Uses of Class
javajs.util.Lst
Packages that use Lst
Package
Description
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
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Uses of Lst in com.sparshui.server
Methods in com.sparshui.server that return LstModifier and TypeMethodDescriptionServerToClientProtocol.getGestures
(int groupID) Retrieve a list of allowed gestures for the provided group id.Methods in com.sparshui.server with parameters of type LstModifier and TypeMethodDescriptionvoid
ServerToClientProtocol.processEvents
(int groupID, Lst<Event> events) Instruct the client to process the events that have been generated by a group.Constructors in com.sparshui.server with parameters of type LstModifierConstructorDescriptionGroup
(int id, Lst<GestureType> gestureTypes, ServerToClientProtocol clientProtocol) Construct a new group with the given gesture IDs and the given connection to the client. -
Uses of Lst in javajs.util
Methods in javajs.util that return LstModifier and TypeMethodDescriptionstatic <type> Lst<type>[]
AU.createArrayOfArrayList
(int size) Helper method for creating a List[] without warnings. Lst
<javajs.util.CompoundDocDirEntry> CompoundDocument.getDirectory()
Measure.getIntersectionPP
(P4 plane1, P4 plane2) Calculate the line that is the intersection of two planes.Measure.getLatticePoints
(Lst<P3> cpts, int h, int k, int l) Based on a set of centering points, creates a list of lattice points in place.Measure.getPointsOnPlane
(P3[] pts, P4 plane) Based on a set of centering points, returns the list of points on a given plane.Measure.transformPoints
(Lst<P3> vPts, M4 m4, P3 center) Methods in javajs.util with parameters of type LstModifier and TypeMethodDescriptionstatic P3[]
Measure.getCenterAndPoints
(Lst<P3> vPts) from a list of points, create an array that includes the center point as the first point.Measure.getLatticePoints
(Lst<P3> cpts, int h, int k, int l) Based on a set of centering points, creates a list of lattice points in place.static float
Fills a 4x4 matrix with rotation-translation of mapped points A to B.static String
static String
static String
AU.sortedItem
(Lst<String> v, int n) Measure.transformPoints
(Lst<P3> vPts, M4 m4, P3 center) -
Uses of Lst in jspecview.api
Methods in jspecview.api that return LstMethods in jspecview.api with parameters of type LstModifier and TypeMethodDescriptionvoid
JSVTree.deleteNodes
(Lst<JSVTreeNode> toDelete) AppletFrame.getJSVPanel
(JSViewer viewer, Lst<Spectrum> specs) void
JSVMainPanel.setSelectedPanel
(JSViewer viewer, JSVPanel jsvp, Lst<PanelNode> panelNodes) ScriptInterface.siGetNewJSVPanel2
(Lst<Spectrum> specs) void
ScriptInterface.siOpenDataOrFile
(Object data, String name, Lst<Spectrum> specs, String url, int firstSpec, int lastSpec, boolean doCheck, String script, String id) from EXPORT command -
Uses of Lst in jspecview.app
Methods in jspecview.app that return LstMethods in jspecview.app with parameters of type Lst -
Uses of Lst in jspecview.appletjs
Methods in jspecview.appletjs with parameters of type Lst -
Uses of Lst in jspecview.application
Methods in jspecview.application that return LstMethods in jspecview.application with parameters of type LstModifier and TypeMethodDescriptionvoid
AwtTree.deleteNodes
(Lst<JSVTreeNode> toDelete) void
ApplicationMenu.setRecentMenu
(Lst<String> recentFilePaths) JSpecView.siGetNewJSVPanel2
(Lst<Spectrum> specs) void
JSpecView.siOpenDataOrFile
(Object data, String name, Lst<Spectrum> specs, String url, int firstSpec, int lastSpec, boolean isAppend, String script, String id) void
ApplicationMenu.updateRecentMenus
(Lst<String> recentFilePaths) -
Uses of Lst in jspecview.common
Subclasses of Lst in jspecview.commonModifier and TypeClassDescriptionclass
from IntegralGraph a data structure for integration settingsclass
class
a data structure for peak listsFields in jspecview.common declared as LstModifier and TypeFieldDescriptionLst
<jspecview.common.GraphSet> PanelData.graphSets
JSViewer.panelNodes
JSViewer.scriptQueue
PanelData.spectra
Methods in jspecview.common that return LstModifier and TypeMethodDescriptionstatic Lst
<Annotation> IntegralData.getIntegrationRatiosFromString
(Spectrum spec, String key_values) Parses x-coordinates and values from a string and returns them asIntegrationRatio
objectsSpectrum.getPeakList()
static Lst
<ScriptToken> ScriptToken.getScriptTokenList
(String name, boolean isExact) Spectrum.getSubSpectra()
read a string for possibly quoted tokens separated by space until // or # is reached.Methods in jspecview.common with parameters of type LstModifier and TypeMethodDescriptionvoid
PanelData.addAnnotation
(Lst<String> tokens) void
static PanelNode
Returns the tree node that is associated with a panelstatic PanelNode
PanelNode.findNodeById
(String id, Lst<PanelNode> panelNodes) static JDXSource
PanelNode.findSourceByNameOrId
(String id, Lst<PanelNode> panelNodes) static Annotation
Annotation.getColoredAnnotation
(GenericGraphics g2d, Spectrum spec, Lst<String> args, Annotation lastAnnotation) static JSVPanel
PanelNode.getLastFileFirstNode
(Lst<PanelNode> panelNodes) static double
Returns the maximum x value value from an array of arrays ofCoordinate
s.static double
Coordinate.getMaxYUser
(Lst<Spectrum> spectra, ViewData vd) Returns the maximum y value value from an array of arrays ofCoordinate
s.static double
Returns the minimum x value value from an array of arrays ofCoordinate
s.static double
Coordinate.getMinYUser
(Lst<Spectrum> spectra, ViewData vd) Returns the minimum y value value from an array of arrays ofCoordinate
s.static String
ScriptToken.getNameList
(Lst<ScriptToken> list) static String
PanelNode.getSpectrumListAsString
(Lst<PanelNode> panelNodes) void
static int
void
ViewData.newSpectrum
(Lst<Spectrum> spectra) int
JSViewer.openDataOrFile
(Object data, String name, Lst<Spectrum> specs, String strUrl, int firstSpec, int lastSpec, boolean isAppend, String id) static boolean
Spectrum.process
(Lst<Spectrum> specs, Spectrum.IRMode irMode) int
JSViewer.selectPanel
(JSVPanel jsvp, Lst<PanelNode> panelNodes) int
Spectrum.setPeakList
(Lst<PeakInfo> list, String peakXLabel, String peakYLabel) Constructors in jspecview.common with parameters of type Lst -
Uses of Lst in jspecview.export
Fields in jspecview.export declared as LstModifier and TypeFieldDescriptionprotected Lst
<Coordinate> XMLExporter.newXYCoords
protected Lst
<Coordinate> XMLExporter.newXYCoords
Methods in jspecview.export with parameters of type Lst -
Uses of Lst in jspecview.java
Methods in jspecview.java with parameters of type LstModifier and TypeMethodDescriptionstatic AwtPanel
AwtPanel.getPanelMany
(JSViewer viewer, Lst<Spectrum> spectra) Constructs aJSVPanel
with List of spectra and corresponding start and end indices of data points that should be displayedvoid
AwtMainPanel.setSelectedPanel
(JSViewer viewer, JSVPanel jsvp, Lst<PanelNode> panelNodes) -
Uses of Lst in jspecview.js2d
Methods in jspecview.js2d with parameters of type LstModifier and TypeMethodDescriptionstatic JsPanel
JsPanel.getPanelMany
(JSViewer viewer, Lst<Spectrum> spectra) Constructs aJSVPanel
with List of spectra and corresponding start and end indices of data points that should be displayedvoid
JsMainPanel.setSelectedPanel
(JSViewer viewer, JSVPanel jsvp, Lst<PanelNode> panelNodes) -
Uses of Lst in jspecview.source
Fields in jspecview.source declared as LstMethods in jspecview.source that return LstModifier and TypeMethodDescriptionJDXHeader.getHeaderTable()
Returns the table of headersJDXSource.getSpectra()
Returns the Vector of SpectraMethods in jspecview.source with parameters of type Lst -
Uses of Lst in jspecview.tree
Methods in jspecview.tree with parameters of type Lst -
Uses of Lst in org.jmol.adapter.readers.cif
Fields in org.jmol.adapter.readers.cif declared as LstMethods in org.jmol.adapter.readers.cif with parameters of type LstModifier and TypeMethodDescriptionboolean
MSRdr.addLatticeVector
(Lst<float[]> lattvecs, String data) -
Uses of Lst in org.jmol.adapter.readers.pymol
Methods in org.jmol.adapter.readers.pymol that return LstModifier and TypeMethodDescriptionMethods in org.jmol.adapter.readers.pymol with parameters of type Lst -
Uses of Lst in org.jmol.adapter.readers.quantum
Fields in org.jmol.adapter.readers.quantum declared as LstModifier and TypeFieldDescriptionGamessReader.atomNames
MOReader.moTypes
BasisFunctionReader.orbitals
Lst
<int[]> BasisFunctionReader.shells
protected Lst
<SlaterData> BasisFunctionReader.slaters
protected Lst
<AdfReader.SymmetryData> AdfReader.vSymmetries
Methods in org.jmol.adapter.readers.quantum that return LstMethods in org.jmol.adapter.readers.quantum with parameters of type LstModifier and TypeMethodDescriptionprotected void
NBOParser.getAllStructures
(String output, Lst<Object> list) NBOParser.getStructureMap
(Lst<Object> structureList, String type, int index) Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structureint
NBOParser.getStructures
(String data, String nrtType, Lst<Object> list) Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.static void
NBOParser.getStructures46
(String[] tokens, String type, Lst<Object> structures, int nAtoms) Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.static void
GenNBOReader.setNboLabels
(String[] tokens, int nLabels, Lst<Map<String, Object>> orbitals, int nOrbitals0, String moType) -
Uses of Lst in org.jmol.adapter.readers.simple
Fields in org.jmol.adapter.readers.simple declared as Lst -
Uses of Lst in org.jmol.adapter.readers.xtal
Fields in org.jmol.adapter.readers.xtal declared as Lst -
Uses of Lst in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter declared as LstModifier and TypeFieldDescriptionAtomSetCollectionReader.lstNCS
Atom.tensors
AtomSetCollectionReader.trajectorySteps
Methods in org.jmol.adapter.smarter that return LstModifier and TypeMethodDescriptionAtomSetCollectionReader.getFortranFormatLengths
(String s) get all integers after letters negative entries are spaces (1Xn)Methods in org.jmol.adapter.smarter with parameters of type LstModifier and TypeMethodDescriptionboolean
MSInterface.addLatticeVector
(Lst<float[]> lattvecs, String substring) boolean
XtalSymmetry.FileSymmetry.addLatticeVectors
(Lst<float[]> lattvecs) void
AtomSetCollection.finalizeTrajectoryAs
(Lst<P3[]> trajectorySteps, Lst<V3[]> vibrationSteps) Constructors in org.jmol.adapter.smarter with parameters of type LstModifierConstructorDescriptionAtomSetCollection
(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, Lst<?> list) -
Uses of Lst in org.jmol.api
Methods in org.jmol.api that return LstModifier and TypeMethodDescriptionJmolAnnotationParser.catalogValidations
(Viewer vwr, SV validation, int[] modelAtomIndices, Map<String, int[]> valResMap, Map<String, Integer> map, Map<String, Integer> modelMap) SymmetryInterface.generateCrystalClass
(P3 pt0) JmolAnnotationParser.getAtomValidation
(Viewer vwr, String type, Atom atom) SymmetryInterface.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) SymmetryInterface.getLatticeCentering()
SymmetryInterface.getMoreInfo()
JmolScriptManager.getScriptItem
(boolean b, boolean startedByCommandThread) JmolScriptManager.getScriptQueue()
JmolNMRInterface.getTensorInfo
(String tensorType, String infoType, BS bs) JmolAdapterAtomIterator.getTensors()
JmolAnnotationParser.initializeAnnotation
(SV objAnn, int type, int modelIndex) JmolJDXMOLParser.readACDAssignments
(int nPoints, boolean isPeakAssignment) Methods in org.jmol.api that return types with arguments of type LstMethods in org.jmol.api with parameters of type LstModifier and TypeMethodDescriptionJmolScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) JmolPropertyManager.extractProperty
(Object property, Object args, int pt, Lst<Object> v2, boolean isCompiled) void
SymmetryInterface.getEquivPointList
(Lst<P3> pts, int nIgnore, String flags, M4[] opsCtr) SymmetryInterface.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) void
SmilesMatcherInterface.getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings) void
JmolNavigatorInterface.navigateList
(JmolScriptEvaluator eval, Lst<Object[]> list) int
JmolJDXMOLParser.setACDAssignments
(String model, String mytype, int peakCount, Lst<String[]> acdlist, String molFile) -
Uses of Lst in org.jmol.awtjs.swing
Fields in org.jmol.awtjs.swing declared as Lst -
Uses of Lst in org.jmol.dssx
Methods in org.jmol.dssx that return LstModifier and TypeMethodDescriptionAnnotationParser.catalogValidations
(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Returns a LstAnnotationParser.getAtomValidation
(Viewer vwr, String type, Atom atom) Get all validation values corresponding to a specific validation type.AnnotationParser.initializeAnnotation
(SV objAnn, int type, int modelIndex) We create a main list of mappings, where each mapping has _atoms and _pathMethods in org.jmol.dssx with parameters of type Lst -
Uses of Lst in org.jmol.export
Methods in org.jmol.export that return LstModifier and TypeMethodDescription___Exporter.getColorList
(int i00, short[] colixes, int nVertices, BS bsSelected, Map<Short, Integer> htColixes) input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color indexMethods in org.jmol.export with parameters of type LstModifier and TypeMethodDescriptionprotected int[]
__CartesianExporter.getNormalMap
(T3[] normals, int nNormals, BS bsValid, Lst<String> vNormals) protected void
_VrmlExporter.outputColors
(Lst<Short> colorList) protected void
_StlExporter.outputGeometry
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, BS bsPolygons, int faceVertexMax, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_VrmlExporter.outputGeometry
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, BS bsPolygons, int faceVertexMax, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_X3dExporter.outputGeometry
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, BS bsPolygons, int faceVertexMax, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_VrmlExporter.outputNormals
(Lst<String> vNormals) protected void
___Exporter.outputSurface
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_IdtfExporter.outputSurface
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_MayaExporter.outputSurface
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_PovrayExporter.outputSurface
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_TachyonExporter.outputSurface
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
_VrmlExporter.outputSurface
(T3[] vertices, T3[] normals, short[] colixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) protected void
JSExporter.outputSurface
(T3[] vertices, T3[] normals, short[] vertexColixes, int[][] indices, short[] polygonColixes, int nVertices, int nPolygons, int nTriangles, BS bsPolygons, int faceVertexMax, short colix, Lst<Short> colorList, Map<Short, Integer> htColixes, P3 offset) -
Uses of Lst in org.jmol.jsv
Methods in org.jmol.jsv that return LstModifier and TypeMethodDescriptionJDXMOLParser.readACDAssignments
(int nPoints, boolean isPeakAssignment) Methods in org.jmol.jsv with parameters of type Lst -
Uses of Lst in org.jmol.jvxl.data
Fields in org.jmol.jvxl.data declared as LstMethods in org.jmol.jvxl.data with parameters of type LstModifier and TypeMethodDescriptionstatic void
JvxlCoder.set3dContourVector
(Lst<Object> v, int[][] polygonIndexes, T3[] vertices) 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. -
Uses of Lst in org.jmol.jvxl.readers
Fields in org.jmol.jvxl.readers declared as LstMethods in org.jmol.jvxl.readers with parameters of type Lst -
Uses of Lst in org.jmol.minimize
Fields in org.jmol.minimize declared as Lst -
Uses of Lst in org.jmol.modelset
Fields in org.jmol.modelset declared as LstModifier and TypeFieldDescriptionMeasurementData.points
ModelSet.stateScripts
ModelSet.vibrationSteps
Fields in org.jmol.modelset with type parameters of type LstMethods in org.jmol.modelset that return LstModifier and TypeMethodDescriptionAtomCollection.generateCrystalClass
(int atomIndex, P3 pt) AtomCollection.getAllAtomTensors
(String type) AtomCollection.getAtomPointVector
(BS bs) ModelSet.getModulationList
(BS bs, char type, P3 t456) Methods in org.jmol.modelset with parameters of type LstModifier and TypeMethodDescriptionModelSet.addAtom
(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, byte specialAtomID, BS atomSymmetry, float bondRadius) ModelSet.addHydrogens
(Lst<Atom> vConnections, P3[] pts) these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEWvoid
ModelSet.calcRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds) These are not actual hydrogen bonds.P3[][]
AtomCollection.calculateHydrogens
(BS bs, int[] nTotal, Lst<Atom> vConnect, int flags) get a list of potential H atom positions based on elemental valence and formal chargestatic int
Measurement.find
(Lst<Measurement> measurements, Measurement m) P3[][]
ModelSet.getCenterAndPoints
(Lst<Object[]> vAtomSets, boolean addCenters) boolean
Atom.getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) Used by SMILES to get vector of cross-linksboolean
Group.getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) void
ModelSet.getPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) void
AtomCollection.setAtomTensors
(int atomIndex, Lst<Object> list) -
Uses of Lst in org.jmol.modelsetbio
Methods in org.jmol.modelsetbio that return LstModifier and TypeMethodDescriptionNucleicMonomer.getBasePairs()
BioModel.getBioBranches
(Lst<BS> biobranches) Methods in org.jmol.modelsetbio with parameters of type LstModifier and TypeMethodDescriptionprotected static int
NucleicPolymer.addHydrogenBond
(Lst<Bond> vAtoms, Atom atom1, Atom atom2) void
BioModelSet.calcAllRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int dsspVersion) only for base models, not trajectoriesvoid
AminoPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
BioPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
NucleicPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
BioModelSet.getAllPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) BioModel.getBioBranches
(Lst<BS> biobranches) protected boolean
Monomer.getCrossLinkGroup
(int i, Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck) boolean
Monomer.getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) boolean
NucleicMonomer.getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) int
BioPolymer.getPolymerPointsAndVectors
(int last, BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) Method parameters in org.jmol.modelsetbio with type arguments of type Lst -
Uses of Lst in org.jmol.multitouch
Methods in org.jmol.multitouch that return Lst -
Uses of Lst in org.jmol.popup
Fields in org.jmol.popup declared as Lst -
Uses of Lst in org.jmol.quantum
Methods in org.jmol.quantum that return Lst -
Uses of Lst in org.jmol.script
Fields in org.jmol.script declared as LstFields in org.jmol.script with type parameters of type LstMethods in org.jmol.script that return LstModifier and TypeMethodDescriptionT.getAtomPropertiesLike
(String type) SV.getList()
ScriptParam.getPointOrCenterVector
(T t) ScriptParam.getPointVector
(T t, int i) ScriptManager.getScriptItem
(boolean watching, boolean isByCommandWatcher) ScriptManager.getScriptQueue()
ScriptParam.listParameter
(int i, int nMin, int nMax) ScriptParam.listParameter4
(int i, int nMin, int nMax, boolean allowString) Methods in org.jmol.script that return types with arguments of type LstMethods in org.jmol.script with parameters of type LstModifier and TypeMethodDescriptionScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) Add hydrogens to a modelboolean
void
ScriptParam.getHklPlane
(T3 pt, float offset, Lst<P3> pts) ScriptEval.getUserFunctionResult
(String name, Lst<SV> params, SV tokenAtom) static SV
SV.getVariableList
(Lst<?> v) ScriptParam.hklParameter
(int i, Lst<P3> pts, boolean allowOffset) void
ScriptManager.runScriptFromThread
(Lst<Object> scriptItem) -
Uses of Lst in org.jmol.scriptext
Methods in org.jmol.scriptext that return LstMethods in org.jmol.scriptext with parameters of type LstModifier and TypeMethodDescriptionfloat
SmilesExt.getSmilesCorrelation
(BS bsA, BS bsB, String smiles, Lst<P3> ptsA, Lst<P3> ptsB, M4 m4, Lst<BS> vReturn, boolean asMap, int[][] mapSet, P3 center, boolean bestMap, int flags) The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality. -
Uses of Lst in org.jmol.shape
Fields in org.jmol.shape declared as LstModifier and TypeFieldDescriptionMeshCollection.displayWithinPoints
Mesh.lineData
final Lst
<Measurement> Measures.measurements
Methods in org.jmol.shape that return LstModifier and TypeMethodDescriptionMeshCollection.getMeshList
(String key, boolean justOne) Get matching list of meshes, order reversedMethods in org.jmol.shape with parameters of type LstModifier and TypeMethodDescriptionstatic boolean
Mesh.checkWithin
(T3 pti, Lst<P3> withinPoints, float withinDistance2, boolean isWithinNot) void
Mesh.setShowWithin
(Lst<P3> showWithinPoints, float showWithinDistance2, boolean isWithinNot) -
Uses of Lst in org.jmol.shapecgo
Fields in org.jmol.shapecgo declared as Lst -
Uses of Lst in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as Lst -
Uses of Lst in org.jmol.shapesurface
Methods in org.jmol.shapesurface that return LstMethods in org.jmol.shapesurface with parameters of type LstModifier and TypeMethodDescriptionstatic void
IsosurfaceMesh.addContourPoints
(Lst<Object> v, BS bsContour, int i, SB fData, T3[] vertices, float[] vertexValues, int iA, int iB, int iC, float value) static void
IsosurfaceMesh.setContourVector
(Lst<Object> v, int nPolygons, BS bsContour, float value, short colix, int color, SB fData) -
Uses of Lst in org.jmol.smiles
Methods in org.jmol.smiles with parameters of type LstModifier and TypeMethodDescriptionvoid
SmilesSearch.SmilesTarget.finalizeAromatic
(Lst<BS> lstAromatic) boolean
SmilesAtom.getCrossLinkVector
(Lst<Integer> vLinks, boolean crosslinkCovalent, boolean crosslinkHBond) void
SmilesMatcher.getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> ret, Lst<BS>[] vRings) called by ForceFieldMMFF.setAtomTypes only -
Uses of Lst in org.jmol.symmetry
Methods in org.jmol.symmetry that return LstModifier and TypeMethodDescriptionSymmetry.generateCrystalClass
(P3 pt00) Symmetry.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) Symmetry.getLatticeCentering()
SymmetryOperation.getLatticeCentering
(SymmetryOperation[] ops) Symmetry.getMoreInfo()
Methods in org.jmol.symmetry with parameters of type LstModifier and TypeMethodDescriptionboolean
SpaceGroup.addLatticeVectors
(Lst<float[]> lattvecs) void
Symmetry.getEquivPointList
(Lst<P3> pts, int nInitial, String flags, M4[] opsCtr) Symmetry.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) -
Uses of Lst in org.jmol.util
Fields in org.jmol.util declared as LstModifier and TypeFieldDescriptionprotected Lst
<org.jmol.util.BZone.BZPoint> BZone.newLatticePts
BZone.newPlanes
protected Lst
<org.jmol.util.BZone.Subzone> BZone.subzones
Methods in org.jmol.util that return LstModifier and TypeMethodDescriptionTriangulator.intersectPlane
(P4 plane, T3[] vertices, int flags) 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.Methods in org.jmol.util with parameters of type LstModifier and TypeMethodDescriptionstatic String
static BS
JmolMolecule.getBranchBitSet
(Node[] atoms, int atomIndex, BS bsToTest, Lst<BS> biobranches, int atomIndexNot, boolean allowCyclic, boolean allowBioResidue) 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.boolean
Node.getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) void
MeshSlicer.getIntersection
(float distance, P4 plane, P3[] ptCenters, Lst<P3[]> vData, float[] fData, BS bsSource, MeshSurface meshSurface, boolean andCap, boolean doClean, int tokType, boolean isGhost) static final JmolMolecule[]
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.ModulationSet.setMod
(String id, P3 r00, P3 r0, int d, Lst<Modulation> mods, M3 gammaE, Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate) A collection of modulations for a specific atom.void
MeshSurface.slabPolygonsList
(Lst<Object[]> slabInfo, boolean allowCap) -
Uses of Lst in org.jmol.viewer
Fields in org.jmol.viewer with type parameters of type LstMethods in org.jmol.viewer that return LstModifier and TypeMethodDescriptionPropertyManager.getAllAtomInfo
(BS bs) PropertyManager.getAllBondInfo
(Object bsOrArray) Viewer.getAtomValidation
(String type, Atom atom) PropertyManager.getMoleculeInfo
(Object atomExpression) Viewer.getStatusChanged
(String statusNameList) Lst
<?> Viewer.getSymmetryEquivPointList
(Lst<P3> pts, String flags) Viewer.getSymmetryEquivPoints
(P3 pt, String flags) Viewer.parseJSONArray
(String jsonArray) Methods in org.jmol.viewer that return types with arguments of type LstModifier and TypeMethodDescriptionPropertyManager.getAllChainInfo
(BS bs) Viewer.getStatusChanged
(String statusNameList) Viewer.getStatusChanged
(String statusNameList) Methods in org.jmol.viewer with parameters of type LstModifier and TypeMethodDescriptionViewer.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) PropertyManager.extractProperty
(Object prop, Object args, int ptr, Lst<Object> v2, boolean isCompiled) P3[]
Viewer.getAdditionalHydrogens
(BS bsAtoms, Lst<Atom> vConnections, int flags) P3[][]
Viewer.getCenterAndPoints
(Lst<Object[]> atomSets, boolean addCenter) static void
void
Viewer.getPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList) Lst
<?> Viewer.getSymmetryEquivPointList
(Lst<P3> pts, String flags) void
TransformManager.navigateList
(JmolScriptEvaluator eval, Lst<Object[]> list) Viewer.newMeasurementData
(String id, Lst<Object> points) boolean
Viewer.rotateAboutPointsInternal
(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, Lst<P3> finalPoints, float[] dihedralList, M4 m4, boolean useModelKit) void
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Uses of Lst in org.openscience.jvxl.simplewriter
Methods in org.openscience.jvxl.simplewriter with parameters of type LstModifier and TypeMethodDescriptionstatic String
ASimpleJvxlWriter.jvxlGetData
(VoxelDataCreator vdc, Parameters params, VolumeData volumeData, String[] title, Lst<P3> surfacePointsReturn, float[] areaVolumeReturn) Constructors in org.openscience.jvxl.simplewriter with parameters of type LstModifierConstructorDescriptionSimpleMarchingCubes
(VoxelDataCreator vdc, VolumeData volumeData, Parameters params, JvxlData jvxlData, Lst<P3> surfacePointsReturn, float[] areaVolumeReturn)