, String, String, int, BS[]) - Constructor for class org.jmol.adapter.smarter.Structure
- STRUCTURE - Enum constant in enum class org.jmol.c.PAL
- structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- structureID - Variable in class org.jmol.adapter.smarter.Structure
- StructureIterator - Class in org.jmol.adapter.smarter
- STRUCTUREMODIFIED - Enum constant in enum class org.jmol.c.CBK
- structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
- structureTainted - Variable in class org.jmol.modelset.Model
- structureType - Variable in class org.jmol.adapter.smarter.Structure
- structureTypes - Variable in class org.jmol.renderbio.BackboneRenderer
- structureTypes - Variable in class org.jmol.renderbio.CartoonRenderer
- structureTypes - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- structureTypes - Variable in class org.jmol.renderbio.RibbonsRenderer
- structureTypes - Variable in class org.jmol.renderbio.RocketsRenderer
- structureTypes - Variable in class org.jmol.renderbio.StrandsRenderer
- structureTypes - Variable in class org.jmol.renderbio.TraceRenderer
- strutdefaultradius - Static variable in class org.jmol.script.T
- strutlengthmaximum - Static variable in class org.jmol.script.T
- struts - Static variable in class org.jmol.script.T
- strutsmultiple - Static variable in class org.jmol.script.T
- strutspacing - Static variable in class org.jmol.script.T
- sType - Variable in class com.sparshui.GestureType
- sType - Variable in class org.jmol.minimize.MinAtom
- sub - Static variable in class org.jmol.script.T
- sub(double[], double[], V3d) - Static method in class org.jmol.minimize.Util
- sub(M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
- sub(M4) - Method in class javajs.util.M4
-
Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
- sub(Matrix) - Method in class javajs.util.Matrix
-
subtract two matrices
- sub(T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
- sub(T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
- sub2(T3d, T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
- sub2(T3, T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
- sub33(M34) - Method in class javajs.util.M34
- sublistAt(Lst<Object>, int...) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- subscripts - Variable in class jme.AtomDisplayLabel
- subset - Static variable in class org.jmol.script.T
- SubSpecChangeEvent - Class in jspecview.common
- SubSpecChangeEvent(int, String) - Constructor for class jspecview.common.SubSpecChangeEvent
- substring(int) - Method in class javajs.util.SB
- substring2(int, int) - Method in class javajs.util.SB
- substructure - Static variable in class org.jmol.script.T
- substructureType - Variable in class org.jmol.adapter.smarter.Structure
- subsystem - Static variable in class org.jmol.script.T
- subsystemCode - Variable in class org.jmol.symmetry.SymmetryOperation
- subzones - Variable in class org.jmol.util.BZone
- sum - Static variable in class org.jmol.script.T
- sum2 - Static variable in class org.jmol.script.T
- sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shape.Mesh
- sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- sumVertexNormals2(Mesh, T3[], V3[]) - Static method in class org.jmol.shape.Mesh
- supercell - Static variable in class org.jmol.script.T
- superscripts - Variable in class jme.AtomDisplayLabel
- surface - Static variable in class org.jmol.script.T
- SURFACE - Enum constant in enum class org.jmol.c.PAL
- SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
- surfaceAtoms - Variable in class org.jmol.jvxl.readers.Parameters
- surfaceAtoms - Variable in class org.jmol.util.MeshSurface
- surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- surfacedistance - Static variable in class org.jmol.script.T
- surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
- SurfaceGenerator - Class in org.jmol.jvxl.readers
- SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
- surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
- SurfaceReader - Class in org.jmol.jvxl.readers
- surfaceSet - Variable in class org.jmol.util.MeshSurface
- SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
-
Class that holds the surface status information that the surface tool needs.
- SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
- surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SurfaceTool - Class in org.openscience.jmol.app.surfacetool
- SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
- SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
- surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SV - Class in org.jmol.script
-
ScriptVariable class
- SV() - Constructor for class org.jmol.script.SV
- SV.Sort - Class in org.jmol.script
- sValue(T) - Static method in class org.jmol.script.SV
- SVG - Enum constant in enum class jspecview.common.ExportType
- SVGExporter - Class in jspecview.export
-
class
SVGExporter
contains static methods to export a Graph as as SVG. - SVGExporter() - Constructor for class jspecview.export.SVGExporter
- SVGI - Enum constant in enum class jspecview.common.ExportType
- swap(Object[], int, int) - Static method in class javajs.util.AU
- swap(T[], int, int) - Static method in class jme.JMEUtil
- swapBytesI(int) - Method in interface javajs.api.GenericBinaryDocument
- swapBytesI(int) - Method in class javajs.util.BinaryDocument
- swapBytesS(short) - Method in interface javajs.api.GenericBinaryDocument
- swapBytesS(short) - Method in class javajs.util.BinaryDocument
- swapInt(int[], int, int) - Static method in class javajs.util.AU
- swapXZ() - Method in class org.jmol.jvxl.readers.JvxlReader
- swapXZ() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- swapXZ() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- SwingConstants - Class in org.jmol.awtjs.swing
- SwingConstants() - Constructor for class org.jmol.awtjs.swing.SwingConstants
- SwingController - Interface in org.jmol.awtjs.swing
-
SwingController is an interface that org.jmol.awtjs.swing classes will need.
- swipeCount - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeCutoff - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeDelayMs - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeFactor - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeStartTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- switchAtoms() - Method in class org.jmol.util.ContactPair
- switchcmd - Static variable in class org.jmol.script.T
- sX - Variable in class org.jmol.util.Point3fi
-
screen X
- sY - Variable in class org.jmol.util.Point3fi
-
screen Y
- symbol - Static variable in class org.jmol.script.T
- symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- symMatrix - Variable in class org.jmol.util.Tensor
- symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- symmetry - Static variable in class org.jmol.script.T
- Symmetry - Class in org.jmol.symmetry
- Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
- SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- SymmetryDesc - Class in org.jmol.symmetry
-
A class to handle requests for information about space groups and symmetry operations.
- SymmetryDesc() - Constructor for class org.jmol.symmetry.SymmetryDesc
- symmetryhermannmauguin - Static variable in class org.jmol.script.T
- SymmetryInterface - Interface in org.jmol.api
- SymmetryOperation - Class in org.jmol.symmetry
- symop - Static variable in class org.jmol.script.T
- symopColixes - Variable in class org.jmol.shape.Mesh
- symopNormixes - Variable in class org.jmol.shape.Mesh
- symops - Variable in class org.jmol.adapter.readers.cif.CifReader
- symops - Variable in class org.jmol.shape.Mesh
- sync - Static variable in class org.jmol.script.T
- sync() - Method in class com.jcraft.jzlib.Inflater
- SYNC - Enum constant in enum class org.jmol.c.CBK
- SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
- SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
- SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
- SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
- SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
- SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
- SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
- SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
- SYNCCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
- syncID - Variable in class jspecview.common.JSViewer
- SYNCID - Enum constant in enum class jspecview.common.ScriptToken
- syncingScripts - Variable in class org.jmol.viewer.StatusManager
- syncmouse - Static variable in class org.jmol.script.T
- syncPoint() - Method in class com.jcraft.jzlib.Inflater
- syncscript - Static variable in class org.jmol.script.T
- syncScript(String) - Method in interface jspecview.api.JSVAppletInterface
-
precede invalid input: '<'Peaks here with full name of Jmol applet (including syncID)
- syncScript(String) - Method in class jspecview.app.JSVApp
- syncScript(String) - Method in class jspecview.appletjs.JSVApplet
- syncScript(String) - Method in class jspecview.application.MainFrame
- syncScript(String) - Method in class jspecview.common.JSViewer
-
incoming script processing of invalid input: '<'PeakAssignment file="" type="xxx"...> record from Jmol
- syncScript(String) - Method in interface org.jmol.api.JmolSyncInterface
- syncScript(String) - Method in class org.jmol.util.GenericApplet
- syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
- syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
- syncScript(Viewer, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- syncSend(String, Object, int) - Method in class org.jmol.viewer.StatusManager
- syncToJmol(String) - Method in interface jspecview.api.ScriptInterface
- syncToJmol(String) - Method in class jspecview.app.JSVApp
- syncToJmol(String) - Method in class jspecview.application.JSpecView
- syncToJmol(String) - Method in class jspecview.application.MainFrame
- syncToJmol(String) - Method in interface org.jmol.api.JSVInterface
- syncToJmol(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- syntaxError(String) - Method in class javajs.util.JSJSONParser
-
Make a JSONException to signal a syntax error.
- sZ - Variable in class org.jmol.util.Point3fi
-
screen Z
T
- t(int) - Static method in class org.jmol.script.T
- T - Class in org.jmol.script
-
Script token class.
- T() - Constructor for class org.jmol.script.T
- T_SHAPED - Static variable in class org.jmol.smiles.SmilesStereo
- T3 - Class in javajs.util
-
A generic 3 element tuple that is represented by single precision floating point x,y and z coordinates.
- T3() - Constructor for class javajs.util.T3
- T3d - Class in javajs.util
-
A generic 3 element tuple that is represented by double precision floating point x,y and z coordinates.
- T3d() - Constructor for class javajs.util.T3d
-
Constructs and initializes a Tuple3d to (0,0,0).
- T3i - Class in javajs.util
-
A 3-element tuple represented by signed integer x,y,z coordinates.
- T3i() - Constructor for class javajs.util.T3i
-
Constructs and initializes a Tuple3i to (0,0,0).
- T4 - Class in javajs.util
-
A generic 4 element tuple that is represented by single precision floating point x,y,z and w coordinates.
- T4() - Constructor for class javajs.util.T4
-
Constructs and initializes a Tuple4f to (0,0,0,0).
- tableCellAlignLeft - Variable in class jspecview.java.AwtDialog
- tableCellAlignLeft - Variable in class jspecview.js2d.JsDialog
- TableCellRenderer - Interface in org.jmol.awtjs.swing
- TableColumn - Interface in org.jmol.awtjs.swing
- tableModel - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter - Class in org.openscience.jmol.app.janocchio
- TableSorter() - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter(TableModel) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter(TableModel, JTableHeader) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
- taConvert(Spectrum, Spectrum.IRMode) - Static method in class jspecview.common.Spectrum
- TAG_NONE - Static variable in class jspecview.source.XMLParser
- tagName - Variable in class jspecview.source.AnIMLReader
- tags - Static variable in class org.jmol.quantum.QS
- tags2 - Static variable in class org.jmol.quantum.QS
- TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_BONDINGRADIUS - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_CHAIN - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_RESNO - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_SEQID - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_SITE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
- taintAtom(int, int) - Method in class org.jmol.modelset.AtomCollection
- taintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
- tainted - Variable in class org.jmol.modelset.AtomCollection
- target - Variable in class org.jmol.modelset.Text
- targetTime - Variable in class org.jmol.thread.JmolThread
- TBI_AB - Static variable in class org.jmol.minimize.forcefield.ForceField
- TBI_BC - Static variable in class org.jmol.minimize.forcefield.ForceField
- TBI_CD - Static variable in class org.jmol.minimize.forcefield.ForceField
- TEAL - Static variable in class org.jmol.util.C
- techname - Variable in class jspecview.source.AnIMLReader
- temp - Static variable in class org.jmol.adapter.readers.cif.BCIFReader
- TEMP - Enum constant in enum class org.jmol.c.PAL
- TEMP - Enum constant in enum class org.jmol.c.VDW
- TempArray - Class in org.jmol.util
- TempArray() - Constructor for class org.jmol.util.TempArray
- temperature - Static variable in class org.jmol.script.T
- templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- tempP1 - Variable in class org.jmol.export.___Exporter
- tempP2 - Variable in class org.jmol.export.___Exporter
- tempP3 - Variable in class org.jmol.export.___Exporter
- tempQ1 - Variable in class org.jmol.export._VrmlExporter
- tempQ2 - Variable in class org.jmol.export._VrmlExporter
- tempQ3 - Variable in class org.jmol.export._VrmlExporter
- tempStatement - Variable in class org.jmol.script.ScriptEval
- tempV1 - Variable in class org.jmol.export.___Exporter
- tempV2 - Variable in class org.jmol.export.___Exporter
- tensor - Static variable in class org.jmol.script.T
- tensor - Variable in class org.jmol.shapespecial.Ellipsoid
- Tensor - Class in org.jmol.util
- Tensor() - Constructor for class org.jmol.util.Tensor
-
Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods.
- tensors - Variable in class org.jmol.adapter.smarter.Atom
- tensScale - Static variable in class javajs.util.PT
- terminateEmptyTag(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
- terminateTag(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
- test() - Static method in class javajs.util.Measure
- test(String) - Static method in class javajs.util.DebugJS
-
Insert a JavaScript debug statement
- Test - Class in org.openscience.jmol.app.webexport
- TEST - Enum constant in enum class jspecview.common.ScriptToken
- testAsync - Variable in class org.jmol.viewer.Viewer
- testflag1 - Static variable in class org.jmol.script.T
- testflag2 - Static variable in class org.jmol.script.T
- testflag3 - Static variable in class org.jmol.script.T
- testflag4 - Static variable in class org.jmol.script.T
- testFlags - Variable in class org.jmol.jvxl.readers.Parameters
- testRule6Full - Variable in class org.jmol.symmetry.CIPData
-
A flag that, if set, returns rr for bicyclo[2.2.2]octane
- TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
- text - Variable in class jspecview.common.Annotation
- text - Variable in class org.jmol.awtjs.swing.Component
- text - Variable in class org.jmol.modelset.Measurement
- text - Variable in class org.jmol.modelset.MeasurementData
- text - Variable in class org.jmol.modelset.Text
- text - Variable in class org.jmol.shape.Hover
- Text - Class in org.jmol.modelset
- Text() - Constructor for class org.jmol.modelset.Text
- TEXT_ALIGN_CENTER - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_LEFT - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_NONE - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_RIGHT - Static variable in class org.jmol.viewer.JC
- textAlign - Variable in class org.jmol.render.LabelsRenderer
- TextShape - Class in org.jmol.shape
- TextShape() - Constructor for class org.jmol.shape.TextShape
- textUnformatted - Variable in class org.jmol.modelset.Text
- textY - Variable in class org.jmol.util.GData
- thePlane - Variable in class org.jmol.jvxl.readers.Parameters
- thePlane - Variable in class org.jmol.render.MeshRenderer
- theta - Static variable in class org.jmol.script.T
- theta0 - Variable in class org.jmol.minimize.MinAngle
- theTok - Variable in class org.jmol.script.ScriptParam
- theTok - Variable in class org.jmol.script.ScriptCompiler
- theToken - Variable in class org.jmol.script.ScriptParam
- theToken - Variable in class org.jmol.script.ScriptCompiler
- THIS_MODEL_ONLY - Static variable in class org.jmol.viewer.JC
-
specifically for ECHO and DRAW to have these specific for a given model and only appearing when there is only one model showing (see MODELKIT SET KEY ON)
- thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
- thisBiomolecule - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- thisCommand - Variable in class org.jmol.script.ScriptEval
- thisContext - Variable in class org.jmol.script.ScriptParam
- thisContour - Variable in class org.jmol.jvxl.data.JvxlData
- thisDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
- thisID - Variable in class org.jmol.modelset.Measurement
- thisID - Variable in class org.jmol.modelset.MeasurementData
- thisID - Variable in class org.jmol.shape.Mesh
- thisID - Variable in class org.jmol.shape.TextShape
- thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- thisJsvp - Variable in class jspecview.popup.JSVGenericPopup
- thisMesh - Variable in class org.jmol.shapesurface.Isosurface
- thismodel - Static variable in class org.jmol.script.T
- thisModelOnly - Variable in class org.jmol.modelset.Text
- thisModelOnly - Variable in class org.jmol.shapespecial.DrawMesh
- thisPopup - Variable in class org.jmol.popup.GenericPopup
- thisSet - Variable in class org.jmol.jvxl.data.JvxlData
- thisValue() - Method in class jspecview.source.XMLParser
-
for value without surrounding tag
- thisWidget - Variable in class jspecview.common.PanelData
- thisWidth - Variable in class jspecview.common.PanelData
- thisx - Variable in class org.jmol.popup.GenericPopup
- thisy - Variable in class org.jmol.popup.GenericPopup
- throwcmd - Static variable in class org.jmol.script.T
- tickA - Variable in class org.jmol.render.FontLineShapeRenderer
- tickAs - Variable in class org.jmol.render.FontLineShapeRenderer
- tickB - Variable in class org.jmol.render.FontLineShapeRenderer
- tickBs - Variable in class org.jmol.render.FontLineShapeRenderer
- tickEdges - Variable in class org.jmol.render.AxesRenderer
- tickEdges - Variable in class org.jmol.render.BbcageRenderer
- tickEdges - Variable in class org.jmol.render.UccageRenderer
- tickInfo - Variable in class org.jmol.modelset.Measurement
- tickInfo - Variable in class org.jmol.modelset.MeasurementData
- tickInfo - Variable in class org.jmol.render.FontLineShapeRenderer
- TickInfo - Class in org.jmol.modelset
- TickInfo(P3) - Constructor for class org.jmol.modelset.TickInfo
- tickInfos - Variable in class org.jmol.shape.FontLineShape
- tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
- tickParamAsStr(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
- ticks - Variable in class org.jmol.modelset.TickInfo
- ticks - Static variable in class org.jmol.script.T
- time - Variable in class jspecview.export.AMLExporter
- time - Variable in class jspecview.export.CMLExporter
- time - Variable in class jspecview.source.JDXHeader
- time - Variable in class org.jmol.viewer.MouseState
- timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- timeout - Static variable in class org.jmol.script.T
- timeouts - Variable in class org.jmol.viewer.Viewer
- TimeoutThread - Class in org.jmol.thread
- TimeoutThread(Viewer, String, int, String) - Constructor for class org.jmol.thread.TimeoutThread
- times - Static variable in class org.jmol.script.T
- timestimes - Static variable in class org.jmol.script.T
- timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- TinkerReader - Class in org.jmol.adapter.readers.simple
-
simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
- TinkerReader() - Constructor for class org.jmol.adapter.readers.simple.TinkerReader
- title - Variable in class jspecview.common.PanelData
- title - Variable in class jspecview.common.PrintLayout
- title - Variable in class jspecview.dialog.JSVDialog
- title - Variable in class jspecview.export.AMLExporter
- title - Variable in class jspecview.export.CMLExporter
- title - Variable in class jspecview.source.JDXHeader
- title - Variable in class jspecview.source.AnIMLReader
- title - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- title - Variable in class org.jmol.console.ScriptEditor
- title - Variable in class org.jmol.jvxl.data.JvxlData
- title - Variable in class org.jmol.jvxl.readers.Parameters
- title - Static variable in class org.jmol.script.T
- title - Variable in class org.jmol.shape.Mesh
- title - Variable in class org.jmol.shape.MeshCollection
- TITLEBOLDON - Enum constant in enum class jspecview.common.ScriptToken
- titleColor - Variable in class jspecview.common.PanelData
- titleColor - Variable in class org.jmol.shapespecial.DrawMesh
- TITLECOLOR - Enum constant in enum class jspecview.common.ScriptToken
- titleDrawn - Variable in class jspecview.common.PanelData
- titleFontName - Variable in class jspecview.common.ColorParameters
- TITLEFONTNAME - Enum constant in enum class jspecview.common.ScriptToken
- titleformat - Static variable in class org.jmol.script.T
- titleOn - Variable in class jspecview.common.PanelData
- TITLEON - Enum constant in enum class jspecview.common.ScriptToken
- TlsDataOnlyReader - Class in org.jmol.adapter.readers.more
- TlsDataOnlyReader() - Constructor for class org.jmol.adapter.readers.more.TlsDataOnlyReader
- tm - Variable in class org.jmol.export.___Exporter
- tm - Variable in class org.jmol.render.ShapeRenderer
- tm - Variable in class org.jmol.viewer.Viewer
- tmpEnd - Variable in class jspecview.source.AnIMLReader
- to - Static variable in class org.jmol.script.T
- TO_ABS - Enum constant in enum class jspecview.common.Spectrum.IRMode
- TO_TRANS - Enum constant in enum class jspecview.common.Spectrum.IRMode
- to3D(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- toArray() - Method in class org.jmol.script.SV
- TOAU_ANGSTROMS - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_AU - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_BOHR - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_CM - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_CM_1 - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_EV - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_HARTREE - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_KCAL_MOL - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_KJ_MOL - Static variable in class org.qcschema.QCSchemaUnits
- TOAU_M - Static variable in class org.qcschema.QCSchemaUnits
- toAxisAngle4f() - Method in class javajs.util.Quat
- toByteArray() - Method in class javajs.util.OC
- toBytes(int, int) - Method in class javajs.util.SB
-
simple byte conversion properly implementing UTF-8.
- toCartesian(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
- toCartesian(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
- toCartesian(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
- toCartesian(T3, boolean) - Method in class org.jmol.viewer.Viewer
-
absolute or relative to origin of UNITCELL {x y z}
- toCartesianUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
- toCDXML() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- toCSSString(GenericColor) - Static method in class javajs.util.CU
- toExternalForm(URL) - Method in class javajs.util.AjaxURLStreamHandler
- toFFGGGfromRGB(int) - Static method in class javajs.util.CU
-
Return a greyscale rgb value 0-FF using NTSC color lightness algorithm
- toFractional(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
- toFractional(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
- toFractional(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
- toFractional(T3, boolean) - Method in class org.jmol.viewer.Viewer
- toFractionalM(M4) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- toFractionalM(M4) - Method in class org.jmol.util.SimpleUnitCell
- toFractionalUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
- toFromPrimitive(boolean, char, T3[], M3) - Method in interface org.jmol.api.SymmetryInterface
- toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.Symmetry
- toFront() - Method in class org.jmol.awtjs.swing.JDialog
- toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- TOGGLE - Enum constant in enum class jspecview.common.IntegralData.IntMode
- TOGGLE - Enum constant in enum class jspecview.common.Spectrum.IRMode
- toggleCoordinate() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that toggles the coordinate on a
JSVPanel
- toggleCoordinate() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that toggles the coordinate on a
JSVPanel
- toggleCoordinate() - Method in class jspecview.appletjs.JSVApplet
- toggleCoordinate() - Method in class jspecview.application.MainFrame
- toggleGrid() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that toggles the grid on a
JSVPanel
- toggleGrid() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that toggles the grid on a
JSVPanel
- toggleGrid() - Method in class jspecview.appletjs.JSVApplet
- toggleGrid() - Method in class jspecview.application.MainFrame
- toggleInPlace(BS, BS) - Static method in class org.jmol.util.BSUtil
-
a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
- toggleIntegration() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that toggles the integration graph of a
JSVPanel
. - toggleIntegration() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that toggles the integration graph of a
JSVPanel
. - toggleIntegration() - Method in class jspecview.appletjs.JSVApplet
- toggleIntegration() - Method in class jspecview.application.MainFrame
- togglelabel - Static variable in class org.jmol.script.T
- toggleMode() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
- toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- toggleOverlayKeyMenuItem() - Method in class jspecview.application.ApplicationMenu
- togglePointsOnly() - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that toggles the flag for points only on a
JSVPanel
- togglePointsOnly() - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that toggles the coordinate on a
JSVPanel
- togglePointsOnly() - Method in class jspecview.appletjs.JSVApplet
- togglePointsOnly() - Method in class jspecview.application.MainFrame
- toHTML() - Method in class org.jmol.awtjs.swing.Component
- toHTML() - Method in class org.jmol.awtjs.swing.JButton
- toHTML() - Method in class org.jmol.awtjs.swing.JCheckBox
- toHTML() - Method in class org.jmol.awtjs.swing.JComboBox
- toHTML() - Method in class org.jmol.awtjs.swing.JContentPane
- toHTML() - Method in class org.jmol.awtjs.swing.JDialog
- toHTML() - Method in class org.jmol.awtjs.swing.JEditorPane
- toHTML() - Method in class org.jmol.awtjs.swing.JLabel
- toHTML() - Method in class org.jmol.awtjs.swing.JMenu
- toHTML() - Method in class org.jmol.awtjs.swing.JMenuItem
- toHTML() - Method in class org.jmol.awtjs.swing.JPanel
- toHTML() - Method in class org.jmol.awtjs.swing.JPopupMenu
- toHTML() - Method in class org.jmol.awtjs.swing.JScrollPane
- toHTML() - Method in class org.jmol.awtjs.swing.JSplitPane
- toHTML() - Method in class org.jmol.awtjs.swing.JTable
- toHTML() - Method in class org.jmol.awtjs.swing.JTextField
- toHTML() - Method in class org.jmol.awtjs.swing.JTextPane
- toHTML(String) - Method in class org.jmol.awtjs.swing.Cell
- toHTML(String) - Method in class org.jmol.awtjs.swing.Grid
- toHTML(SB, String, BS) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
- toJSON() - Method in interface javajs.api.JSONEncodable
- toJSON() - Method in class javajs.util.A4
- toJSON() - Method in class javajs.util.BS
- toJSON() - Method in class javajs.util.T3
- toJSON() - Method in class javajs.util.T4
- toJSON() - Method in class org.jmol.script.SV
- toJSON(String, Object) - Static method in class javajs.util.PT
- toJSONBytes(Map<String, Object>) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
-
Guaranteed to create a clean no-whitespace JSON stream terminated by a single \n.
- tok - Variable in class org.jmol.script.T
- tokAction - Variable in class org.jmol.modelset.MeasurementData
- tokAt(int) - Method in class org.jmol.script.ScriptCompiler
- tokAt(int) - Method in class org.jmol.script.ScriptParam
- tokAt(int) - Method in class org.jmol.scriptext.ScriptExt
- tokAttr(int, int) - Static method in class org.jmol.script.T
- tokAttrOr(int, int, int) - Static method in class org.jmol.script.T
- tokCommand - Variable in class org.jmol.script.ScriptCompiler
- tokenAll - Static variable in class org.jmol.script.T
- tokenAnd - Static variable in class org.jmol.script.T
- tokenAndEquals - Variable in class org.jmol.script.ScriptCompiler
- tokenAndFALSE - Static variable in class org.jmol.script.T
- tokenAndSpec - Static variable in class org.jmol.script.T
- tokenArrayClose - Static variable in class org.jmol.script.T
- tokenArrayOpen - Static variable in class org.jmol.script.T
- tokenArraySquare - Static variable in class org.jmol.script.T
- tokenAttr(T, int) - Static method in class org.jmol.script.ScriptCompiler
- tokenColon - Static variable in class org.jmol.script.T
- tokenComma - Static variable in class org.jmol.script.T
- tokenCommand - Variable in class org.jmol.script.ScriptCompiler
- tokenConnected - Static variable in class org.jmol.script.T
- tokenCoordinateBegin - Static variable in class org.jmol.script.T
- tokenCoordinateEnd - Static variable in class org.jmol.script.T
- tokenDefineString - Static variable in class org.jmol.script.T
- tokenDivide - Static variable in class org.jmol.script.T
- tokenEquals - Static variable in class org.jmol.script.T
- tokenExpressionBegin - Static variable in class org.jmol.script.T
- tokenExpressionEnd - Static variable in class org.jmol.script.T
- tokenIf - Static variable in class org.jmol.script.T
- tokenize(String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
-
Take the given string and chop it up into a series of strings on whitespace boundries.
- tokenLeftBrace - Static variable in class org.jmol.script.T
- tokenLeftParen - Static variable in class org.jmol.script.T
- tokenMinus - Static variable in class org.jmol.script.T
- tokenMul3 - Static variable in class org.jmol.script.T
- tokenOff - Static variable in class org.jmol.script.T
- tokenOn - Static variable in class org.jmol.script.T
- tokenOpIf - Static variable in class org.jmol.script.T
- tokenOr - Static variable in class org.jmol.script.T
- tokenOrTRUE - Static variable in class org.jmol.script.T
- tokenPlus - Static variable in class org.jmol.script.T
- tokenRightBrace - Static variable in class org.jmol.script.T
- tokenRightParen - Static variable in class org.jmol.script.T
- tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- tokenScript - Static variable in class org.jmol.script.T
- tokenSet - Static variable in class org.jmol.script.T
- tokenSetArray - Static variable in class org.jmol.script.T
- tokenSetCmd - Static variable in class org.jmol.script.T
- tokenSetProperty - Static variable in class org.jmol.script.T
- tokenSetVar - Static variable in class org.jmol.script.T
- tokenSpaceBeforeSquare - Static variable in class org.jmol.script.T
- tokenSwitch - Static variable in class org.jmol.script.T
- tokenTimes - Static variable in class org.jmol.script.T
- toLABnorm(int) - Method in class javajs.img.GifEncoder
- toMap(byte[]) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- toMOL() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- toOABC(P3[], T3) - Static method in class org.jmol.util.BoxInfo
-
Delivers [center a b c] for generation of unit cells from a boundbox
- toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- top - Static variable in class org.jmol.script.T
- topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- toPeak(int) - Method in class jspecview.common.PanelData
- topMargin - Static variable in class jspecview.common.PanelData
- toPNG(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- TopoCifParser - Class in org.jmol.adapter.readers.cif
-
see https://github.com/COMCIFS/TopoCif Basic idea: We have TLinks, TNodes, and TAtoms TLinks each have two TNodes and may also be associated with bridging TAtom sets.
- TopoCifParser() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser
- toPoint4f() - Method in class javajs.util.Quat
-
Quaternions are saved as {q1, q2, q3, q0} While this may seem odd, it is so that for any point4 -- planes, axisangles, and quaternions -- we can use the first three coordinates to determine the relavent axis the fourth then gives us offset to {0,0,0} (plane), rotation angle (axisangle), and cos(theta/2) (quaternion).
- toRadians - Static variable in class org.jmol.util.SimpleUnitCell
- toReadable(String, Object) - Static method in class org.jmol.util.Escape
-
Used only for getProperty("readable",...)
- toRGB(P3) - Method in class javajs.img.GifEncoder
- toRGB3f(int, float[]) - Static method in class javajs.util.CU
- toRGBHexString(GenericColor) - Static method in class javajs.util.CU
- torsion - Static variable in class org.jmol.script.T
- toStdAmino3(String) - Method in class org.jmol.modelsetbio.BioResolver
- toString() - Method in class com.sparshui.common.Location
- toString() - Method in class com.sparshui.common.messages.events.DragEvent
- toString() - Method in class com.sparshui.common.messages.events.FlickEvent
- toString() - Method in class com.sparshui.common.messages.events.RotateEvent
- toString() - Method in class com.sparshui.common.messages.events.SpinEvent
- toString() - Method in class com.sparshui.common.messages.events.TouchEvent
- toString() - Method in class com.sparshui.common.messages.events.ZoomEvent
- toString() - Method in class javajs.util.A4
-
Returns a string that contains the values of this AxisAngle4f.
- toString() - Method in class javajs.util.BArray
- toString() - Method in class javajs.util.BS
-
Returns a string representation of this bit set.
- toString() - Method in class javajs.util.M3
-
Returns a string that contains the values of this Matrix3f.
- toString() - Method in class javajs.util.M4
-
Returns a string that contains the values of this Matrix4f.
- toString() - Method in class javajs.util.Matrix
- toString() - Method in class javajs.util.OC
- toString() - Method in class javajs.util.Quat
-
Java axisAngle / plane / Point4f format all have the format {x y z w} so we go with that here as well
- toString() - Method in class javajs.util.SB
- toString() - Method in class javajs.util.T3
-
Returns a string that contains the values of this Tuple3f.
- toString() - Method in class javajs.util.T3d
-
Returns a string that contains the values of this Tuple3d.
- toString() - Method in class javajs.util.T3i
-
Returns a string that contains the values of this Tuple3i.
- toString() - Method in class javajs.util.T4
-
Returns a string that contains the values of this Tuple4f.
- toString() - Method in class jspecview.common.Annotation
-
Overrides Objects toString() method
- toString() - Method in class jspecview.common.Coordinate
-
Overides Objects toString() method
- toString() - Method in class jspecview.common.Measurement
-
Overrides Objects toString() method
- toString() - Method in class jspecview.common.PanelNode
- toString() - Method in class jspecview.common.PeakInfo
- toString() - Method in class jspecview.common.PeakPickEvent
- toString() - Method in class jspecview.common.Spectrum
- toString() - Method in class jspecview.common.SubSpecChangeEvent
- toString() - Method in class jspecview.java.AwtPanel
- toString() - Method in class jspecview.js2d.JsPanel
- toString() - Method in class jspecview.tree.SimpleTreeNode
- toString() - Method in class org.jmol.adapter.smarter.Bond
- toString() - Method in class org.jmol.adapter.writers.CIFWriter
- toString() - Method in class org.jmol.adapter.writers.CMLWriter
- toString() - Method in class org.jmol.adapter.writers.PDBWriter
- toString() - Method in class org.jmol.adapter.writers.PWMATWriter
- toString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- toString() - Method in class org.jmol.adapter.writers.QCJSONWriter
- toString() - Method in class org.jmol.adapter.writers.XSFWriter
- toString() - Method in class org.jmol.atomdata.RadiusData
- toString() - Method in class org.jmol.awtjs.swing.Color
- toString() - Method in class org.jmol.minimize.MinAtom
- toString() - Method in class org.jmol.minimize.Minimizer
- toString() - Method in class org.jmol.minimize.MinObject
- toString() - Method in class org.jmol.modelset.Atom
- toString() - Method in class org.jmol.modelset.Bond
- toString() - Method in class org.jmol.modelset.Group
- toString() - Method in class org.jmol.modelset.Measurement
- toString() - Method in class org.jmol.modelset.StateScript
- toString() - Method in class org.jmol.modelset.Text
- toString() - Method in class org.jmol.modelsetbio.BasePair
- toString() - Method in class org.jmol.modelsetbio.BioPolymer
- toString() - Method in class org.jmol.modelsetbio.Monomer
- toString() - Method in class org.jmol.modelsetbio.ProteinStructure
- toString() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- toString() - Method in class org.jmol.quantum.NMRNoeMatrix
- toString() - Method in class org.jmol.quantum.SlaterData
- toString() - Method in class org.jmol.script.ScriptEval
- toString() - Method in exception class org.jmol.script.ScriptException
- toString() - Method in class org.jmol.script.ScriptFunction
- toString() - Method in class org.jmol.script.SV
- toString() - Method in class org.jmol.script.T
- toString() - Method in class org.jmol.smiles.SmilesAtom
- toString() - Method in class org.jmol.smiles.SmilesBond
- toString() - Method in class org.jmol.smiles.SmilesMeasure
- toString() - Method in class org.jmol.smiles.SmilesSearch
- toString() - Method in class org.jmol.symmetry.SpaceGroup
- toString() - Method in class org.jmol.symmetry.SymmetryOperation
- toString() - Method in class org.jmol.thread.JmolThread
- toString() - Method in class org.jmol.thread.TimeoutThread
- toString() - Method in class org.jmol.util.BoxInfo
- toString() - Method in class org.jmol.util.ContactPair
- toString() - Method in class org.jmol.util.Font
- toString() - Method in class org.jmol.util.Modulation
- toString() - Method in class org.jmol.util.Rgb16
- toString() - Method in class org.jmol.util.SimpleUnitCell
- toString() - Method in class org.jmol.util.Tensor
- toString() - Method in class org.openscience.jmol.app.janocchio.Measure
- toString2() - Method in class org.jmol.script.T
- toStringNormRow() - Method in class org.jmol.quantum.NMRNoeMatrix
- toSupercell(P3) - Method in interface org.jmol.api.SymmetryInterface
- toSupercell(P3) - Method in class org.jmol.symmetry.Symmetry
- toSupercell(P3) - Method in class org.jmol.util.SimpleUnitCell
-
convenience return only after changing fpt
- toTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
- total_in - Variable in class com.jcraft.jzlib.ZStream
- total_out - Variable in class com.jcraft.jzlib.ZStream
- toTrm(String, M4) - Static method in class org.jmol.symmetry.UnitCell
- TOUCH_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- TOUCH_EVENT - Static variable in class com.sparshui.GestureType
- TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- TOUCH_GESTURE - Static variable in class com.sparshui.GestureType
- TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- TouchData() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- TouchDataComparator() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator.TouchDataComparator
- TouchEvent - Class in com.sparshui.common.messages.events
- TouchEvent() - Constructor for class com.sparshui.common.messages.events.TouchEvent
- TouchEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.TouchEvent
-
Constructs a new TouchEvent from a serialized version - 4 bytes : id - 4 bytes : x - 4 bytes : y - 4 bytes : state - 8 bytes : time - 24 bytes total
- TouchEvent(int, float, float, int) - Constructor for class com.sparshui.common.messages.events.TouchEvent
- TouchEvent(TouchPoint) - Constructor for class com.sparshui.common.messages.events.TouchEvent
- TouchHandler() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- TouchPoint - Class in com.sparshui.server
-
Represents a touch point.
- TouchPoint(int, Location, long) - Constructor for class com.sparshui.server.TouchPoint
- TouchPoint(TouchPoint) - Constructor for class com.sparshui.server.TouchPoint
-
Copy constructor
- TouchState - Class in com.sparshui.common
-
Defines the types of touches that can ocurr in sparsh-UI: Birth, Move, and Death.
- TouchState() - Constructor for class com.sparshui.common.TouchState
- toUnicode(String) - Method in interface javajs.api.GenericCifDataParser
- toUnicode(String) - Method in class javajs.util.CifDataParser
-
Only translating the basic Greek set here, not all the other stuff.
- toUnicode(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
There is no need to convert to unicode in CIF 2.0.
- toUnitCell(P3, P3) - Method in class org.jmol.viewer.Viewer
-
Returns the relative to origin without regard to offset created using the UNITCELL command.
- toUnitCell(T3, T3) - Method in interface org.jmol.api.SymmetryInterface
- toUnitCell(T3, T3) - Method in class org.jmol.symmetry.Symmetry
- toUnitCellRnd(T3, T3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- toUnitCellRnd(T3, T3) - Method in class org.jmol.symmetry.UnitCell
-
when offset is null, use the current cell, otherwise use the original unit cell
- toUnits(float, String, boolean) - Static method in class org.jmol.modelset.Measurement
- toUserUnits(double) - Method in class org.jmol.minimize.forcefield.ForceField
- toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
- toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- tQuiet - Variable in class org.jmol.script.ScriptEval
- trace - Static variable in class org.jmol.script.T
- trace() - Method in class javajs.util.Matrix
-
Matrix trace.
- Trace - Class in org.jmol.shapebio
- Trace() - Constructor for class org.jmol.shapebio.Trace
- tracealpha - Static variable in class org.jmol.script.T
- tracePt - Variable in class org.jmol.util.Vibration
- TraceRenderer - Class in org.jmol.renderbio
- TraceRenderer() - Constructor for class org.jmol.renderbio.TraceRenderer
- traceX - Variable in class org.jmol.modelset.Measurement
- traceY - Variable in class org.jmol.modelset.Measurement
- trajectory - Variable in class org.jmol.modelset.AtomCollection
- trajectory - Static variable in class org.jmol.script.T
- Trajectory - Class in org.jmol.modelset
- Trajectory() - Constructor for class org.jmol.modelset.Trajectory
- trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
- trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- transform - Static variable in class org.jmol.script.T
- transform(T4) - Method in class javajs.util.M4
-
Transform the vector vec using this Matrix4f and place the result back into vec.
- transform(V3, V3) - Method in class org.jmol.jvxl.data.VolumeData
- transform2(T3, T3) - Method in class javajs.util.Quat
- transform2(T4, T4) - Method in class javajs.util.M4
-
Transform the vector vec using this Matrix4f and place the result into vecOut.
- transformAtomsToUnitCell(SymmetryInterface, T3[], String) - Method in class org.jmol.modelkit.ModelKit
-
Transform the atoms to fractional coordinate, set the unit cell to a new cell, and then transform them back to Cartesians.
- transformedVectors - Variable in class org.jmol.render.MeshRenderer
- transformedVectors - Variable in class org.jmol.util.GData
- TransformManager - Class in org.jmol.viewer
- TransformManager() - Constructor for class org.jmol.viewer.TransformManager
- TransformManager4D - Class in org.jmol.viewer
- TransformManager4D() - Constructor for class org.jmol.viewer.TransformManager4D
- transformPoints(Lst<P3>, M4, P3) - Static method in class javajs.util.Measure
- transformPt(T3) - Method in class org.jmol.viewer.TransformManager
-
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
- transformPt2D(T3) - Method in class org.jmol.viewer.TransformManager
- transformPt2Df(T3, P3) - Method in class org.jmol.viewer.TransformManager
- transformPt3f(T3, P3) - Method in class org.jmol.viewer.TransformManager
- transformPtNoClip(T3, T3) - Method in class org.jmol.viewer.TransformManager
- transformPtScr(T3, P3i) - Method in class org.jmol.viewer.TransformManager
- transformPtScrT3(T3, T3) - Method in class org.jmol.viewer.TransformManager
- transformPtScrT32D(T3, P3) - Method in class org.jmol.viewer.TransformManager
- transformPtVib(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
- transformUnitCell(M4) - Method in class org.jmol.symmetry.Symmetry
- transformXYZ(M4, BS) - Method in class org.jmol.atomdata.AtomData
-
allow for transformed XYZ
- translate - Static variable in class org.jmol.script.T
- translate(char, float, char, BS) - Method in class org.jmol.viewer.Viewer
- translate(String) - Method in interface org.jmol.api.Translator
- translate(String) - Method in class org.jmol.i18n.GT
-
used in custom menu translation only
- translate(String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- translateModel(int, T3) - Method in class org.jmol.modelset.ModelSet
-
move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE
- translateScale(float, float, float) - Method in class javajs.export.PDFCreator
- translateScale(Object, double, double, double) - Method in class jspecview.common.PDFWriter
- translateScale(Object, double, double, double) - Method in class jspecview.java.AwtG2D
- translateScale(Object, double, double, double) - Method in class jspecview.js2d.JsG2D
- translateScale(Object, double, double, double) - Method in interface org.jmol.api.GenericGraphics
- translateScale(Object, double, double, double) - Method in class org.jmol.awt.AwtG2D
- translateScale(Object, double, double, double) - Method in class org.jmol.awtjs2d.JsG2D
- translateSelected - Static variable in class org.jmol.script.T
- translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
- translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
- translation - Static variable in class org.jmol.script.T
- translations - Variable in class org.jmol.modelset.ModelSet
- Translator - Interface in org.jmol.api
- translucency - Variable in class org.jmol.jvxl.data.JvxlData
- translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
- translucencyMask - Variable in class org.jmol.g3d.Graphics3D
- translucent - Static variable in class org.jmol.script.T
- TRANSLUCENT_MASK - Static variable in class org.jmol.util.C
- TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.C
- TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.C
- translucentAllowed - Variable in class org.jmol.shape.Shape
- translucentCoverOnly - Variable in class org.jmol.util.GData
- translucentLevel - Variable in class org.jmol.shape.Shape
- TRANSPARENT - Static variable in class org.jmol.util.C
- transpose() - Method in class javajs.util.M3
-
Sets the value of this matrix to its transpose.
- transpose() - Method in class javajs.util.M4
-
Sets the value of this matrix to its transpose.
- transpose() - Method in class javajs.util.Matrix
-
Matrix transpose.
- transpose33() - Method in class javajs.util.M34
- transposeM(M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to the transpose of the argument matrix
- treeNode - Variable in class jspecview.common.PanelNode
- TriangleData - Class in org.jmol.util
-
An adaptation of Marching Cubes that allows for indicating edges on triangles.
- TriangleData() - Constructor for class org.jmol.util.TriangleData
- triangleHeight(double, double, double) - Static method in class jme.JMEUtil
-
Compute the height of a triangle knowing the length of each side.
- TriangleRenderer - Class in org.jmol.g3d
-
renders triangles
- TriangleRenderer() - Constructor for class org.jmol.g3d.TriangleRenderer
- triangles - Static variable in class org.jmol.script.T
- triangles - Variable in class org.jmol.shapespecial.Polyhedron
- triangleTable2 - Static variable in class org.jmol.util.TriangleData
-
The new triangle table developed specifically for Jmol.
- triangulateFaces(int[][], P3[], int[][]) - Method in class org.jmol.util.MeshCapper
-
generic entry for a set of faces
- triangulatePolygon(P3[], int) - Method in class org.jmol.util.MeshCapper
-
generic entry for a polygon
- Triangulator - Class in org.jmol.util
- Triangulator() - Constructor for class org.jmol.util.Triangulator
- TRICOLOR_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
- trigger(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
- triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
- TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
- TRIGONAL_PYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
- trim - Static variable in class org.jmol.script.T
- trim(String, String) - Static method in class javajs.util.PT
- trimGUI(String) - Method in class org.jmol.console.GenericConsole
- trimQuotes(String) - Static method in class javajs.util.PT
- trycmd - Static variable in class org.jmol.script.T
- tryPt - Variable in class org.jmol.viewer.Viewer
- TURN - Enum constant in enum class org.jmol.c.STR
- tv(int, int, Object) - Static method in class org.jmol.script.T
- twelfthify(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- twelfthify(P3) - Method in class org.jmol.util.SimpleUnitCell
- twelfthsOf(float) - Method in class org.jmol.util.SimpleUnitCell
- twistedsheets - Static variable in class org.jmol.script.T
- twistedSheets - Variable in class org.jmol.modelsetbio.BioPolymer
- twoDEditorAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- TwoDEditorAction(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
- twoDEditorActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- twodots - Static variable in class org.jmol.render.FontLineShapeRenderer
- twoPI - Static variable in class org.jmol.util.Vibration
- TwoPointGesture - Class in org.jmol.multitouch.sparshui
-
TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
- TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
- Txt - Class in org.jmol.util
- Txt() - Constructor for class org.jmol.util.Txt
- txt1 - Variable in class jspecview.dialog.JSVDialog
- txt2 - Variable in class jspecview.dialog.JSVDialog
- txt3 - Variable in class jspecview.dialog.JSVDialog
- type - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- type - Variable in class jspecview.dialog.JSVDialog
- type - Variable in class jspecview.source.JDXSource
- type - Variable in class org.jmol.minimize.MinObject
- type - Variable in class org.jmol.minimize.MMConstraint
- type - Variable in class org.jmol.modelset.TickInfo
- type - Variable in class org.jmol.modelsetbio.BioPolymer
- type - Static variable in class org.jmol.script.T
- type - Variable in class org.jmol.util.Tensor
- TYPE - Enum constant in enum class org.jmol.c.PAL
- TYPE_ADP - Static variable in class org.jmol.util.Tensor
- TYPE_AMINO - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_ANGLE - Static variable in class org.jmol.minimize.MMConstraint
- TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_ATROPISOMER - Static variable in class org.jmol.util.Edge
- TYPE_ATROPISOMER_REV - Static variable in class org.jmol.util.Edge
- TYPE_BIO_CROSSLINK - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_BLOCK - Static variable in class jspecview.source.JDXSource
- TYPE_BUTTON - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_CHARGE - Static variable in class org.jmol.util.Tensor
- TYPE_CHECKBOX - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_CSA - Static variable in class org.jmol.util.Tensor
- TYPE_DIHEDRAL - Static variable in class org.jmol.minimize.MMConstraint
- TYPE_DISP_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_DISP_LEGENDRE - Static variable in class org.jmol.util.Modulation
- TYPE_DISP_SAWTOOTH - Static variable in class org.jmol.util.Modulation
- TYPE_DISTANCE - Static variable in class org.jmol.minimize.MMConstraint
- TYPE_EFG - Static variable in class org.jmol.util.Tensor
- TYPE_ISC - Static variable in class org.jmol.util.Tensor
- TYPE_ISO - Static variable in class org.jmol.util.Tensor
- TYPE_MENU - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_MS - Static variable in class org.jmol.util.Tensor
- TYPE_NOBONDING - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_NTUPLE - Static variable in class jspecview.source.JDXSource
- TYPE_NUCLEIC - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_OCC_CRENEL - Static variable in class org.jmol.util.Modulation
- TYPE_OCC_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_OTHER - Static variable in class org.jmol.util.Tensor
- TYPE_QUADRUPOLE - Static variable in class org.jmol.util.Tensor
- TYPE_RADIO - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_RAMAN - Static variable in class org.jmol.util.Tensor
- TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_SEPARATOR - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_SIMPLE - Static variable in class jspecview.source.JDXSource
- TYPE_SPIN - Static variable in class org.jmol.util.Vibration
- TYPE_SPIN_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_SPIN_SAWTOOTH - Static variable in class org.jmol.util.Modulation
- TYPE_TLS_R - Static variable in class org.jmol.util.Tensor
- TYPE_TLS_U - Static variable in class org.jmol.util.Tensor
- TYPE_U_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_U_LEGENDRE - Static variable in class org.jmol.util.Modulation
- TYPE_UNKNOWN - Static variable in class jspecview.source.JDXSource
- TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_VIBRATION - Static variable in class org.jmol.util.Vibration
- TYPE_VIEW - Static variable in class jspecview.source.JDXSource
- TYPE_WYCKOFF - Static variable in class org.jmol.util.Vibration
- typeName - Variable in class org.jmol.script.ScriptFunction
- TYPES - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- typeSymbol - Variable in class org.jmol.adapter.smarter.Atom
U
- U_LIST - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- uABsM(String) - Static method in class org.jmol.util.Escape
- UC_TOLERANCE2 - Static variable in class org.jmol.viewer.JC
- Uccage - Class in org.jmol.shape
- Uccage() - Constructor for class org.jmol.shape.Uccage
- UccageRenderer - Class in org.jmol.render
- UccageRenderer() - Constructor for class org.jmol.render.UccageRenderer
- uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
- ucItems - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
- unaryMinus - Static variable in class org.jmol.script.T
- unbind - Static variable in class org.jmol.script.T
- unbindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
- unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
- unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
- unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
- unbindName(int, String) - Method in class org.jmol.viewer.binding.Binding
- unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
- undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
-
called from org.jmol.modelsetbio.resolver when adding hydrogens.
- undo - Static variable in class org.jmol.script.T
- undoauto - Static variable in class org.jmol.script.T
- undomax - Static variable in class org.jmol.script.T
- undomove - Static variable in class org.jmol.script.T
- undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
- undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.Viewer
- unescape(String) - Static method in class javajs.util.BS
- unescapeMatrix(String) - Static method in class org.jmol.util.Escape
- unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.SV
- unescapeString(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
- unescapeStringArray(String) - Static method in class org.jmol.util.Escape
- unescapeUnicode(String) - Static method in class org.jmol.util.Escape
- uniqueID - Variable in class org.jmol.adapter.smarter.Bond
- unitAxisVectors - Static variable in class org.jmol.viewer.JC
- unitcell - Static variable in class org.jmol.script.T
- unitCell - Variable in class org.jmol.shape.Mesh
- unitCell - Variable in class org.jmol.symmetry.Symmetry
- UnitCell - Class in org.jmol.symmetry
-
a class pseudoprivate to the org.jmol.symmetry and org.jmol.applet.smarter.FileSymmetry to be accessed generally only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
- unitcellcolor - Static variable in class org.jmol.script.T
- unitCellEquals(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
- unitCellEquals(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
- UnitCellIterator - Class in org.jmol.symmetry
- UnitCellIterator() - Constructor for class org.jmol.symmetry.UnitCellIterator
- unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- unitCellParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- unitCellParams - Variable in class org.jmol.util.SimpleUnitCell
- unitCells - Variable in class org.jmol.modelset.ModelSet
- unitCubePoints - Static variable in class org.jmol.util.BoxInfo
- unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
- UNITID_ATOM - Static variable in class org.jmol.viewer.JC
- UNITID_INSCODE - Static variable in class org.jmol.viewer.JC
- UNITID_MODEL - Static variable in class org.jmol.viewer.JC
- UNITID_RESIDUE - Static variable in class org.jmol.viewer.JC
- UNITID_TRIM - Static variable in class org.jmol.viewer.JC
- unitize(T3) - Method in interface org.jmol.api.SymmetryInterface
- unitize(T3) - Method in class org.jmol.symmetry.Symmetry
- unitizeDim(int, T3) - Method in class org.jmol.util.SimpleUnitCell
-
Used for just about everything; via UnitCell including SpaceGroup.getSiteMultiplicity, Symmetry.getInvariantSymops, Symmetry.removeDuplicates, Symmetry.unitize, Symmetry.toUnitCell, SymmetryDesc.getTransform.
- unitizeDimRnd(int, T3, float) - Static method in class org.jmol.util.SimpleUnitCell
-
Only used for getting equivalent points and checking for duplicates.
- unitizeX(float, float) - Static method in class org.jmol.util.SimpleUnitCell
- unitizeXRnd(float, float) - Static method in class org.jmol.util.SimpleUnitCell
-
Slightly higher precision -- only used for cmdAssignSpaceGroup checking for duplicates
- units - Variable in class jspecview.common.MeasurementData
- units - Variable in class org.jmol.minimize.Minimizer
- units - Variable in class org.jmol.modelset.Measurement
- units - Variable in class org.jmol.modelset.MeasurementData
- UNITS_ANGSTROMS - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_AU - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_BOHR - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_CM - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_CM_1 - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_EV - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_FRACTIONAL - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_HARTREE - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_KCAL_MOL - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_KJ_MOL - Static variable in class org.qcschema.QCSchemaUnits
- UNITS_M - Static variable in class org.qcschema.QCSchemaUnits
- unitsColor - Variable in class jspecview.common.PanelData
- UNITSCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
- unitx - Static variable in class org.jmol.script.T
- unitxyz - Static variable in class org.jmol.script.T
- unity - Static variable in class org.jmol.script.T
- unitz - Static variable in class org.jmol.script.T
- UNK - Enum constant in enum class jspecview.common.ExportType
- UNKNOWN - Enum constant in enum class jspecview.common.ScriptToken
- UNKNOWN - Enum constant in enum class org.jmol.c.HB
- UNKNOWN - Enum constant in enum class org.jmol.c.PAL
- UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.C
- unpack(byte[], int, int) - Static method in class javajs.util.MessagePackReader
-
mmtf type 14 and 15 Unpack an array of int8 or int16 to int32.
- unpack16Deltaf(byte[], int, float) - Static method in class javajs.util.MessagePackReader
-
mmtf type 10 Decode an array of int16 using run-length decoding of a difference array.
- unpackf(byte[], int, int, float) - Static method in class javajs.util.MessagePackReader
-
mmtf type 12 and 13 Unpack an array of int8 or int16 to int32 and divide to give a float32.
- unquoted(String) - Method in class javajs.util.CifDataParser
-
In CIF 2.0, this method turns a String into an Integer or Float In CIF 1.0 (here) just return the unchanged value.
- unquoted(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Handle unquoted value as Integer or Float if we can.
- unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
- unsetProperty(String) - Method in class org.jmol.viewer.Viewer
- unTaintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
- untransformedPoint - Variable in class org.jmol.viewer.TransformManager
- unTransformPoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
- unwrapCdata(String) - Static method in class org.jmol.jvxl.readers.XmlReader
- uP(String) - Static method in class org.jmol.util.Escape
- UP - Static variable in class org.jmol.viewer.binding.Binding
- update() - Method in interface javajs.api.JSInterface
- update() - Method in class jspecview.appletjs.JSVApplet
- update() - Method in class org.jmol.util.GenericApplet
- update(byte[], int, int) - Method in class com.jcraft.jzlib.Adler32
- update(byte[], int, int) - Method in interface com.jcraft.jzlib.Checksum
- update(byte[], int, int) - Method in class com.jcraft.jzlib.CRC32
- update(double, double, double) - Method in class jspecview.common.IntegralData
-
minY is ignored
- update(Location, long, int) - Method in class com.sparshui.server.TouchPoint
-
Update this touch point with a new location and state.
- update(TouchPoint) - Method in class com.sparshui.server.Group
-
Update the given touch point that belongs to this group.
- update(Graphics) - Method in class jme.JME
- update(Graphics) - Method in class jspecview.java.AwtPanel
- update(String) - Method in class org.jmol.viewer.ChimeMessenger
-
called upon script exit and file opening
- update(String) - Method in interface org.jmol.viewer.JmolChimeMessenger
- update(LineEvent) - Method in class org.jmol.util.JmolAudio
- update(Coordinate, double, int) - Method in class jspecview.dialog.JSVDialog
- update(Parameters) - Method in class jspecview.common.IntegralData
- UPDATE - Enum constant in enum class jspecview.common.IntegralData.IntMode
- UPDATE_ALL - Static variable in class org.jmol.popup.JmolPopup
- UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolPopup
- UPDATE_NEVER - Static variable in class jspecview.popup.JSVGenericPopup
- UPDATE_NEVER - Static variable in class org.jmol.popup.JmolPopup
- UPDATE_SHOW - Static variable in class org.jmol.popup.JmolPopup
- updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
- updateAllXtalMenuOptions() - Method in class org.jmol.modelkit.ModelKitPopup
- updateAtomXYZ(boolean) - Method in class org.jmol.minimize.Minimizer
- updateAwtMenus(String) - Method in class org.jmol.awt.AwtJmolPopup
- updateAwtMenus(String) - Method in class org.jmol.awt.AwtModelKitPopup
- updateBasisFromSite(int) - Method in class org.jmol.modelset.ModelSet
- updateButton(SC, String, String) - Method in class org.jmol.popup.GenericPopup
- updateByteAsInt(int) - Method in class com.jcraft.jzlib.Adler32
- updateByteAsInt(int) - Method in interface com.jcraft.jzlib.Checksum
- updateByteAsInt(int) - Method in class com.jcraft.jzlib.CRC32
- updateCheckBoxesForModelKit(String) - Method in class org.jmol.modelkit.ModelKitPopup
- updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateConsoleFont() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- updateControlPressed(int) - Method in class jspecview.common.PanelData
- updateCoordinates(M4, BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
bs will be null if this is a set from the new isosurface MOVE [mat4] command
- updateDrawAtomSets(String, BS) - Method in class org.jmol.modelkit.ModelKit
- updateElementsComputedMenu(BS) - Method in class org.jmol.popup.JmolPopup
- updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- updateFileMenu() - Method in class org.jmol.popup.JmolPopup
- updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolPopup
- updateFontSize() - Method in class org.jmol.console.JmolConsole
- updateFontSize() - Method in class org.jmol.console.ScriptEditor
- updateFontSize() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateHeteroComputedMenu(Map<String, String>) - Method in class org.jmol.popup.JmolPopup
- updateInvalidatedVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
- updateJS() - Method in class jspecview.common.JSViewer
-
for JavaScript only; this is the call to draw the spectrum
- updateJS() - Method in class org.jmol.viewer.Viewer
-
for JavaScript only
- updateJS(int, int) - Method in class jspecview.app.JSVApp
- updateLabels() - Method in class org.jmol.console.GenericConsole
- updateLabels() - Method in class org.jmol.console.JmolConsole
- updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
- updateMark(int) - Method in class jme.JME
- updateMenu() - Method in class org.jmol.modelkit.ModelKit
- updateMenus() - Method in class org.jmol.popup.JmolPopup
- updateMode - Variable in class jspecview.popup.JSVGenericPopup
- updateMode - Variable in class org.jmol.popup.JmolPopup
- updateModel(int) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateOperatorMenu() - Method in class org.jmol.modelkit.ModelKitPopup
- updatePDBResidueComputedMenus() - Method in class org.jmol.popup.JmolPopup
- updateRecentMenus(String) - Method in class jspecview.application.MainFrame
- updateRecentMenus(Lst<String>) - Method in class jspecview.application.ApplicationMenu
- updateSceneComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Update screen informations
- updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
- updateSignedAppletItems() - Method in class org.jmol.popup.GenericPopup
- updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- updateSpecialMenuItem(SC) - Method in class org.jmol.popup.JmolPopup
- updateSpectraMenu() - Method in class org.jmol.popup.JmolPopup
- updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
- updateSurfMoComputedMenu(Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
- updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolPopup
- updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateTables() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- updateTables() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- updateToolbar(ScriptToken, boolean) - Method in class jspecview.application.MainFrame
- updatingForShow - Variable in class org.jmol.popup.GenericPopup
- url - Static variable in class org.jmol.script.T
- URL_CACHE - Static variable in class javajs.util.OC
- URL_LOCAL - Static variable in class javajs.util.OC
- URL_LOCAL - Static variable in class jspecview.common.JSVFileManager
- urlPrefixes - Static variable in class javajs.util.OC
- urlTypeIndex(String) - Static method in class javajs.util.OC
- urlTypeIndex(String) - Static method in class jspecview.common.JSVFileManager
- USE_PALETTE - Static variable in class org.jmol.util.C
- useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- useAuthorChainID - Variable in class org.jmol.adapter.readers.cif.CifReader
- useColix - Variable in class org.jmol.shape.Mesh
- useDirLastExported - Variable in class jspecview.java.AwtFileHelper
- useDirLastOpened - Variable in class jspecview.java.AwtFileHelper
- useFileModelNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- useminimizationthread - Static variable in class org.jmol.script.T
- useMinimizationThread() - Method in class org.jmol.viewer.Viewer
- usenumberlocalization - Static variable in class org.jmol.script.T
- usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
- user - Static variable in class org.jmol.script.T
- USER - Enum constant in enum class org.jmol.c.VDW
- USER - Static variable in class org.jmol.util.ColorEncoder
- userAction(int, Object[]) - Method in class org.jmol.viewer.ActionManager
-
If the user has created a function to handle this action, run it and cancel action processing if that function returns an explicit FALSE;
- userActionEnabled(int) - Method in class org.jmol.viewer.ActionManager
- usercolorscheme - Static variable in class org.jmol.script.T
- userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
- userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
- useScriptQueue - Variable in class org.jmol.viewer.GlobalSettings
- useTable - Variable in class org.jmol.export._VrmlExporter
- useThreads() - Method in class org.jmol.script.ScriptEval
- useTimeout - Variable in class org.jmol.thread.JmolThread
- UTF_16BE - Enum constant in enum class javajs.util.Encoding
- UTF_16LE - Enum constant in enum class javajs.util.Encoding
- UTF_32BE - Enum constant in enum class javajs.util.Encoding
- UTF_32LE - Enum constant in enum class javajs.util.Encoding
- UTF8 - Enum constant in enum class javajs.util.Encoding
- Util - Class in org.jmol.minimize
- Util() - Constructor for class org.jmol.minimize.Util
V
- v1 - Variable in class org.jmol.modelset.BondCollection
- v2 - Variable in class org.jmol.modelset.BondCollection
- V3 - Class in javajs.util
-
A 3-element vector that is represented by single precision floating point x,y,z coordinates.
- V3() - Constructor for class javajs.util.V3
- V3000Rdr - Class in org.jmol.adapter.readers.molxyz
-
A reader for Accelrys V3000 files.
- V3000Rdr() - Constructor for class org.jmol.adapter.readers.molxyz.V3000Rdr
- V3d - Class in javajs.util
-
A 3 element vector that is represented by double precision floating point x,y,z coordinates.
- V3d() - Constructor for class javajs.util.V3d
- vAB - Variable in class org.jmol.shape.Mesh
- val - Static variable in class org.jmol.script.T
- valence - Static variable in class org.jmol.script.T
- validate() - Method in interface jspecview.api.AppletFrame
- validate() - Method in class jspecview.appletjs.JSVApplet
- validate() - Method in class org.jmol.awtjs.swing.JDialog
- validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
- validateAndRepaint(boolean) - Method in class jspecview.application.MainFrame
- validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
- validateContent(int) - Method in interface jspecview.api.AppletFrame
- validateContent(int) - Method in class jspecview.appletjs.JSVApplet
- validateModel(int, boolean) - Method in class org.jmol.bspt.Bspf
- validation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- validation - Static variable in class org.jmol.script.T
- valign - Variable in class org.jmol.modelset.Text
- value - Variable in class jspecview.common.Measurement
- value - Variable in class org.jmol.atomdata.RadiusData
- value - Variable in class org.jmol.minimize.MMConstraint
- value - Variable in class org.jmol.modelset.Measurement
- value - Variable in class org.jmol.script.T
- value() - Element in annotation interface javajs.J2SIgnoreImport
- value() - Element in annotation interface javajs.J2SRequireImport
- valueChanged() - Method in class jspecview.tree.SimpleTree
- valueChanged(ListSelectionEvent) - Method in class jspecview.java.AwtDialogManager
-
ListSelectionListener callback
- valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- valueExtended - Variable in class org.jmol.atomdata.RadiusData
- valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
- valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
- valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
- valueOf(String) - Static method in enum class javajs.util.Encoding
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class jspecview.common.Annotation.AType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class jspecview.common.ExportType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class jspecview.common.IntegralData.IntMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class jspecview.common.PanelData.LinkMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class jspecview.common.ScriptToken
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class jspecview.common.Spectrum.IRMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.atomdata.RadiusData.EnumType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.CBK
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.FIL
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.HB
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.PAL
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.STER
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.STR
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.c.VDW
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.jmol.viewer.Viewer.ACCESS
-
Returns the enum constant of this class with the specified name.
- values - Variable in class org.jmol.atomdata.RadiusData
- values() - Static method in enum class javajs.util.Encoding
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class jspecview.common.Annotation.AType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class jspecview.common.ExportType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class jspecview.common.IntegralData.IntMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class jspecview.common.PanelData.LinkMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class jspecview.common.ScriptToken
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class jspecview.common.Spectrum.IRMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.atomdata.RadiusData.EnumType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.CBK
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.FIL
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.HB
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.PAL
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.STER
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.STR
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.c.VDW
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.jmol.viewer.Viewer.ACCESS
-
Returns an array containing the constants of this enum class, in the order they are declared.
- vanderwaals - Static variable in class org.jmol.script.T
- vanderwaalsMars - Static variable in class org.jmol.util.Elements
-
Default table of van der Waals Radii.
- var - Static variable in class org.jmol.script.T
- varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
- variable - Static variable in class org.jmol.script.T
- VARIABLE - Enum constant in enum class org.jmol.c.PAL
- variables - Static variable in class org.jmol.script.T
- varray - Static variable in class org.jmol.script.T
- vars - Variable in class org.jmol.script.ScriptContext
- VaspChgcarReader - Class in org.jmol.adapter.readers.xtal
-
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
- VaspChgcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspChgcarReader
- VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
-
http://cms.mpi.univie.ac.at/vasp/
- VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
- VaspPoscarReader - Class in org.jmol.adapter.readers.xtal
-
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
- VaspPoscarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspPoscarReader
- vAtoms - Variable in class org.jmol.adapter.readers.simple.InputReader
- vBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- vBiomolecules - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- vc - Variable in class org.jmol.util.MeshSurface
-
vertex count
- vContours - Variable in class org.jmol.jvxl.data.JvxlData
- vcs - Variable in class org.jmol.util.MeshSurface
-
vertex color index "colix" array
- VDW - Enum Class in org.jmol.c
- vdwKey - Variable in class org.jmol.minimize.MinAtom
- VdwPROBE - Static variable in class org.jmol.util.Elements
- vdws - Variable in class org.jmol.util.ContactPair
- vdwType - Variable in class org.jmol.atomdata.RadiusData
- vdwVolume - Variable in class org.jmol.util.ContactPair
- vector - Static variable in class org.jmol.script.T
- vector - Variable in class org.jmol.shapespecial.Dipole
- vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
- Vectors - Class in org.jmol.shapespecial
- Vectors() - Constructor for class org.jmol.shapespecial.Vectors
- vectorscale - Static variable in class org.jmol.script.T
- vectorscentered - Static variable in class org.jmol.script.T
- VectorsRenderer - Class in org.jmol.renderspecial
- VectorsRenderer() - Constructor for class org.jmol.renderspecial.VectorsRenderer
- vectorsymmetry - Static variable in class org.jmol.script.T
- vectorT - Variable in class org.jmol.render.FontLineShapeRenderer
- vectorT2 - Variable in class org.jmol.render.FontLineShapeRenderer
- vectorT3 - Variable in class org.jmol.render.FontLineShapeRenderer
- vectorTemp - Variable in class org.jmol.viewer.TransformManager
- vectortrail - Static variable in class org.jmol.script.T
- vendor - Variable in class jspecview.export.AMLExporter
- vendor - Variable in class jspecview.export.CMLExporter
- vendor - Variable in class jspecview.source.AnIMLReader
- version - Variable in class org.jmol.jvxl.data.JvxlData
- version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- version - Static variable in class org.jmol.viewer.JC
- version - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- version - Static variable in class org.qcschema.QCSchemaUnits
- version() - Static method in class com.jcraft.jzlib.JZlib
- VERSION - Enum constant in enum class jspecview.common.ScriptToken
- VERSION - Static variable in class jspecview.common.JSVersion
- VERSION - Static variable in class org.openscience.jmol.app.janocchio.Nmr
- VERSION - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- VERSION_SHORT - Static variable in class jspecview.common.JSVersion
- versionInt - Static variable in class jspecview.common.JSVersion
- versionInt - Static variable in class org.jmol.viewer.JC
- VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
- VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
- vertexColorMap - Variable in class org.jmol.shape.Mesh
- vertexColors - Variable in class org.jmol.jvxl.data.JvxlData
- vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
- vertexCount - Variable in class org.jmol.render.MeshRenderer
- vertexCount0 - Variable in class org.jmol.util.MeshSurface
- vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
- VertexDataServer - Interface in org.jmol.jvxl.api
- vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
- vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- vertexSets - Variable in class org.jmol.util.MeshSurface
- vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
- vertexSource - Variable in class org.jmol.util.MeshSurface
- vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
- vertexValues - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- vertices - Variable in class org.jmol.render.MeshRenderer
- vertices - Static variable in class org.jmol.script.T
- vertices - Variable in class org.jmol.shapespecial.Polyhedron
- vf - Variable in class org.jmol.shape.Shape
-
shape visibility flag
- vF - Static variable in class org.jmol.script.SV
- vib - Variable in class org.jmol.adapter.smarter.Atom
- vib - Variable in class org.jmol.util.ModulationSet
-
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
- vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- vibration - Static variable in class org.jmol.script.T
- Vibration - Class in org.jmol.util
-
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
- Vibration() - Constructor for class org.jmol.util.Vibration
- vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- vibrationOn - Variable in class org.jmol.viewer.TransformManager
- vibrationperiod - Static variable in class org.jmol.script.T
- vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
- vibrations - Variable in class org.jmol.modelset.AtomCollection
- vibrationscale - Static variable in class org.jmol.script.T
- vibrationSteps - Variable in class org.jmol.modelset.ModelSet
- vibrationThread - Variable in class org.jmol.viewer.TransformManager
- VibrationThread - Class in org.jmol.thread
- VibrationThread() - Constructor for class org.jmol.thread.VibrationThread
- vibScale - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- vibsFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- vibx - Static variable in class org.jmol.script.T
- vibxyz - Static variable in class org.jmol.script.T
- viby - Static variable in class org.jmol.script.T
- vibz - Static variable in class org.jmol.script.T
- VIEW - Enum constant in enum class jspecview.common.ScriptToken
- ViewCoupleTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
- ViewData - Class in jspecview.common
-
Stores information that
GraphSet
needs to display a view with one or more spectra. - ViewData(Lst<Spectrum>, double, double, boolean) - Constructor for class jspecview.common.ViewData
- ViewData(Lst<Spectrum>, double, double, int[], int[], boolean, boolean) - Constructor for class jspecview.common.ViewData
- viewer - Variable in class jspecview.appletjs.JSVApplet
- viewer - Variable in class jspecview.application.ApplicationMenu
- viewer - Variable in class org.jmol.util.GenericApplet
- viewer - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- Viewer - Class in org.jmol.viewer
- Viewer(Map<String, Object>) - Constructor for class org.jmol.viewer.Viewer
-
new way...
- Viewer.ACCESS - Enum Class in org.jmol.viewer
- viewerOptions - Variable in class jspecview.appletjs.JSVApplet
- viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
- ViewNoeTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
- viewOffset - Variable in class jspecview.common.Parameters
- viewpoint - Variable in class org.jmol.export.__CartesianExporter
- Views - Enum constant in enum class jspecview.common.Annotation.AType
- ViewsDialog - Class in jspecview.dialog
-
Dialog for managing overlaying spectra and closing files
- ViewsDialog() - Constructor for class jspecview.dialog.ViewsDialog
- viewSelected() - Method in class jspecview.dialog.ViewsDialog
- VIS_BACKBONE_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_BALLS_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_BOND_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_CARTOON_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_LABEL_FLAG - Static variable in class org.jmol.viewer.JC
- visibilityFlags - Variable in class org.jmol.shape.Mesh
- visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
- visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedron
- visible - Variable in class org.jmol.modelset.Text
- visible - Static variable in class org.jmol.script.T
- visible - Variable in class org.jmol.shape.Mesh
- visible - Variable in class org.jmol.shapespecial.Ellipsoid
- Visible - Class in jspecview.common
-
Visible class - for prediction of colour from visible spectrum see Robert J.
- Visible() - Constructor for class jspecview.common.Visible
- VisibleInterface - Interface in jspecview.api
- visualrange - Static variable in class org.jmol.script.T
- visualRangeAngstroms - Variable in class org.jmol.viewer.TransformManager
- VK_ALT - Static variable in class org.jmol.awtjs.Event
- VK_BACK_SPACE - Static variable in class org.jmol.awtjs.Event
- VK_CONTROL - Static variable in class org.jmol.awtjs.Event
- VK_DELETE - Static variable in class org.jmol.awtjs.Event
- VK_DOWN - Static variable in class org.jmol.awtjs.Event
- VK_ESCAPE - Static variable in class org.jmol.awtjs.Event
- VK_LEFT - Static variable in class org.jmol.awtjs.Event
- VK_META - Static variable in class org.jmol.awtjs.Event
- VK_PAGE_DOWN - Static variable in class org.jmol.awtjs.Event
- VK_PAGE_UP - Static variable in class org.jmol.awtjs.Event
- VK_PERIOD - Static variable in class org.jmol.awtjs.Event
- VK_RIGHT - Static variable in class org.jmol.awtjs.Event
- VK_SHIFT - Static variable in class org.jmol.awtjs.Event
- VK_SPACE - Static variable in class org.jmol.awtjs.Event
- VK_UP - Static variable in class org.jmol.awtjs.Event
- vNaN - Static variable in class org.jmol.script.SV
- vNorm - Variable in class org.jmol.symmetry.CIPData
- vOcc - Variable in class org.jmol.util.ModulationSet
-
the current value of the occupancy modulation
- volume - Variable in class org.jmol.quantum.QuantumCalculation
- volume - Static variable in class org.jmol.script.T
- volume - Variable in class org.jmol.util.BZone
- volume - Variable in class org.jmol.util.ContactPair
- volume - Variable in class org.jmol.util.SimpleUnitCell
- volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
- volumeData - Variable in class org.jmol.jvxl.readers.Parameters
- VolumeData - Class in org.jmol.jvxl.data
- VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
- volumeDataTemp - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- volumeRender - Variable in class org.jmol.render.MeshRenderer
- volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
- volumeRender(boolean) - Method in class org.jmol.export.Export3D
- volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
- volumeRender4(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- volumeRender4(int, int, int, int) - Method in class org.jmol.export.Export3D
- volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- volumeRenderPointSize - Variable in class org.jmol.shape.Mesh
- volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
- volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
- voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
- voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
- voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- voxelData - Variable in class org.jmol.quantum.QuantumCalculation
- VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
- voxelDataTemp - Variable in class org.jmol.quantum.QuantumCalculation
- voxelPtToXYZ(int, int, int, T3) - Method in class org.jmol.jvxl.data.VolumeData
- voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
- voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
- voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
- vs - Variable in class org.jmol.util.MeshSurface
-
vertices
- vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- vT - Static variable in class org.jmol.script.SV
- vTemp - Variable in class org.jmol.renderspecial.DrawRenderer
- vTemp - Variable in class org.jmol.shape.Mesh
- vTemp - Variable in class org.jmol.symmetry.CIPData
- vTemp2 - Variable in class org.jmol.renderspecial.DrawRenderer
- vvs - Variable in class org.jmol.util.MeshSurface
-
vertex values
- vwr - Variable in class jspecview.app.JSVApp
- vwr - Variable in class jspecview.application.AppToolBar
- vwr - Variable in class jspecview.application.AwtTree
- vwr - Variable in class jspecview.dialog.DialogManager
- vwr - Variable in class jspecview.dialog.JSVDialog
- vwr - Variable in class jspecview.export.AMLExporter
- vwr - Variable in class jspecview.export.CMLExporter
- vwr - Variable in class jspecview.export.SVGExporter
- vwr - Variable in class jspecview.popup.JSVGenericPopup
- vwr - Variable in class jspecview.tree.SimpleTree
- vwr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- vwr - Variable in class org.jmol.adapter.writers.CMLWriter
- vwr - Variable in class org.jmol.console.GenericConsole
- vwr - Variable in class org.jmol.console.ImageDialog
- vwr - Variable in class org.jmol.dialog.Dialog
- vwr - Variable in class org.jmol.export.___Exporter
- vwr - Variable in class org.jmol.minimize.Minimizer
- vwr - Variable in class org.jmol.modelkit.ModelKit
- vwr - Variable in class org.jmol.modelset.AtomCollection
- vwr - Variable in class org.jmol.popup.JmolGenericPopup
- vwr - Variable in class org.jmol.render.ShapeRenderer
- vwr - Variable in class org.jmol.script.ScriptError
- vwr - Variable in class org.jmol.script.ScriptCompiler
- vwr - Variable in class org.jmol.scriptext.ScriptExt
- vwr - Variable in class org.jmol.shape.Shape
- vwr - Variable in class org.jmol.thread.JmolThread
- vwr - Variable in class org.jmol.util.GData
- vwr - Variable in class org.jmol.util.MeshSurface
- vwr - Variable in class org.jmol.viewer.ActionManager
- vwr - Variable in class org.jmol.viewer.AnimationManager
- vwr - Variable in class org.jmol.viewer.FileManager
- vwr - Variable in class org.jmol.viewer.OutputManagerAwt
- vwr - Variable in class org.jmol.viewer.OutputManagerJS
- vwr - Variable in class org.jmol.viewer.ShapeManager
- vwr - Variable in class org.jmol.viewer.StateManager
- vwr - Variable in class org.jmol.viewer.StatusManager
- vwr - Variable in class org.jmol.viewer.TransformManager
- vwr - Variable in class org.molecularplayground.MPJmolApp
- vwr - Variable in class org.openscience.jmol.app.JmolData
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- vwr - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- vwrFrame - Variable in class org.jmol.console.JmolConsole
- vwrOptions - Variable in class org.jmol.util.GenericApplet
- vwrOptions - Variable in class org.jmol.viewer.Viewer
- vwrOptions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
W
- w - Variable in class javajs.util.T4
-
The w coordinate.
- w - Static variable in class org.jmol.script.T
- waitForDisplay(Object, Object) - Method in class jspecview.java.AwtPlatform
- waitForDisplay(Object, Object) - Method in class jspecview.js2d.JsPlatform
- waitForDisplay(Object, Object) - Method in interface org.jmol.api.GenericPlatform
-
can be ignored (return false) if platform cannot save images
- waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
- waitForDisplay(Object, Object) - Method in class org.jmol.awtjs2d.Platform
- waitformoveto - Static variable in class org.jmol.script.T
- waitForMoveTo - Variable in class org.jmol.viewer.GlobalSettings
- waitForQueue() - Method in interface org.jmol.api.JmolScriptManager
- waitForQueue() - Method in class org.jmol.script.ScriptManager
- warn(String) - Method in class org.jmol.util.DefaultLogger
- warn(String) - Static method in class org.jmol.util.Logger
-
Writes a log at WARN level.
- warn(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at WARN level.
- warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
- warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at WARN level with detail on exception.
- warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at WARN level with detail on exception.
- warning(int, String, String) - Method in class org.jmol.script.ScriptError
- warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- WARNING_MESSAGE - Static variable in class jspecview.dialog.DialogManager
- wasClicked(int, int) - Method in class org.jmol.shape.Frank
- wasClicked(int, int) - Method in class org.jmol.shape.Shape
- wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
- wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
- wasmInchiHack(String) - Method in class org.jmol.viewer.Viewer
-
WASM inchi must be initialized asynchronously
- wasPerspective - Variable in class org.jmol.export._PovrayExporter
- wasPerspective - Variable in class org.jmol.export._TachyonExporter
- wasRotating() - Method in class org.jmol.modelkit.ModelKit
- wasSpinOn - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- wasUnquoted - Variable in class javajs.util.CifDataParser
-
whether we are processing an unquoted value or key
- wasX - Variable in class org.jmol.script.ScriptMathProcessor
- WB - Static variable in class org.jmol.util.ColorEncoder
- WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- WebExport - Class in org.openscience.jmol.app.webexport
- webme - Variable in class jme.JME
- WebMOReader - Class in org.jmol.adapter.readers.quantum
-
A molecular orbital reader for WebMO files.
- WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
- WEST - Static variable in class org.jmol.awtjs.swing.BorderLayout
- WEST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
- WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
- WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
- WHEEL - Static variable in class org.jmol.viewer.binding.Binding
- wheeled(long, int, int) - Method in class jspecview.app.GenericMouse
- WHEELED - Static variable in class org.jmol.awtjs.Event
- when - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- whilecmd - Static variable in class org.jmol.script.T
- WHITE - Static variable in class jspecview.common.ColorParameters
- WHITE - Static variable in class org.jmol.util.C
- why - Variable in class org.jmol.script.ScriptContext
- width - Variable in class javajs.img.ImageEncoder
- width - Variable in class org.jmol.awtjs.swing.Component
- width - Variable in class org.jmol.awtjs.swing.Dimension
- width - Variable in class org.jmol.render.FontLineShapeRenderer
- width - Variable in class org.jmol.render.MeshRenderer
- width - Static variable in class org.jmol.script.T
- width - Variable in class org.jmol.shape.Mesh
- width - Variable in class org.jmol.util.GData
- width - Variable in class org.jmol.util.Rectangle
- width - Variable in class org.jmol.viewer.TransformManager
- WIDTHSCALE - Static variable in class org.jmol.shapecgo.CGOMesh
- Wien2kReader - Class in org.jmol.adapter.readers.xtal
-
A reader for Wein2k DFT files.
- Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
- wigner - Static variable in class org.jmol.script.T
- window - Static variable in class org.jmol.script.T
- WINDOW - Enum constant in enum class jspecview.common.ScriptToken
- windowActivated(WindowEvent) - Method in class jspecview.java.AwtDialogManager
- windowActivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowActivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowcentered - Static variable in class org.jmol.script.T
- windowCentered - Variable in class org.jmol.viewer.TransformManager
- windowClosed(WindowEvent) - Method in class jspecview.java.AwtDialogManager
- windowClosed(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowClosed(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowClosing(WindowEvent) - Method in class jspecview.java.AwtDialogManager
-
WindowListener callback
- windowClosing(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowClosing(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowClosing(HTMLElement) - Method in interface org.jmol.awtjs.swing.SwingController
-
Called by clicking the [x] in the corner of the dialog; send a notification back to the manager via processWindowClosing(key) var id = $("div.JDialog:has(#" + element.id + ")")[0].id var dialog = Jmol.Swing.htDialogs[id]; dialog.manager.processWindowClosing(dialog.registryKey);
- windowClosing_actionPerformed() - Method in class jspecview.application.MainFrame
- windowDeactivated(WindowEvent) - Method in class jspecview.java.AwtDialogManager
- windowDeactivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowDeactivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowDeiconified(WindowEvent) - Method in class jspecview.java.AwtDialogManager
- windowDeiconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowDeiconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowHeight - Variable in class org.jmol.modelset.Text
- windowHeight - Variable in class org.jmol.util.GData
- windowIconified(WindowEvent) - Method in class jspecview.java.AwtDialogManager
- windowIconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowIconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowName - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- windowOpened(WindowEvent) - Method in class jspecview.java.AwtDialogManager
- windowOpened(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowOpened(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
- windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowWidth - Variable in class org.jmol.modelset.Text
- windowWidth - Variable in class org.jmol.util.GData
- wingVectors - Variable in class org.jmol.modelsetbio.BioPolymer
- wingVectors - Variable in class org.jmol.renderbio.BackboneRenderer
- wingVectors - Variable in class org.jmol.renderbio.CartoonRenderer
- wingVectors - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- wingVectors - Variable in class org.jmol.renderbio.RibbonsRenderer
- wingVectors - Variable in class org.jmol.renderbio.RocketsRenderer
- wingVectors - Variable in class org.jmol.renderbio.StrandsRenderer
- wingVectors - Variable in class org.jmol.renderbio.TraceRenderer
- wingVectors - Variable in class org.jmol.shapebio.BioShape
- wireframe - Static variable in class org.jmol.script.T
- wireframeOnly - Variable in class org.jmol.renderbio.BackboneRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.CartoonRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.MeshRibbonRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.RibbonsRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.RocketsRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.StrandsRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.TraceRenderer
- wireframerotation - Static variable in class org.jmol.script.T
- within - Static variable in class org.jmol.script.T
- within(float, P3, Lst<P3>) - Static method in class org.jmol.util.BZone
- withinDistPoints(float, P3, P3[], P3[], BS, Object[]) - Static method in class org.jmol.bspt.PointIterator
-
carry out various functions of the within() script function
- words - Variable in class org.jmol.popup.PopupResource
- wrap(String, SB) - Static method in class org.jmol.symmetry.WyckoffFinder
-
Just wrap the coordinate with parentheses.
- wrapCdata(Object) - Static method in class javajs.util.XmlUtil
-
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
- wrapCData(String) - Static method in class org.jmol.adapter.writers.CDXMLWriter
-
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
- wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManagerAwt
- wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManagerJS
- write - Static variable in class org.jmol.script.T
- write(byte[], int, int) - Method in class com.jcraft.jzlib.DeflaterOutputStream
- write(byte[], int, int) - Method in interface javajs.api.GenericOutputChannel
- write(byte[], int, int) - Method in class javajs.util.OC
- write(int) - Method in class javajs.util.OC
-
Deprecated.
- write(BS) - Method in class org.jmol.adapter.writers.CDXMLWriter
- write(BS) - Method in class org.jmol.adapter.writers.CIFWriter
- write(BS) - Method in class org.jmol.adapter.writers.CMLWriter
- write(BS) - Method in class org.jmol.adapter.writers.PDBWriter
- write(BS) - Method in class org.jmol.adapter.writers.PWMATWriter
- write(BS) - Method in class org.jmol.adapter.writers.QCJSONWriter
- write(BS) - Method in class org.jmol.adapter.writers.XSFWriter
- write(BS) - Method in interface org.jmol.api.JmolWriter
- write(JSViewer, Lst<String>, boolean) - Method in interface jspecview.api.ExportInterface
-
from EXPORT command
- write(JSViewer, Lst<String>, boolean) - Method in class jspecview.export.Exporter
- WRITE - Enum constant in enum class jspecview.common.ScriptToken
- writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
- writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- writeArray(Object) - Method in class org.jmol.util.JSONWriter
- writeAtoms(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeBonds(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeBoolean(Boolean) - Method in class org.jmol.util.JSONWriter
- writeByte(int) - Method in class javajs.img.PngEncoder
-
Write a single byte into the pngBytes array at a given position.
- writeByteAsInt(int) - Method in class com.jcraft.jzlib.DeflaterOutputStream
- writeByteAsInt(int) - Method in interface javajs.api.GenericOutputChannel
- writeByteAsInt(int) - Method in class javajs.util.OC
- writeBytes(byte[]) - Method in class javajs.img.PngEncoder
-
Write an array of bytes into the pngBytes array.
- writeCRC() - Method in class javajs.img.PngEncoder
- writeFile(String, Object, String) - Method in class org.jmol.viewer.Viewer
- writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
- writeFloat(float) - Method in class javajs.util.OC
- writeForm(String) - Method in class jspecview.export.AMLExporter
- writeForm(String) - Method in class jspecview.export.CMLExporter
- writeForm(String) - Method in class jspecview.export.SVGExporter
- writeInt(int) - Method in interface javajs.api.GenericOutputChannel
- writeInt(int) - Method in class javajs.util.OC
- writeInt2(int) - Method in class javajs.img.PngEncoder
-
Write a two-byte integer into the pngBytes array at a given position.
- writeInt4(int) - Method in class javajs.img.PngEncoder
-
Write a four-byte integer into the pngBytes array at a given position.
- writeJob(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeJobMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeJobs() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeJSON() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeList(List<Object>) - Method in class org.jmol.util.JSONWriter
- writeLong(long) - Method in interface javajs.api.GenericOutputChannel
- writeLong(long) - Method in class javajs.util.OC
- writeMagic() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeMap(Map<String, Object>) - Method in class org.jmol.util.JSONWriter
- writemi - Variable in class jme.JME
- writeMOBases() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeModel(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeModelMetadata(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeModels() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writemol - Variable in class jme.JME
- WriteNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
- writeNamfisFiles(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- writeNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- writeNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- writeNull() - Method in class org.jmol.util.JSONWriter
- writeNumber(Number) - Method in class org.jmol.util.JSONWriter
- writeObject(Object) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeObject(Object) - Method in class org.jmol.util.JSONWriter
- writeSchemaMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeShort(short) - Method in interface javajs.api.GenericOutputChannel
- writeShort(short) - Method in class javajs.util.OC
- writesmi - Variable in class jme.JME
- writeStatus(String) - Method in interface jspecview.api.JSVAppletInterface
-
Writes a message to the status label
- writeStatus(String) - Method in interface jspecview.api.ScriptInterface
- writeStatus(String) - Method in class jspecview.app.JSVApp
-
Writes a message to the status label
- writeStatus(String) - Method in class jspecview.appletjs.JSVApplet
- writeStatus(String) - Method in class jspecview.application.JSpecView
- writeStatus(String) - Method in class jspecview.application.MainFrame
-
Writes a message to the status bar
- writeString(String) - Method in class javajs.img.PngEncoder
-
Write a string into the pngBytes array at a given position.
- writeString(String) - Method in class org.jmol.util.JSONWriter
- writeString(String, SB) - Method in class org.jmol.util.JSONWriter
- writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
- writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
- writeTopology(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeVibrations(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- wyckoff - Static variable in class org.jmol.script.T
- WYCKOFF_RET_CENTERING - Static variable in class org.jmol.symmetry.WyckoffFinder
- WYCKOFF_RET_CENTERING_STRING - Static variable in class org.jmol.symmetry.WyckoffFinder
- WYCKOFF_RET_COORD - Static variable in class org.jmol.symmetry.WyckoffFinder
- WYCKOFF_RET_COORDS - Static variable in class org.jmol.symmetry.WyckoffFinder
- WYCKOFF_RET_COORDS_ALL - Static variable in class org.jmol.symmetry.WyckoffFinder
- WYCKOFF_RET_GENERAL - Static variable in class org.jmol.symmetry.WyckoffFinder
- WYCKOFF_RET_LABEL - Static variable in class org.jmol.symmetry.WyckoffFinder
-
positive numbers will be label characters or '*'
- WYCKOFF_RET_WITH_MULT - Static variable in class org.jmol.symmetry.WyckoffFinder
- WyckoffFinder - Class in org.jmol.symmetry
-
A class to calculate, store, and retrieve Wyckoff information as per BCS nph-trgen at https://www.cryst.ehu.es/cgi-bin/cryst/programs//nph-trgen?gnum=146invalid input: '&what'=wposinvalid input: '&trmat'=2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3cinvalid input: '&unconv'=R%203%20:Rinvalid input: '&from'=ita For the 611 standard setting in ITA GENPOS, we are just reading the json file and loading its information.
- WyckoffFinder() - Constructor for class org.jmol.symmetry.WyckoffFinder
- wyckoffm - Static variable in class org.jmol.script.T
X
- x - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- x - Variable in class javajs.util.T3
- x - Variable in class javajs.util.T3d
-
The x coordinate.
- x - Variable in class javajs.util.T3i
-
The x coordinate.
- x - Variable in class org.jmol.quantum.SlaterData
- x - Static variable in class org.jmol.script.T
- x - Variable in class org.jmol.util.Rectangle
- x - Variable in class org.jmol.viewer.MouseState
- X - Variable in class org.jmol.quantum.QuantumCalculation
- X - Static variable in class org.jmol.util.BoxInfo
- X2 - Variable in class org.jmol.quantum.QuantumCalculation
- xaxisData - Variable in class jspecview.source.AnIMLReader
- xAxisLeftToRight - Variable in class jspecview.common.PanelData
- xBohr - Variable in class org.jmol.quantum.QuantumCalculation
- xButton - Variable in class jme.JME
- XcrysdenReader - Class in org.jmol.adapter.readers.xtal
- XcrysdenReader() - Constructor for class org.jmol.adapter.readers.xtal.XcrysdenReader
- xFactor - Variable in class jspecview.source.JDXDataObject
-
Also used in JDXExport
- xFactor - Variable in class jspecview.source.AnIMLReader
- xGT - Static variable in class org.jmol.util.GData
- xLabel - Variable in class jspecview.source.JDXDataObject
- xLast - Variable in class org.jmol.util.GData
- xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- xLT - Static variable in class org.jmol.util.GData
- xMax - Variable in class org.jmol.quantum.QuantumCalculation
- xMin - Variable in class org.jmol.quantum.QuantumCalculation
- XmlArgusReader - Class in org.jmol.adapter.readers.xml
-
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
- XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
- XmlCdxReader - Class in org.jmol.adapter.readers.xml
-
A reader for CambridgeSoft CDXML files.
- XmlCdxReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCdxReader
- XmlChem3dReader - Class in org.jmol.adapter.readers.xml
-
An chem3d c3xml reader
- XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
- XmlCmlReader - Class in org.jmol.adapter.readers.xml
-
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
- XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
- xmlData - Variable in class org.jmol.jvxl.data.VolumeData
- XmlHandler - Class in org.jmol.adapter.readers.xml
-
a SAX handler -- Java only
- XmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlHandler
- XmlMagResReader - Class in org.jmol.adapter.readers.xml
- XmlMagResReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMagResReader
- XmlMolproReader - Class in org.jmol.adapter.readers.xml
-
A Molpro 2005 reader
- XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
- XmlMOReader - Class in org.jmol.adapter.readers.xml
-
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
- XmlMOReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMOReader
- XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
-
An Odyssey xodydata reader
- XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
- XMLParser - Class in jspecview.source
- XMLParser(BufferedReader) - Constructor for class jspecview.source.XMLParser
- XmlQEReader - Class in org.jmol.adapter.readers.xml
-
QuantumEspresso XML reader
- XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
- XmlReader - Class in org.jmol.adapter.readers.xml
-
A generic XML reader template -- by itself, does nothing.
- XmlReader - Class in org.jmol.jvxl.readers
- XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
- XmlReader(BufferedReader) - Constructor for class org.jmol.jvxl.readers.XmlReader
- XmlUtil - Class in javajs.util
-
A very simplistic XML generator
- XmlUtil() - Constructor for class javajs.util.XmlUtil
- XmlVaspReader - Class in org.jmol.adapter.readers.xml
-
Vasp vasprun.xml reader
- XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
- XmlXsdReader - Class in org.jmol.adapter.readers.xml
-
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
- XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
- xor(BS) - Method in class javajs.util.BS
-
Performs a logical XOR of this bit set with the bit set argument.
- xPixelClicked - Variable in class jspecview.common.PanelData
- XSCALEON - Enum constant in enum class jspecview.common.ScriptToken
- XSFWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer.
- XSFWriter() - Constructor for class org.jmol.adapter.writers.XSFWriter
- xtalSymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- XtalSymmetry - Class in org.jmol.adapter.smarter
-
A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
- XtalSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry
- XtalSymmetry.FileSymmetry - Class in org.jmol.adapter.smarter
-
A class only used by adapter.smarter.XtalSymmetry while building the file-based model.
- XtlWriter - Class in org.jmol.adapter.writers
- XtlWriter() - Constructor for class org.jmol.adapter.writers.XtlWriter
- xUnitExponent - Variable in class jspecview.export.AMLExporter
- xUnitExponent - Variable in class jspecview.export.CMLExporter
- xUnitFactor - Variable in class jspecview.export.AMLExporter
- xUnitFactor - Variable in class jspecview.export.CMLExporter
- xUnitLabel - Variable in class jspecview.export.AMLExporter
- xUnitLabel - Variable in class jspecview.export.CMLExporter
- xUnits - Variable in class jspecview.export.AMLExporter
- xUnits - Variable in class jspecview.export.CMLExporter
- xUnits - Variable in class jspecview.source.JDXDataObject
- xUnits - Variable in class jspecview.source.AnIMLReader
- XUNITSON - Enum constant in enum class jspecview.common.ScriptToken
- xVdwClash - Variable in class org.jmol.util.ContactPair
- xWhenPressed - Variable in class jspecview.app.GenericMouse
- xy - Variable in class org.jmol.render.LabelsRenderer
- xy - Variable in class org.jmol.shape.Hover
- XY - Enum constant in enum class jspecview.common.ExportType
- XY_RANGE - Static variable in class org.jmol.viewer.ActionManager
- XY_ZTOP - Static variable in class org.jmol.viewer.JC
- xyCoords - Variable in class jspecview.export.AMLExporter
- xyCoords - Variable in class jspecview.export.CMLExporter
- xyCoords - Variable in class jspecview.source.JDXDataObject
-
array of x,y coordinates
- xyData - Variable in class jspecview.dialog.JSVDialog
- xypParameter(int) - Method in class org.jmol.script.ScriptParam
- xyz - Variable in class org.jmol.atomdata.AtomData
- xyz - Variable in class org.jmol.modelset.Text
- xyz - Static variable in class org.jmol.script.T
- XYZ - Static variable in class org.jmol.util.BoxInfo
- xyzIsSlabbedInternal(T3) - Method in class org.jmol.viewer.TransformManager
- xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
- xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
- xyzpParameter(int) - Method in class org.jmol.script.ScriptParam
- XyzReader - Class in org.jmol.adapter.readers.molxyz
-
Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
- XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
- xyzToLab(P3, P3) - Method in class javajs.img.GifEncoder
- xyzToRgb(P3, P3) - Method in class javajs.img.GifEncoder
- xyzToVoxelPt(float, float, float, T3i) - Method in class org.jmol.jvxl.data.VolumeData
Y
- y - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
- y - Variable in class javajs.util.T3
- y - Variable in class javajs.util.T3d
-
The y coordinate.
- y - Variable in class javajs.util.T3i
-
The y coordinate.
- y - Variable in class org.jmol.quantum.SlaterData
- y - Static variable in class org.jmol.script.T
- y - Variable in class org.jmol.util.Rectangle
- y - Variable in class org.jmol.viewer.MouseState
- Y - Variable in class org.jmol.quantum.QuantumCalculation
- Y - Static variable in class org.jmol.util.BoxInfo
- Y2 - Variable in class org.jmol.quantum.QuantumCalculation
- y2DUnits - Variable in class jspecview.source.JDXDataObject
- yaxisData - Variable in class jspecview.source.AnIMLReader
- yBohr - Variable in class org.jmol.quantum.QuantumCalculation
- YELLOW - Static variable in class org.jmol.util.C
- yFactor - Variable in class jspecview.source.JDXDataObject
-
Also used in JDXExport
- yFactor - Variable in class jspecview.source.AnIMLReader
- yGT - Static variable in class org.jmol.util.GData
- yLabel - Variable in class jspecview.source.JDXDataObject
- yLast - Variable in class org.jmol.util.GData
- yLT - Static variable in class org.jmol.util.GData
- yMax - Variable in class org.jmol.quantum.QuantumCalculation
- yMin - Variable in class org.jmol.quantum.QuantumCalculation
- YSCALE - Enum constant in enum class jspecview.common.ScriptToken
- YSCALEON - Enum constant in enum class jspecview.common.ScriptToken
- yUnitLabel - Variable in class jspecview.export.AMLExporter
- yUnitLabel - Variable in class jspecview.export.CMLExporter
- yUnits - Variable in class jspecview.export.AMLExporter
- yUnits - Variable in class jspecview.export.CMLExporter
- yUnits - Variable in class jspecview.source.JDXDataObject
- yUnits - Variable in class jspecview.source.AnIMLReader
- YUNITSON - Enum constant in enum class jspecview.common.ScriptToken
- yWhenPressed - Variable in class jspecview.app.GenericMouse
- yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
- yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
- yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader
Z
- z - Variable in class javajs.util.T3
- z - Variable in class javajs.util.T3d
-
The z coordinate.
- z - Variable in class javajs.util.T3i
-
The z coordinate.
- z - Variable in class org.jmol.modelset.Text
- z - Variable in class org.jmol.quantum.SlaterData
- z - Static variable in class org.jmol.script.T
- Z - Variable in class org.jmol.quantum.QuantumCalculation
- Z - Static variable in class org.jmol.util.BoxInfo
- Z_ASCII - Static variable in class com.jcraft.jzlib.JZlib
- Z_BEST_COMPRESSION - Static variable in class com.jcraft.jzlib.JZlib
- Z_BEST_SPEED - Static variable in class com.jcraft.jzlib.JZlib
- Z_BINARY - Static variable in class com.jcraft.jzlib.JZlib
- Z_BUF_ERROR - Static variable in class com.jcraft.jzlib.JZlib
- Z_DATA_ERROR - Static variable in class com.jcraft.jzlib.JZlib
- Z_DEFAULT_COMPRESSION - Static variable in class com.jcraft.jzlib.JZlib
- Z_DEFAULT_STRATEGY - Static variable in class com.jcraft.jzlib.JZlib
- Z_ERRNO - Static variable in class com.jcraft.jzlib.JZlib
- Z_FILTERED - Static variable in class com.jcraft.jzlib.JZlib
- Z_FINISH - Static variable in class com.jcraft.jzlib.JZlib
- Z_FULL_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
- Z_HUFFMAN_ONLY - Static variable in class com.jcraft.jzlib.JZlib
- Z_MEM_ERROR - Static variable in class com.jcraft.jzlib.JZlib
- Z_NEED_DICT - Static variable in class com.jcraft.jzlib.JZlib
- Z_NO_COMPRESSION - Static variable in class com.jcraft.jzlib.JZlib
- Z_NO_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
- Z_OK - Static variable in class com.jcraft.jzlib.JZlib
- Z_PARTIAL_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
- Z_STREAM_END - Static variable in class com.jcraft.jzlib.JZlib
- Z_STREAM_ERROR - Static variable in class com.jcraft.jzlib.JZlib
- Z_SYNC_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
- Z_UNKNOWN - Static variable in class com.jcraft.jzlib.JZlib
- Z_VERSION_ERROR - Static variable in class com.jcraft.jzlib.JZlib
- Z2 - Variable in class org.jmol.quantum.QuantumCalculation
- zap - Static variable in class org.jmol.script.T
- zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
- zap() - Method in class org.jmol.console.GenericConsole
- zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- ZAP_TITLE - Static variable in class org.jmol.viewer.JC
- ZAPPED - Enum constant in enum class org.jmol.c.FIL
- zBohr - Variable in class org.jmol.quantum.QuantumCalculation
- zbuf - Variable in class org.jmol.g3d.Graphics3D
- zbufT - Variable in class org.jmol.g3d.Graphics3D
- zdepth - Static variable in class org.jmol.script.T
- zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
- zDepthValue - Variable in class org.jmol.viewer.TransformManager
- zerobasedxyzrasmol - Static variable in class org.jmol.script.T
- zeroFontId - Variable in class org.jmol.shape.Labels
- zeta - Variable in class org.jmol.quantum.SlaterData
- zGT - Static variable in class org.jmol.util.GData
- ZInputStream - Interface in javajs.api
- ZipData - Class in javajs.util
- ZipData(int) - Constructor for class javajs.util.ZipData
- ZipTools - Class in javajs.util
-
Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
- ZipTools() - Constructor for class javajs.util.ZipTools
- zLT - Static variable in class org.jmol.util.GData
- zMargin - Variable in class org.jmol.g3d.Graphics3D
- zMax - Variable in class org.jmol.quantum.QuantumCalculation
- zMin - Variable in class org.jmol.quantum.QuantumCalculation
- zmPct - Variable in class org.jmol.viewer.TransformManager
-
zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled
- zoom - Static variable in class org.jmol.script.T
- ZOOM - Enum constant in enum class jspecview.common.ScriptToken
- ZOOM_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
- ZOOM_EVENT - Static variable in class com.sparshui.GestureType
- ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- ZOOM_GESTURE - Static variable in class com.sparshui.GestureType
- ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- zoomBoxColor - Variable in class jspecview.common.PanelData
- ZOOMBOXCOLOR - Enum constant in enum class jspecview.common.ScriptToken
- zoomBoxColor2 - Variable in class jspecview.common.PanelData
- ZOOMBOXCOLOR2 - Enum constant in enum class jspecview.common.ScriptToken
- zoomBy(int) - Method in class org.jmol.viewer.TransformManager
-
standard response to user mouse vertical shift-drag
- zoomByFactor(float, int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
- zoomByFactor(float, int, int) - Method in class org.jmol.navigate.Navigator
- zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
- zoomenabled - Static variable in class org.jmol.script.T
- zoomEnabled - Variable in class org.jmol.viewer.TransformManager
- ZoomEvent - Class in com.sparshui.common.messages.events
- ZoomEvent - Class in jspecview.common
- ZoomEvent() - Constructor for class com.sparshui.common.messages.events.ZoomEvent
- ZoomEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.ZoomEvent
-
Constructs a ZoomEvent from a serialized version of ZoomEvent.
- ZoomEvent(float, Location, long) - Constructor for class com.sparshui.common.messages.events.ZoomEvent
- zoomFactor - Variable in class org.jmol.viewer.TransformManager
- zoomheight - Static variable in class org.jmol.script.T
- zoomlarge - Static variable in class org.jmol.script.T
- zoomTo - Static variable in class org.jmol.script.T
- zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
- zoomTrigger - Variable in class org.jmol.viewer.ActionManager
- zshade - Static variable in class org.jmol.script.T
- zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
- zshadepower - Static variable in class org.jmol.script.T
- zslab - Static variable in class org.jmol.script.T
- zSlab - Variable in class org.jmol.modelset.Text
- zSlab - Variable in class org.jmol.render.LabelsRenderer
- zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
- zSlabPoint - Variable in class org.jmol.viewer.TransformManager
- zSlabValue - Variable in class org.jmol.viewer.TransformManager
- ZStream - Class in com.jcraft.jzlib
-
Bob Hanson -- using this for Jmol; added ZStream.getBytes(s) ZStream deprecated? Not for public use in the future.
- ZStream() - Constructor for class com.jcraft.jzlib.ZStream
- ZStreamException - Exception Class in com.jcraft.jzlib
- ZStreamException() - Constructor for exception class com.jcraft.jzlib.ZStreamException
- ZStreamException(String) - Constructor for exception class com.jcraft.jzlib.ZStreamException
- zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager
_
- __ - Static variable in class org.jmol.script.T
- ___Exporter - Class in org.jmol.export
- ___Exporter() - Constructor for class org.jmol.export.___Exporter
- __CartesianExporter - Class in org.jmol.export
- __CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.AdfReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.AmsReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.DgridReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- _active - Variable in class com.sparshui.inputdevice.JmolTouchSimulator
- _args - Static variable in class org.jmol.script.T
- _atomPickedCallback(int, int) - Method in interface org.jmol.api.js.JSmolAppletObject
- _IdtfExporter - Class in org.jmol.export
- _IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
- _in - Variable in class com.sparshui.common.ClientProtocol
- _MayaExporter - Class in org.jmol.export
- _MayaExporter() - Constructor for class org.jmol.export._MayaExporter
- _ObjExporter - Class in org.jmol.export
-
Class to export Wavefront OBJ files.
- _ObjExporter() - Constructor for class org.jmol.export._ObjExporter
- _offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _out - Variable in class com.sparshui.common.ClientProtocol
- _PovrayExporter - Class in org.jmol.export
- _PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
- _refresh() - Method in interface org.jmol.api.js.JSmolAppletObject
- _search(String) - Method in interface jspecview.api.js.JSVAppletObject
- _showStatus(String, String) - Method in interface jspecview.api.js.JSVAppletObject
- _showTooltip(String, int, int) - Method in interface jspecview.api.js.JSVAppletObject
- _socket - Variable in class com.sparshui.common.ClientProtocol
- _StlExporter - Class in org.jmol.export
-
STereoLithography file format exporter for 3D printing.
- _StlExporter() - Constructor for class org.jmol.export._StlExporter
- _TachyonExporter - Class in org.jmol.export
- _TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
- _updateView(Object, String) - Method in interface jspecview.api.js.JSVAppletObject
- _VrmlExporter - Class in org.jmol.export
-
A basic VRML generator.
- _VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
- _X3dExporter - Class in org.jmol.export
- _X3dExporter() - Constructor for class org.jmol.export._X3dExporter
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