Uses of Class
javajs.util.P3
Packages that use P3
Package
Description
Provides Binary Space Partitioning Functionality to spacially
separate data structures in n-dimensions
Provides a software implementation of complete 3D graphics engine
for rendering molecules and associated shapes.
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
-
Uses of P3 in javajs.img
Methods in javajs.img that return P3Methods in javajs.img with parameters of type P3 -
Uses of P3 in javajs.util
Subclasses of P3 in javajs.utilModifier and TypeClassDescriptionclass
A 4 element axis angle represented by single precision floating point x,y,z,angle components.Methods in javajs.util that return P3Modifier and TypeMethodDescriptionstatic final P3
CU.colorPtFromInt
(int color, P3 pt) static final P3
CU.colorPtFromString
(String colorName) static P3[]
Measure.getBestLineThroughPoints
(P3[] points, int nPoints) Get the endpoints of the best line through N points, where N >= 2static P3[]
Measure.getCenterAndPoints
(Lst<P3> vPts) from a list of points, create an array that includes the center point as the first point.static P3
Calculate the intersection of a line with a plane.static P3[]
Measure.getProjectedLineSegment
(P3[] points, int nPoints, P3 ptA, V3 unitVector, V3 vTemp) static P3
P3.getUnlikely()
static P3
Convert HSL (hue/saturation/luninance) values to RGBstatic P3
P3.new3
(float x, float y, float z) static P3
P3.newA
(float[] a) static P3
static P3
Convert RGB values to HSL (hue/saturation/lightness)Methods in javajs.util that return types with arguments of type P3Modifier and TypeMethodDescriptionMeasure.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 P3Modifier and TypeMethodDescriptionstatic void
Measure.calcAveragePoint
(P3 pointA, P3 pointB, P3 pointC) static void
Measure.calcAveragePointN
(P3[] points, int nPoints, P3 averagePoint) static void
Measure.calcBestAxisThroughPoints
(P3[] points, int nPoints, P3 axisA, V3 axisUnitVector, V3 vectorProjection, int nTriesMax) static float
Measure.calcBestPlaneThroughPoints
(P3[] points, int nPoints, P4 plane) 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.static float
Measure.calcPlaneForMode
(P3[] points, int nPoints, P4 plane, char mode) 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.static Quat
Measure.calculateQuaternionRotation
(P3[][] centerAndPoints, float[] retStddev) Closed-form solution of absolute orientation requiring 1:1 mapping of positions.static final P3
CU.colorPtFromInt
(int color, P3 pt) static T3[]
Measure.computeHelicalAxis
(P3 a, P3 b, Quat dq) This method calculates measures relating to two points in space with related quaternion frame difference.static float
Measure.directedDistanceToPlane
(P3 pt, P4 plane, P3 ptref) static float
Measure.distanceToPlaneD
(P4 plane, float d, P3 pt) static float
Measure.distanceToPlaneV
(V3 norm, float w, P3 pt) static float
static P3[]
Measure.getBestLineThroughPoints
(P3[] points, int nPoints) Get the endpoints of the best line through N points, where N >= 2static void
static P3
Calculate the intersection of a line with a plane.static boolean
Measure.getNormalFromCenter
(P3 ptCenter, P3 ptA, P3 ptB, P3 ptC, boolean isOutward, V3 normal, V3 vTemp) static void
Measure.getNormalToLine
(P3 pointA, P3 pointB, V3 vNormNorm) Measure.getPointsOnPlane
(P3[] pts, P4 plane) Based on a set of centering points, returns the list of points on a given plane.static P3[]
Measure.getProjectedLineSegment
(P3[] points, int nPoints, P3 ptA, V3 unitVector, V3 vTemp) static final Quat
Quat.getQuaternionFrame
(P3 center, T3 x, T3 xy) returns a quaternion frame based on three points (center, x, and any point in xy plane) or two vectors (vA, vB).static float
static float
Fills a 4x4 matrix with rotation-translation of mapped points A to B.static P3
Convert HSL (hue/saturation/luninance) values to RGBstatic boolean
Measure.isInTetrahedron
(P3 pt, P3 ptA, P3 ptB, P3 ptC, P3 ptD, P4 plane, V3 vTemp, V3 vTemp2, boolean fullyEnclosed) static boolean
static float
Measure.projectOntoAxis
(P3 pt, P3 ptA, V3 axisUnitVector, V3 vectorProjection) 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 vectorProjectionstatic P3
Convert RGB values to HSL (hue/saturation/lightness)Measure.transformPoints
(Lst<P3> vPts, M4 m4, P3 center) Method parameters in javajs.util with type arguments of type P3Modifier 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.Measure.transformPoints
(Lst<P3> vPts, M4 m4, P3 center) -
Uses of P3 in jspecview.java
Methods in jspecview.java with parameters of type P3Modifier and TypeMethodDescriptionvoid
AwtPlatform.convertPointFromScreen
(Object display, P3 ptTemp) -
Uses of P3 in jspecview.js2d
Methods in jspecview.js2d with parameters of type P3Modifier and TypeMethodDescriptionvoid
JsPlatform.convertPointFromScreen
(Object canvas, P3 ptTemp) -
Uses of P3 in org.jmol.adapter.readers.cif
Methods in org.jmol.adapter.readers.cif with parameters of type P3 -
Uses of P3 in org.jmol.adapter.smarter
Subclasses of P3 in org.jmol.adapter.smarterFields in org.jmol.adapter.smarter declared as P3Modifier and TypeFieldDescriptionprotected P3
AtomSetCollectionReader.fileOffset
protected P3
AtomSetCollectionReader.fileScaling
protected P3
AtomSetCollectionReader.ptSupercell
protected P3
AtomSetCollectionReader.unitCellOffset
Methods in org.jmol.adapter.smarter with parameters of type P3Modifier and TypeMethodDescriptionboolean
XtalSymmetry.FileSymmetry.checkDistance
(P3 f1, P3 f2, float distance, float dx, int iRange, int jRange, int kRange, P3 ptOffset) protected int
AtomSetCollectionReader.cloneLastAtomSet
(int ac, P3[] pts) int
AtomSetCollection.cloneLastAtomSetFromPoints
(int ac, P3[] pts) Atom.copyTo
(P3 pt, AtomSetCollection asc) void
AtomSetCollectionReader.fixFloatPt
(P3 pt, float prec) boolean
XtalSymmetry.isWithinCell
(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop) boolean
XtalSymmetry.removePacking
(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop) void
MSInterface.setMinMax0
(P3 minXYZ0, P3 maxXYZ0) void
XtalSymmetry.FileSymmetry.twelfthify
(P3 pt) -
Uses of P3 in org.jmol.api
Methods in org.jmol.api that return P3Modifier and TypeMethodDescriptionabstract P3
JmolViewer.getBoundBoxCenter()
P3[]
SymmetryInterface.getCanonicalCopy
(float scale, boolean withOffset) SymmetryInterface.getCartesianOffset()
P3[]
JmolAnnotationParser.getDSSRFrame
(Map<String, Object> dssrNT) SymmetryInterface.getFractionalOffset()
SymmetryInterface.getFractionalOrigin()
P3[]
JmolEnvCalc.getPoints()
AtomIndexIterator.getPosition()
P3[]
SymmetryInterface.getUnitCellVectors()
P3[]
SymmetryInterface.getUnitCellVerticesNoOffset()
JmolAdapterAtomIterator.getXYZ()
SymmetryInterface.toSupercell
(P3 fpt) Methods in org.jmol.api that return types with arguments of type P3Modifier and TypeMethodDescriptionSymmetryInterface.generateCrystalClass
(P3 pt0) SymmetryInterface.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) SymmetryInterface.getLatticeCentering()
Methods in org.jmol.api with parameters of type P3Modifier and TypeMethodDescriptionJmolScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) boolean
SymmetryInterface.checkPeriodic
(P3 pt) void
GenericPlatform.convertPointFromScreen
(Object display, P3 ptTemp) void
JmolRendererInterface.drawBond
(P3 atomA, P3 atomB, short colixA, short colixB, byte endcaps, short mad, int bondOrder) void
JmolRendererInterface.drawDashedLineBits
(int run, int rise, P3 screenA, P3 screenB) boolean
JmolRendererInterface.drawEllipse
(P3 ptAtom, P3 ptX, P3 ptY, boolean fillArc, boolean wireframeOnly) void
JmolRendererInterface.drawHermite4
(int tension, P3 s0, P3 s1, P3 s2, P3 s3) void
JmolRendererInterface.drawHermite7
(boolean fill, boolean border, int tension, P3 s0, P3 s1, P3 s2, P3 s3, P3 s4, P3 s5, P3 s6, P3 s7, int aspectRatio, short colixBack) void
JmolRendererInterface.drawLineAB
(P3 pointA, P3 pointB) void
JmolRendererInterface.drawLineBits
(short colixA, short colixB, P3 pointA, P3 pointB) void
JmolRendererInterface.fillConeScreen3f
(byte endcap, int screenDiameter, P3 screenBase, P3 screenTip, boolean isBarb) void
JmolRendererInterface.fillCylinderBits
(byte endcaps, int diameter, P3 screenA, P3 screenB) void
JmolRendererInterface.fillCylinderBits2
(short colixA, short colixB, byte endcaps, int diameter, P3 screenA, P3 screenB) void
JmolRendererInterface.fillCylinderScreen3I
(byte endcaps, int diameter, P3 s0f, P3 s1f, P3 pt0f, P3 pt1f, float radius) void
JmolRendererInterface.fillEllipsoid
(P3 center, P3[] points, int x, int y, int z, int diameter, M3 mToEllipsoidal, double[] coef, M4 mDeriv, int selectedOctant, P3[] octantPoints) void
JmolRendererInterface.fillHermite
(int tension, int diameterBeg, int diameterMid, int diameterEnd, P3 s0, P3 s1, P3 s2, P3 s3) void
JmolRendererInterface.fillQuadrilateral
(P3 screenA, P3 screenB, P3 screenC, P3 screenD, boolean isSolid) void
JmolRendererInterface.fillSphereBits
(int diameter, P3 center) fills a solid spherevoid
JmolRendererInterface.fillTriangle3CNBits
(P3 pA, short colixA, short nA, P3 pB, short colixB, short nB, P3 pC, short colixC, short nC, boolean twoSided) void
JmolRendererInterface.fillTriangle3f
(P3 screenA, P3 screenB, P3 screenC, boolean setNoisy) void
JmolRendererInterface.fillTriangle3i
(P3 screenA, P3 screenB, P3 screenC, T3 ptA, T3 ptB, T3 ptC, boolean doShade) void
JmolRendererInterface.fillTriangleTwoSided
(short normix, P3 a, P3 b, P3 c) SymmetryInterface.generateCrystalClass
(P3 pt0) float
SymmetryInterface.getCellWeight
(P3 pt) SymmetryInterface.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) int[]
SymmetryInterface.getInvariantSymops
(P3 p3, int[] v0) int
SymmetryInterface.getSiteMultiplicity
(P3 a) SymmetryInterface.getSymmetryInfoAtom
(ModelSet ms, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] oplist) SymmetryInterface.getTransform
(P3 fracA, P3 fracB, boolean debug) SymmetryInterface.getWyckoffPosition
(Viewer vwr, P3 pt, String letter) boolean
SymmetryInterface.isWithinUnitCell
(P3 pt, float x, float y, float z) void
SymmetryInterface.newSpaceGroupPoint
(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint) SmilesMatcherInterface.polyhedronToSmiles
(Node center, int[][] faces, int atomCount, P3[] points, int flags, String details) void
JmolRendererInterface.renderCrossHairs
(int[] minMax, int screenWidth, int screenHeight, P3 navigationOffset, float navigationDepthPercent) V3[]
SymmetryInterface.rotateAxes
(int iop, V3[] axes, P3 ptTemp, M3 mTemp) void
SymmetryInterface.setFinalOperations
(int dim, String name, P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, String filterSymop) SymmetryInterface.staticToRationalXYZ
(P3 fPt, String sep) SymmetryInterface.toSupercell
(P3 fpt) Method parameters in org.jmol.api with type arguments of type P3 -
Uses of P3 in org.jmol.atomdata
Fields in org.jmol.atomdata declared as P3 -
Uses of P3 in org.jmol.awt
Methods in org.jmol.awt with parameters of type P3Modifier and TypeMethodDescriptionvoid
Platform.convertPointFromScreen
(Object display, P3 ptTemp) -
Uses of P3 in org.jmol.awtjs2d
Methods in org.jmol.awtjs2d with parameters of type P3 -
Uses of P3 in org.jmol.bspt
Methods in org.jmol.bspt with parameters of type P3Modifier and TypeMethodDescriptionvoid
void
Bspf.initialize
(int modelIndex, P3[] atoms, BS modelAtomBitSet) static int
PointIterator.withinDistPoints
(float distance, P3 pt, P3[] ap3, P3[] ap31, BS bsSelected, Object[] ret) carry out various functions of the within() script function -
Uses of P3 in org.jmol.dssx
Methods in org.jmol.dssx that return P3Modifier and TypeMethodDescriptionP3[]
AnnotationParser.getDSSRFrame
(Map<String, Object> dssrNT) P3[]
DSSR1.getDSSRFrame
(Map<String, Object> nt) -
Uses of P3 in org.jmol.export
Fields in org.jmol.export declared as P3Modifier and TypeFieldDescriptionprotected P3
___Exporter.cameraPosition
protected final P3
___Exporter.center
protected P3
___Exporter.fixedRotationCenter
protected P3
___Exporter.referenceCenter
protected final P3
___Exporter.tempP1
protected final P3
___Exporter.tempP2
protected final P3
___Exporter.tempP3
protected P3
_VrmlExporter.tempQ1
protected P3
_VrmlExporter.tempQ2
protected P3
_VrmlExporter.tempQ3
Methods in org.jmol.export that return P3Modifier and TypeMethodDescriptionprotected P3
__CartesianExporter.getCameraPosition()
protected P3
__CartesianExporter.getModelCenter()
Methods in org.jmol.export with parameters of type P3Modifier and TypeMethodDescriptionvoid
Export3D.drawBond
(P3 atomA, P3 atomB, short colixA, short colixB, byte endcaps, short mad, int bondOrder) void
Export3D.drawDashedLineBits
(int run, int rise, P3 pointA, P3 pointB) boolean
Export3D.drawEllipse
(P3 ptAtom, P3 ptX, P3 ptY, boolean fillArc, boolean wireframeOnly) void
Export3D.drawHermite4
(int tension, P3 s0, P3 s1, P3 s2, P3 s3) void
Export3D.drawHermite7
(boolean fill, boolean border, int tension, P3 s0, P3 s1, P3 s2, P3 s3, P3 s4, P3 s5, P3 s6, P3 s7, int aspectRatio, short colixBack) void
Export3D.drawLineAB
(P3 pointA, P3 pointB) void
Export3D.drawLineBits
(short colixA, short colixB, P3 pointA, P3 pointB) void
Export3D.drawLineBits
(P3 screenA, P3 screenB, short colixA, short colixB) void
Export3D.fillConeScreen3f
(byte endcap, int screenDiameter, P3 pointBase, P3 screenTip, boolean isBarb) protected void
_TachyonExporter.fillConicalCylinder
(P3 screenA, P3 screenB, int madBond, short colix, byte endcaps) void
Export3D.fillCylinderBits
(byte endcaps, int diameter, P3 pointA, P3 pointB) void
Export3D.fillCylinderBits2
(short colixA, short colixB, byte endcaps, int mad, P3 screenA, P3 screenB) void
Export3D.fillCylinderScreen3I
(byte endcaps, int diameter, P3 pointA, P3 pointB, P3 pt0f, P3 pt1f, float radius) void
Export3D.fillEllipsoid
(P3 center, P3[] points, int x, int y, int z, int diameter, M3 mToEllipsoidal, double[] coef, M4 mDeriv, int selectedOctant, P3[] octantPoints) void
Export3D.fillHermite
(int tension, int diameterBeg, int diameterMid, int diameterEnd, P3 s0, P3 s1, P3 s2, P3 s3) void
Export3D.fillQuadrilateral
(P3 pointA, P3 pointB, P3 pointC, P3 pointD, boolean isSolid) void
Export3D.fillSphereBits
(int diameter, P3 center) fills a solid spherevoid
Export3D.fillTriangle3CNBits
(P3 pA, short colixA, short nA, P3 pB, short colixB, short nB, P3 pC, short colixC, short nC, boolean twoSided) void
Export3D.fillTriangle3f
(P3 pointA, P3 pointB, P3 pointC, boolean setNoisy) void
Export3D.fillTriangle3i
(P3 screenA, P3 screenB, P3 screenC, T3 ptA0, T3 ptB0, T3 ptC0, boolean doShade) void
Export3D.fillTriangleTwoSided
(short normix, P3 a, P3 b, P3 c) protected static MeshSurface
___Exporter.getConeMesh
(P3 centerBase, M3 matRotateScale, short colix) protected M3
___Exporter.getRotationMatrix
(P3 pt1, P3 pt2, float radius) protected M3
___Exporter.getRotationMatrix
(P3 pt1, P3 ptZ, float radius, P3 ptX, P3 ptY) protected abstract void
__CartesianExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
_IdtfExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
_MayaExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
_ObjExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
_StlExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
_VrmlExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
_X3dExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected void
JSExporter.outputCircle
(P3 pt1, P3 pt2, float radius, short colix, boolean doFill) protected abstract void
__CartesianExporter.outputCone
(P3 ptBase, P3 ptTip, float radius, short colix) protected void
_IdtfExporter.outputCone
(P3 ptBase, P3 ptTip, float radius, short colix) protected void
_MayaExporter.outputCone
(P3 ptBase, P3 ptTip, float radius, short colix) protected void
_ObjExporter.outputCone
(P3 ptBase, P3 ptTip, float radius, short colix) protected void
_PovrayExporter.outputCone
(P3 screenBase, P3 screenTip, float radius, short colix, boolean isBarb) protected void
_TachyonExporter.outputCone
(P3 screenBase, P3 screenTip, float radius, short colix, boolean isBarb) protected void
_VrmlExporter.outputCone
(P3 ptBase, P3 ptTip, float radius, short colix) protected void
JSExporter.outputCone
(P3 ptBase, P3 ptTip, float radius, short colix) protected abstract boolean
__CartesianExporter.outputCylinder
(P3 ptCenter, P3 pt1, P3 pt2, short colix1, byte endcaps, float radius, P3 ptX, P3 ptY, boolean checkRadius) protected boolean
_IdtfExporter.outputCylinder
(P3 ptCenter, P3 pt1, P3 pt2, short colix, byte endcaps, float radius, P3 ptX, P3 ptY, boolean checkRadius) protected boolean
_MayaExporter.outputCylinder
(P3 ptCenter, P3 pt1, P3 pt2, short colix, byte endcaps, float radius, P3 ptX, P3 ptY, boolean checkRadius) protected boolean
_ObjExporter.outputCylinder
(P3 ptCenter, P3 pt1, P3 pt2, short colix, byte endcaps, float radius, P3 ptX, P3 ptY, boolean checkRadius) protected void
_PovrayExporter.outputCylinder
(P3 screenA, P3 screenB, float radius, short colix, boolean withCaps) protected void
_TachyonExporter.outputCylinder
(P3 screenA, P3 screenB, float radius, short colix, boolean withCaps) protected boolean
_VrmlExporter.outputCylinder
(P3 ptCenter, P3 pt1, P3 pt2, short colix, byte endcaps, float radius, P3 ptX, P3 ptY, boolean checkRadius) protected boolean
JSExporter.outputCylinder
(P3 ptCenter, P3 pt1, P3 pt2, short colix, byte endcaps, float radius, P3 ptX, P3 ptY, boolean checkRadius) protected void
_PovrayExporter.outputCylinderConical
(P3 screenA, P3 screenB, float radius1, float radius2, short colix) protected void
_TachyonExporter.outputCylinderConical
(P3 screenA, P3 screenB, float radius1, float radius2, short colix) protected abstract void
__CartesianExporter.outputEllipsoid
(P3 center, P3[] points, short colix) protected void
_IdtfExporter.outputEllipsoid
(P3 center, P3[] points, short colix) protected void
_MayaExporter.outputEllipsoid
(P3 center, P3[] points, short colix) protected void
_ObjExporter.outputEllipsoid
(P3 center, P3[] points, short colix) protected void
_PovrayExporter.outputEllipsoid
(P3 center, float radius, double[] coef, short colix) protected void
_TachyonExporter.outputEllipsoid
(P3 center, float radius, double[] coef, short colix) protected void
_VrmlExporter.outputEllipsoid
(P3 ptCenter, P3[] points, short colix) protected void
JSExporter.outputEllipsoid
(P3 center, P3[] points, short colix) 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.outputQuaternionFrame
(P3 ptCenter, P3 ptX, P3 ptY, P3 ptZ, float xScale, float yScale, float zScale) protected void
__CartesianExporter.outputSolidPlate
(P3 tempP1, P3 tempP2, P3 tempP3, short colix) protected void
_VrmlExporter.outputSolidPlate
(P3 tempP1, P3 tempP2, P3 tempP3, short colix) protected abstract void
__CartesianExporter.outputSphere
(P3 ptCenter, float f, short colix, boolean checkRadius) protected void
_IdtfExporter.outputSphere
(P3 center, float radius, short colix, boolean checkRadius) protected void
_MayaExporter.outputSphere
(P3 pt, float radius, short colix, boolean checkRadius) protected void
_ObjExporter.outputSphere
(P3 center, float radius, short colix, boolean checkRadius) protected void
_VrmlExporter.outputSphere
(P3 ptCenter, float radius, short colix, boolean checkRadius) protected void
JSExporter.outputSphere
(P3 ptCenter, float radius, short colix, boolean checkRadius) 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) protected abstract void
__CartesianExporter.outputTextPixel
(P3 pt, int argb) protected void
_IdtfExporter.outputTextPixel
(P3 pt, int argb) protected void
_MayaExporter.outputTextPixel
(P3 pt, int argb) protected void
_ObjExporter.outputTextPixel
(P3 pt, int argb) protected void
_VrmlExporter.outputTextPixel
(P3 pt, int argb) protected void
_X3dExporter.outputTextPixel
(P3 pt, int argb) protected void
JSExporter.outputTextPixel
(P3 pt, int argb) protected void
_VrmlExporter.outputTransRot
(P3 pt1, P3 pt2, int x, int y, int z) void
Export3D.renderCrossHairs
(int[] minMax, int screenWidth, int screenHeight, P3 navigationOffset, float navigationDepthPercent) -
Uses of P3 in org.jmol.g3d
Methods in org.jmol.g3d with parameters of type P3Modifier and TypeMethodDescriptionvoid
Graphics3D.drawBond
(P3 atomA, P3 atomB, short colixA, short colixB, byte endcaps, short mad, int bondOrder) void
Graphics3D.drawDashedLineBits
(int run, int rise, P3 pointA, P3 pointB) boolean
Graphics3D.drawEllipse
(P3 ptAtom, P3 ptX, P3 ptY, boolean fillArc, boolean wireframeOnly) void
Graphics3D.drawHermite4
(int tension, P3 s0, P3 s1, P3 s2, P3 s3) void
Graphics3D.drawHermite7
(boolean fill, boolean border, int tension, P3 s0, P3 s1, P3 s2, P3 s3, P3 s4, P3 s5, P3 s6, P3 s7, int aspectRatio, short colixBack) void
Graphics3D.drawLineAB
(P3 pointA, P3 pointB) void
Graphics3D.drawLineBits
(short colixA, short colixB, P3 pointA, P3 pointB) void
Graphics3D.fillConeScreen3f
(byte endcap, int screenDiameter, P3 screenBase, P3 screenTip, boolean isBarb) void
Graphics3D.fillCylinderBits
(byte endcaps, int diameter, P3 screenA, P3 screenB) void
Graphics3D.fillCylinderBits2
(short colixA, short colixB, byte endcaps, int diameter, P3 screenA, P3 screenB) void
Graphics3D.fillCylinderScreen3I
(byte endcaps, int diameter, P3 screenA, P3 screenB, P3 pt0f, P3 pt1f, float radius) void
Graphics3D.fillEllipsoid
(P3 center, P3[] points, int x, int y, int z, int diameter, M3 mToEllipsoidal, double[] coef, M4 mDeriv, int selectedOctant, P3[] octantPoints) void
Graphics3D.fillHermite
(int tension, int diameterBeg, int diameterMid, int diameterEnd, P3 s0, P3 s1, P3 s2, P3 s3) void
Graphics3D.fillQuadrilateral
(P3 screenA, P3 screenB, P3 screenC, P3 screenD, boolean isSolid) void
Graphics3D.fillSphereBits
(int diameter, P3 center) fills a solid spherevoid
Graphics3D.fillTriangle3CNBits
(P3 screenA, short colixA, short normixA, P3 screenB, short colixB, short normixB, P3 screenC, short colixC, short normixC, boolean twoSided) void
Graphics3D.fillTriangle3f
(P3 screenA, P3 screenB, P3 screenC, boolean isSolid) void
Graphics3D.fillTriangle3i
(P3 screenA, P3 screenB, P3 screenC, T3 ptA, T3 ptB, T3 ptC, boolean doShade) void
Graphics3D.fillTriangleTwoSided
(short normix, P3 screenA, P3 screenB, P3 screenC) void
Graphics3D.renderCrossHairs
(int[] minMax, int screenWidth, int screenHeight, P3 navOffset, float navDepth) void
HermiteRenderer.renderHermiteRibbon
(boolean fill, boolean border, int tension, P3 p0, P3 p1, P3 p2, P3 p3, P3 p4, P3 p5, P3 p6, P3 p7, int aspectRatio, int fillType) void
HermiteRenderer.renderHermiteRope
(boolean fill, int tension, int diameterBeg, int diameterMid, int diameterEnd, P3 p0, P3 p1, P3 p2, P3 p3) -
Uses of P3 in org.jmol.geodesic
Methods in org.jmol.geodesic that return P3 -
Uses of P3 in org.jmol.jvxl.api
Methods in org.jmol.jvxl.api that return P3Modifier and TypeMethodDescriptionP3[]
MeshDataServer.calculateGeodesicSurface
(BS bsSelected, float envelopeRadius) -
Uses of P3 in org.jmol.jvxl.calc
Fields in org.jmol.jvxl.calc declared as P3Modifier and TypeFieldDescriptionprotected final P3
MarchingCubes.pointA
protected final P3
MarchingCubes.pt0
Methods in org.jmol.jvxl.calc with parameters of type P3Modifier and TypeMethodDescriptionint
MarchingSquares.addContourVertex
(P3 vertexXYZ, float value) void
MarchingCubes.calcVertexPoint
(int x, int y, int z, int vertex, P3 pt) -
Uses of P3 in org.jmol.jvxl.data
Fields in org.jmol.jvxl.data declared as P3Modifier and TypeFieldDescriptionP3[]
JvxlData.boundingBox
JvxlData.fixedLattice
JvxlData.mapLattice
final P3
VolumeData.volumetricOrigin
Methods in org.jmol.jvxl.data with parameters of type P3Modifier and TypeMethodDescriptionfloat
VolumeData.calculateFractionalPoint
(float cutoff, P3 pointA, P3 pointB, float valueA, float valueB, P3 pt) void
void
JvxlData.setSurfaceInfo
(P4 thePlane, P3 mapLattice, int nSurfaceInts, String surfaceData) void
JvxlData.setSurfaceInfoFromBitSetPts
(BS bs, P4 thePlane, P3 mapLattice) -
Uses of P3 in org.jmol.jvxl.readers
Fields in org.jmol.jvxl.readers declared as P3Modifier and TypeFieldDescriptionP3[]
Parameters.boundingBox
protected P3[]
VolumeFileReader.boundingBox
protected P3[]
VolumeFileReader.boundingBox
protected P3[]
VolumeFileReader.boundingBox
protected P3
SurfaceReader.center
Parameters.mapLattice
Parameters.origin
Parameters.points
P3[]
Parameters.probes
protected final P3
SurfaceReader.ptTemp
Parameters.steps
protected P3
SurfaceReader.volumetricOrigin
protected P3
SurfaceReader.xyzMax
protected P3
SurfaceReader.xyzMin
Methods in org.jmol.jvxl.readers that return P3Modifier and TypeMethodDescriptionXmlReader.getXmlPoint
(String data, String key) P3[]
JvxlXmlReader.jvxlDecodeVertexData
(String data, boolean asArray) decode vertex data found withinelement as created by jvxlEncodeVertexData (see above) -
Uses of P3 in org.jmol.modelkit
Methods in org.jmol.modelkit with parameters of type P3Modifier and TypeMethodDescriptionint
ModelKit.checkMovedAtoms
(BS bsFixed, BS bsAtoms, P3[] apos0) Something has changed atom positions.void
ModelKit.clickAssignAtom
(int atomIndex, String element, P3 ptNew) From Mouse or handleAtomOrBondBickedint
MODELKIT ADD @3 ...void
ModelKit.cmdAssignAtom
(BS bs, P3 pt, String type, String cmd) A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom via MODELKIT ASSIGN ATOMint
ModelKit.cmdAssignMoveAtoms
(BS bsSelected, int iatom, P3 p, P3[] pts, boolean allowProjection, boolean isMolecule) int
ModelKit.cmdRotateAtoms
(BS bsAtoms, P3[] points, float endDegrees) int
ModelKit.moveMinConstrained
(int iatom, P3 p, BS bsAtoms) -
Uses of P3 in org.jmol.modelset
Subclasses of P3 in org.jmol.modelsetFields in org.jmol.modelset declared as P3Modifier and TypeFieldDescriptionText.pointerPt
TickInfo.reference
Measurement.renderArc
TickInfo.scale
TickInfo.ticks
P3[]
ModelSet.translations
Text.xyz
Methods in org.jmol.modelset that return P3Modifier and TypeMethodDescriptionP3[][]
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 chargeP3[]
AtomCollection.calculateSurface
(BS bsSelected, float envelopeRadius) ModelSet.getAtomSetCenter
(BS bs) ModelSet.getAverageAtomPoint()
ModelSet.getBoundBoxCenter
(int modelIndex) P3[][]
ModelSet.getCenterAndPoints
(Lst<Object[]> vAtomSets, boolean addCenters) Atom.getFractionalCoordPt
(boolean fixJavaFloat, boolean ignoreOffset, P3 pt) P3[]
ModelSet.getFrameOffsets
(BS bsAtoms, boolean isFull) AtomIteratorWithinModel.getPosition()
ModelSet.getTranslation
(int iModel) Atom.getXYZ()
P3[]
ModelSet.saveAtomPositions()
Methods in org.jmol.modelset that return types with arguments of type P3Modifier and TypeMethodDescriptionAtomCollection.generateCrystalClass
(int atomIndex, P3 pt) AtomCollection.getAtomPointVector
(BS bs) Methods in org.jmol.modelset with parameters of type P3Modifier 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 NEWfloat
Atom.atomPropertyFloat
(Viewer vwr, int tokWhat, P3 ptTemp) called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()Atom.atomPropertyTuple
(Viewer vwr, int tok, P3 ptTemp) float
ModelSet.calcRotationRadius
(int modelIndex, P3 center, boolean useBoundBox) LabelToken.formatLabel
(Viewer vwr, Atom atom, String strFormat, P3 ptTemp) static String
LabelToken.formatLabelAtomArray
(Viewer vwr, Atom atom, LabelToken[] tokens, char chAtom, int[] indices, P3 ptTemp) returns a formatted string based on the precompiled label tokensstatic String
LabelToken.formatLabelBond
(Viewer vwr, Bond bond, LabelToken[] tokens, Map<String, Object> values, int[] indices, P3 ptTemp) AtomCollection.generateCrystalClass
(int atomIndex, P3 pt) void
AtomCollection.getAtomIdentityInfo
(int i, Map<String, Object> info, P3 ptTemp) AtomCollection.getAtomInfo
(int i, String format, P3 ptTemp) ModelSet.getBoundBoxOrientation
(int type, BS bsAtoms, P3[] points) void
Trajectory.getFractional
(Atom a, P3 ptTemp) Atom.getFractionalCoordPt
(boolean fixJavaFloat, boolean ignoreOffset, P3 pt) Group.getGroupInfo
(int igroup, P3 ptTemp) Atom.getIdentityXYZ
(P3 pt, int mode) ModelSet.getModulationList
(BS bs, char type, P3 t456) ModelSet.getPointGroupAsString
(BS bsAtoms, String type, int index, float scale, P3[] pts, P3 center, String id) void
ModelSet.getPointTransf
(int i, Atom a, Quat q, P3 pTemp) pick up the appropriate value for this atomvoid
Text.getPymolScreenOffset
(P3 atomPt, P3i screen, int zSlab, P3 pTemp, double sppm) PyMOL will use 1 here for pymolOffset[0] for relative, 0 or absolute.ModelSet.getUnitCellPointsWithin
(float distance, BS bs, P3 pt, boolean asMap) void
ModelSet.invertSelected
(P3 pt, P4 plane, int iAtom, BS bsAtoms) Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.void
ModelSet.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs, P3 center, boolean isInternal, boolean translationOnly) void
ModelSet.restoreAtomPositions
(P3[] apos0) Atom.setAtom
(int modelIndex, int atomIndex, P3 xyz, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero) void
Atom.setFractionalCoordPt
(P3 pt, P3 ptNew, boolean asAbsolute) void
ModelSet.setModulation
(BS bs, boolean isOn, P3 qtOffset, boolean isQ) Sets the modulation for all atoms in bs.void
Constructors in org.jmol.modelset with parameters of type P3 -
Uses of P3 in org.jmol.modelsetbio
Fields in org.jmol.modelsetbio declared as P3Modifier and TypeFieldDescriptionprotected P3
ProteinStructure.axisA
protected P3
ProteinStructure.axisB
protected P3[]
BioPolymer.controlPoints
P3[]
NucleicMonomer.dssrBox
P3[]
NucleicMonomer.dssrFrame
protected P3[]
BioPolymer.leadMidpoints
protected P3[]
BioPolymer.leadPoints
protected P3
AlphaMonomer.nitrogenHydrogenPoint
Methods in org.jmol.modelsetbio that return P3Modifier and TypeMethodDescriptionfinal P3
AlphaMonomer.getAtomPoint
(byte specialAtomID) ProteinStructure.getAxisEndPoint()
ProteinStructure.getAxisStartPoint()
protected P3
AlphaPolymer.getControlPoint
(int i, V3 v) protected P3
BioPolymer.getControlPoint
(int i, V3 v) P3[]
BioPolymer.getControlPoints
(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate) P3[]
NucleicMonomer.getDSSRFrame
(Viewer vwr) P3[]
BioPolymer.getLeadMidpoints()
protected P3
AlphaMonomer.getQuaternionFrameCenterAlpha
(char qType) P3[]
ProteinStructure.getSegments()
protected final P3
Monomer.getSpecialAtomPoint
(byte[] interestingIDs, byte specialAtomID) Methods in org.jmol.modelsetbio with parameters of type P3Modifier and TypeMethodDescriptionvoid
NucleicMonomer.getBaseRing6Points
(P3[] pts) boolean
NucleicMonomer.getEdgePoints
(P3[] pts) boolean
AminoMonomer.getNHPoint
(P3 aminoHydrogenPoint, V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens) void
NucleicMonomer.getRiboseRing5Points
(P3[] pts) boolean
NucleicMonomer.maybeGetBaseRing5Points
(P3[] pts) void
-
Uses of P3 in org.jmol.multitouch
Fields in org.jmol.multitouch declared as P3Methods in org.jmol.multitouch with parameters of type P3Modifier and TypeMethodDescriptionvoid
ActionManagerMT.processMultitouchEvent
(int groupID, int eventType, int touchID, int iData, P3 pt, long time) void
JmolMultiTouchClient.processMultitouchEvent
(int groupID, int eventType, int touchID, int iData, P3 pt, long time) -
Uses of P3 in org.jmol.quantum
Methods in org.jmol.quantum with parameters of type P3Modifier and TypeMethodDescriptionvoid
MepCalculation.calculate
(VolumeData volumeData, BS bsSelected, P3[] xyz, Atom[] atoms, float[] potentials, int calcType) float
MepCalculation.getValueAtPoint
(P3 pt) void
-
Uses of P3 in org.jmol.render
Fields in org.jmol.render declared as P3Modifier and TypeFieldDescriptionprotected P3
MeshRenderer.latticeOffset
protected final P3[]
CageRenderer.p3Screens
protected final P3[]
CageRenderer.p3Screens
protected final P3[]
CageRenderer.p3Screens
protected P3[]
MeshRenderer.p3Screens
protected final P3
FontLineShapeRenderer.pointT
protected final P3
FontLineShapeRenderer.pointT2
protected final P3
FontLineShapeRenderer.pointT3
protected P3
FontLineShapeRenderer.pt0
protected P3
FontLineShapeRenderer.pt1
protected final P3
MeshRenderer.pt1f
protected final P3
MeshRenderer.pt2f
protected P3
LabelsRenderer.pTemp
protected P3
FontLineShapeRenderer.tickA
protected P3
FontLineShapeRenderer.tickAs
protected P3
FontLineShapeRenderer.tickB
protected P3
FontLineShapeRenderer.tickBs
Methods in org.jmol.render with parameters of type P3Modifier and TypeMethodDescriptionprotected void
FontLineShapeRenderer.renderLine
(P3 p0, P3 p1, int diameter, boolean drawTicks) -
Uses of P3 in org.jmol.renderbio
Fields in org.jmol.renderbio declared as P3Modifier and TypeFieldDescriptionprotected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPoints
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
BioShapeRenderer.controlPointScreens
protected P3[]
RocketsRenderer.cordMidPoints
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonBottomScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
protected P3[]
BioShapeRenderer.ribbonTopScreens
-
Uses of P3 in org.jmol.renderspecial
Fields in org.jmol.renderspecial declared as P3 -
Uses of P3 in org.jmol.script
Fields in org.jmol.script declared as P3Methods in org.jmol.script that return P3Modifier and TypeMethodDescriptionScriptParam.atomCenterOrCoordinateParameter
(int i, Object[] ret) ScriptParam.centerParameter
(int i, Object[] ret) protected P3
ScriptParam.centerParameterForModel
(int i, int modelIndex, Object[] ret) protected P3
ScriptEval.getObjectCenter
(String axisID, int index, int modelIndex) ScriptParam.getPoint3f
(int i, boolean allowFractional, boolean throwE) Get an {x,y,z} value, possibly fractional, with option to throw an error.P3[]
ScriptParam.getPointArray
(int i, int nPoints, boolean allowNull) may return null values in some casesScriptParam.getUnitCellCenter()
static P3
ScriptParam.xypParameter
(int index) Methods in org.jmol.script that return types with arguments of type P3Modifier and TypeMethodDescriptionScriptParam.getPointOrCenterVector
(T t) ScriptParam.getPointVector
(T t, int i) Methods in org.jmol.script with parameters of type P3Modifier and TypeMethodDescriptionScriptManager.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) Add hydrogens to a modelboolean
Method parameters in org.jmol.script with type arguments of type P3Modifier and TypeMethodDescriptionScriptParam.getHklPlane
(T3 pt, float offset, Lst<P3> pts) ScriptParam.hklParameter
(int i, Lst<P3> pts, boolean allowOffset) -
Uses of P3 in org.jmol.scriptext
Methods in org.jmol.scriptext that return P3Modifier and TypeMethodDescriptionprotected P3[]
protected P3
ScriptExt.centerParameter
(int i) protected P3[]
ScriptExt.getAllPoints
(int index, int nmin) protected P3
ScriptExt.getPoint3f
(int i, boolean allowFractional) Methods in org.jmol.scriptext with parameters of type P3Modifier 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.Method parameters in org.jmol.scriptext with type arguments of type P3Modifier 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 P3 in org.jmol.shape
Fields in org.jmol.shape declared as P3Modifier and TypeFieldDescriptionfinal P3[]
Axes.axisPoints
[x, y, z, -x, -y, -z] or [a, b, c, -a, -b, -c]Axes.axisXY
Axes.fixedOrigin
final P3
Axes.fixedOriginUC
Mesh.lattice
final P3
Axes.originPoint
Mesh.ptCenter
Fields in org.jmol.shape with type parameters of type P3Methods in org.jmol.shape that return P3Modifier and TypeMethodDescriptionAxes.getAxisPoint
(int i, boolean unscaled, P3 ptTemp) get actual point or 1/2 vector from origin to this pointP3[]
Mesh.getBoundingBox()
P3[]
Mesh.getOffsetVertices
(P4 thePlane) Methods in org.jmol.shape with parameters of type P3Modifier and TypeMethodDescriptionvoid
Shape.checkBoundsMinMax
(P3 pointMin, P3 pointMax) Axes.getAxisPoint
(int i, boolean unscaled, P3 ptTemp) get actual point or 1/2 vector from origin to this pointMethod parameters in org.jmol.shape with type arguments of type P3Modifier 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 P3 in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as P3Modifier and TypeFieldDescriptionDipole.center
Ellipsoid.center
Polyhedron.center
Dipole.offsetPt
Dipole.origin
P3[]
Polyhedron.vertices
Methods in org.jmol.shapespecial that return P3Methods in org.jmol.shapespecial with parameters of type P3 -
Uses of P3 in org.jmol.shapesurface
Methods in org.jmol.shapesurface that return P3Modifier and TypeMethodDescriptionP3[]
Isosurface.calculateGeodesicSurface
(BS bsSelected, float envelopeRadius) P3[]
IsosurfaceMesh.getBoundingBox()
Methods in org.jmol.shapesurface with parameters of type P3 -
Uses of P3 in org.jmol.smiles
Subclasses of P3 in org.jmol.smilesModifier and TypeClassDescriptionclass
This class represents an atom in aSmilesMolecule
.Fields in org.jmol.smiles declared as P3Methods in org.jmol.smiles that return P3Methods in org.jmol.smiles with parameters of type P3Modifier and TypeMethodDescriptionSmilesMatcher.polyhedronToSmiles
(Node center, int[][] faces, int atomCount, P3[] points, int flags, String details) Generate a topological SMILES string from a set of faces -
Uses of P3 in org.jmol.symmetry
Fields in org.jmol.symmetry declared as P3Methods in org.jmol.symmetry that return P3Modifier and TypeMethodDescriptionP3[]
Symmetry.getCanonicalCopy
(float scale, boolean withOffset) P3[]
UnitCell.getCanonicalCopyTrimmed
(P3 frac, float scale) Symmetry.getCartesianOffset()
Symmetry.getFractionalOffset()
Symmetry.getFractionalOrigin()
SymmetryOperation.getOpPoint()
SymmetryOperation.getOpPoint2()
UnitCellIterator.getPosition()
P3[]
Symmetry.getUnitCellVectors()
P3[]
Symmetry.getUnitCellVerticesNoOffset()
Symmetry.toSupercell
(P3 fpt) Methods in org.jmol.symmetry that return types with arguments of type P3Modifier and TypeMethodDescriptionSymmetry.generateCrystalClass
(P3 pt00) Symmetry.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) Symmetry.getLatticeCentering()
SymmetryOperation.getLatticeCentering
(SymmetryOperation[] ops) Methods in org.jmol.symmetry with parameters of type P3Modifier and TypeMethodDescriptionboolean
UnitCell.checkDistance
(P3 f1, P3 f2, float distance, float dx, int iRange, int jRange, int kRange, P3 ptOffset) boolean
Symmetry.checkPeriodic
(P3 pt) SpaceGroupFinder.checkSupercell
(Viewer vwr, Symmetry uc, BS bsPoints, int abc, P3 scaling) Look for a supercell and adjust lattice down if necessary.Symmetry.generateCrystalClass
(P3 pt00) P3[]
UnitCell.getCanonicalCopyTrimmed
(P3 frac, float scale) float
Symmetry.getCellWeight
(P3 pt) Symmetry.getEquivPoints
(Lst<P3> pts, P3 pt, String flags) int[]
Symmetry.getInvariantSymops
(P3 pt, int[] v0) int
Symmetry.getSiteMultiplicity
(P3 pt) Symmetry.getSymmetryInfoAtom
(ModelSet modelSet, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] opList) Symmetry.getTransform
(P3 fracA, P3 fracB, boolean best) SymmetryDesc.getTransform
(UnitCell uc, SymmetryOperation[] ops, P3 fracA, P3 fracB, boolean best) Symmetry.getWyckoffPosition
(Viewer vwr, P3 p, String letter) boolean
Symmetry.isWithinUnitCell
(P3 pt, float x, float y, float z) void
Symmetry.newSpaceGroupPoint
(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint) static void
SymmetryOperation.normalizeOperationToCentroid
(int dim, M4 m, P3[] fracPts, int i0, int n) Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.V3[]
Symmetry.rotateAxes
(int iop, V3[] axes, P3 ptTemp, M3 mTemp) void
Symmetry.setFinalOperations
(int dim, String name, P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, String filterSymop) Symmetry.staticToRationalXYZ
(P3 fPt, String sep) Symmetry.toSupercell
(P3 fpt) Method parameters in org.jmol.symmetry with type arguments of type P3 -
Uses of P3 in org.jmol.util
Subclasses of P3 in org.jmol.utilModifier and TypeClassDescriptionclass
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)Fields in org.jmol.util declared as P3Modifier and TypeFieldDescriptionfinal P3
BoxInfo.bbCorner0
final P3
BoxInfo.bbCorner1
protected P3
BZone.center
MeshSurface.offset
ContactPair.pt
static final P3[]
BoxInfo.unitCubePoints
Methods in org.jmol.util that return P3Modifier and TypeMethodDescriptionP3[]
Vibration.addTracePt
(int n, Point3fi ptNew) P3[]
TempArray.allocTempPoints
(int size) BoxInfo.getBoundBoxCenter()
P3[]
BoxInfo.getBoundBoxPoints
(boolean isAll) Return basic info on boundbox in the form of an array.static final P3[]
BoxInfo.getCanonicalCopy
(P3[] boxPoints, float scale) Change points references to canonical form used in Triangulator, while also scaling.SimpleUnitCell.getFractionalOrigin()
Get the fractional origin for the UccageRenderer.static final P3[]
BoxInfo.getVerticesFromOABC
(T3[] oabc) Node.getXYZ()
SimpleNode.getXYZ()
P3[]
Triangulator.intersectLine
(P3[] points, int nPoints, P3 ptA, V3 unitVector) static final P3[]
Delivers [center a b c] for generation of unit cells from a boundboxSimpleUnitCell.toSupercell
(P3 fpt) convenience return only after changing fptMethods in org.jmol.util that return types with arguments of type P3Modifier and TypeMethodDescriptionMethods in org.jmol.util with parameters of type P3Modifier and TypeMethodDescriptionstatic void
BoxInfo.addPointXYZ
(float x, float y, float z, P3 xyzMin, P3 xyzMax, float margin) void
BZone.createBZ
(Viewer vwr, int n, Object[] array, boolean isK, String id, float scale, float foffset, P3 offset) Create a Brillouin zone.void
void
GData.drawQuadrilateralBits
(JmolRendererInterface jmolRenderer, short colix, P3 screenA, P3 screenB, P3 screenC, P3 screenD) static String
void
GData.drawTriangleBits
(JmolRendererInterface renderer, P3 screenA, short colixA, P3 screenB, short colixB, P3 screenC, short colixC, int check) static Object
Escape.escapeHelical
(String id, int tokType, P3 a, P3 b, T3[] pts) Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxisvoid
TempArray.freeTempPoints
(P3[] tempPoints) static P4[]
BoxInfo.getBoxFacesFromOABC
(P3[] oabc) static final P3[]
BoxInfo.getCanonicalCopy
(P3[] boxPoints, float scale) Change points references to canonical form used in Triangulator, while also scaling.static int
SimpleUnitCell.getCellRange
(T3 fset, P3[] cellRange) 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 void
SimpleUnitCell.ijkToPoint3f
(int nnn, P3 cell, int offset, int kcode) 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}P3[]
Triangulator.intersectLine
(P3[] points, int nPoints, P3 ptA, V3 unitVector) boolean
static void
void
MeshSurface.setBoundingBox
(P3[] boundBoxPoints) void
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.protected void
MeshSlicer.slabBrillouin
(P3[] unitCellPoints) "slabs" an isosurface into the first Brillouin zone moving points as necessary.protected void
MeshSurface.slabBrillouin
(P3[] unitCellVectors) static final P3[]
Delivers [center a b c] for generation of unit cells from a boundboxSimpleUnitCell.toSupercell
(P3 fpt) convenience return only after changing fptint[][]
MeshCapper.triangulateFaces
(int[][] faces, P3[] vertices, int[][] faceTriangles) generic entry for a set of facesint[][]
MeshCapper.triangulatePolygon
(P3[] points, int nPoints) generic entry for a polygonvoid
SimpleUnitCell.twelfthify
(P3 pt) Method parameters in org.jmol.util with type arguments of type P3 -
Uses of P3 in org.jmol.viewer
Fields in org.jmol.viewer declared as P3Modifier and TypeFieldDescriptionfinal P3
TransformManager.camera
final P3
TransformManager.cameraSetting
final P3
TransformManager.fixedRotationCenter
final P3
TransformManager.fixedRotationOffset
final P3
TransformManager.fixedTranslation
protected final P3
TransformManager.fScrPt
final P3
TransformManager.navigationCenter
final P3
TransformManager.navigationOffset
final P3
TransformManager.navigationShiftXY
protected final P3
TransformManager.perspectiveOffset
protected final P3
TransformManager.perspectiveShiftXY
protected final P3
TransformManager.ptTest1
protected final P3
TransformManager.ptTest2
protected final P3
TransformManager.ptTest3
protected final P3
TransformManager.untransformedPoint
TransformManager.zSlabPoint
Methods in org.jmol.viewer that return P3Modifier and TypeMethodDescriptionP3[]
Viewer.allocTempPoints
(int size) P3[]
Viewer.calculateSurface
(BS bsSelected, float envelopeRadius) P3[]
Viewer.getAdditionalHydrogens
(BS bsAtoms, Lst<Atom> vConnections, int flags) Viewer.getBoundBoxCenter()
P3[]
TransformManager.getCameraFactors()
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.P3[][]
Viewer.getCenterAndPoints
(Lst<Object[]> atomSets, boolean addCenter) Viewer.getColorPointForPropertyValue
(float val) Viewer.getDefaultLattice()
TransformManager.getNavigationOffset()
Methods in org.jmol.viewer that return types with arguments of type P3Methods in org.jmol.viewer with parameters of type P3Modifier and TypeMethodDescriptionViewer.addHydrogensInline
(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String, Object> htParams) void
Viewer.addUnitCellOffset
(P3 pt) void
void
Viewer.freeTempPoints
(P3[] tempPoints) Viewer.getAtomsNearPt
(float distance, P3 coord, BS bs) Viewer.getOrientation
(int type, String name, BS bs, P3[] points) Viewer.getSymmetryEquivPoints
(P3 pt, String flags) Viewer.getSymmetryInfo
(int iatom, String xyz, int iOp, P3 translation, P3 pt1, P3 pt2, int type, String desc, float scaleFactor, int nth, int options, int[] opList) A general method for retrieving symmetry information with full capability of the symop() scripting function.void
Viewer.invertAtomCoord
(P3 pt, P4 plane, BS bs, int ringAtomIndex, boolean isClick) void
Viewer.invertSelected
(P3 pt, P4 plane, int iAtom, BS bsAtoms) void
Viewer.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly, boolean useModelKit) int
Viewer.moveAtomWithHydrogens
(int atomIndex, int deltaX, int deltaY, int deltaZ, P3 ptNew, BS bsAtoms) void
TransformManager.moveRotationCenter
(P3 center, boolean toXY) void
Viewer.moveTo
(JmolScriptEvaluator eval, float floatSecondsTotal, P3 center, V3 rotAxis, float degrees, M3 rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY) void
Viewer.navigatePt
(P3 center) void
ActionManager.processMultitouchEvent
(int groupID, int eventType, int touchID, int iData, P3 pt, long time) Specific to ActionManagerMT -- for processing SparshUI gesturesboolean
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) boolean
Viewer.rotateAxisAngleAtCenter
(JmolScriptEvaluator eval, P3 rotCenter, V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected) void
TransformManager.setAll
(P3 center, M3 m, P3 navCenter, float zoom, float xTrans, float yTrans, float rotationRadius, float pixelScale, float navDepth, float xNav, float yNav, float cameraDepth, float cameraX, float cameraY) void
TransformManager.setCenterAt
(int relativeTo, P3 pt) void
Viewer.setDefaultLattice
(P3 p) void
Viewer.setModulation
(BS bs, boolean isOn, P3 t1, boolean isQ) void
TransformManager.setNavigatePt
(P3 pt) scripted entry point for navigationvoid
Viewer.setNewRotationCenter
(P3 center) void
Viewer.toUnitCell
(P3 pt, P3 offset) Returns the relative to origin without regard to offset created using the UNITCELL command.void
TransformManager.transformPt2Df
(T3 v, P3 pt) void
TransformManager.transformPt3f
(T3 ptXYZ, P3 screen) void
TransformManager.transformPtScrT32D
(T3 v, P3 pt) TransformManager.transformPtVib
(P3 ptXYZ, Vibration v) Method parameters in org.jmol.viewer with type arguments of type P3Modifier and TypeMethodDescriptionLst
<?> Viewer.getSymmetryEquivPointList
(Lst<P3> pts, String flags) 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) -
Uses of P3 in org.openscience.jvxl.simplewriter
Methods in org.openscience.jvxl.simplewriter with parameters of type P3Modifier and TypeMethodDescriptionprotected int
Method parameters in org.openscience.jvxl.simplewriter with type arguments of type P3Modifier and TypeMethodDescriptionstatic String
ASimpleJvxlWriter.jvxlGetData
(VoxelDataCreator vdc, Parameters params, VolumeData volumeData, String[] title, Lst<P3> surfacePointsReturn, float[] areaVolumeReturn) Constructor parameters in org.openscience.jvxl.simplewriter with type arguments of type P3ModifierConstructorDescriptionSimpleMarchingCubes
(VoxelDataCreator vdc, VolumeData volumeData, Parameters params, JvxlData jvxlData, Lst<P3> surfacePointsReturn, float[] areaVolumeReturn)