Uses of Class
javajs.util.T3
Packages that use T3
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
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Uses of T3 in javajs.util
Subclasses of T3 in javajs.utilModifier and TypeClassDescriptionclass
A 4 element axis angle represented by single precision floating point x,y,z,angle components.class
A 3 element point that is represented by single precision floating point x,y,z coordinates.class
A 4 element point that is represented by single precision floating point x,y,z,w coordinates.class
A generic 4 element tuple that is represented by single precision floating point x,y,z and w coordinates.class
A 3-element vector that is represented by single precision floating point x,y,z coordinates.Methods in javajs.util that return T3Modifier and TypeMethodDescriptionstatic T3[]
AU.arrayCopyPt
(T3[] array, int newLength) 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.Transforms the point parameter with this Matrix4f and places the result into pointOut.Quat.transform2
(T3 pt, T3 ptNew) Methods in javajs.util with parameters of type T3Modifier and TypeMethodDescriptionvoid
add to translationfinal void
Sets the value of this tuple to the vector sum of itself and tuple t1.final void
Sets the value of this tuple to the vector sum of tuples t1 and t2.static T3[]
AU.arrayCopyPt
(T3[] array, int newLength) void
average of two tuplesstatic void
note that if vAB or vAC is dispensible, vNormNorm can be one of themstatic int
CU.colorPtToFFRGB
(T3 pt) static float
static float
Measure.computeAngleABC
(T3 pointA, T3 pointB, T3 pointC, boolean asDegrees) static float
Measure.computeTorsion
(T3 p1, T3 p2, T3 p3, T3 p4, boolean asDegrees) final void
Sets this tuple to be the vector cross product of vectors v1 and v2.final float
Returns the distance between this point and point p1.final float
T3.distanceSquared
(T3 p1) Computes the square of the distance between this point and point p1.static float
Measure.distanceToPlane
(P4 plane, T3 pt) final float
Vector dot product.static void
PT.fixPtFloats
(T3 pt, float f) static void
void
M3.getColumnV
(int column, T3 v) Copies the matrix values in the specified column into the vector parameter.static float
static float
static float
Measure.getPlaneProjection
(T3 pt, P4 plane, T3 retPtProj, V3 retNorm) Project a point onto a plane, also returning the normal vector and the directed distance to the plane.static void
Measure.getPlaneThroughPoint
(T3 pt, V3 normal, P4 plane) static P4
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).void
M4.getTranslation
(T3 trans) Retrieves the translational components of this matrix.static M4
Constructs and initializes a Matrix4f from the rotation matrix and translation.static P3
static Matrix
static V3
static Quat
static V3
void
void
Transform the vector vec using this Matrix3f and place the result into vecOut.void
Transforms the point parameter with this Matrix4f and places the result back into point.Transforms the point parameter with this Matrix4f and places the result into pointOut.final void
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).final void
{x*p.x, y*p.y, z*p.z) used for three-way scalingvoid
M3.setColumnV
(int column, T3 v) Sets the specified column of this matrix3d to the vector provided.void
Initializes a Matrix4f from the rotation matrix and translation.void
Sets the specified row of this matrix3d to the Vector provided.final void
Sets the value of this tuple to the value of the Tuple3f argument.void
q = (cos(theta/2), sin(theta/2) * n)void
M4.setTranslation
(T3 trans) Modifies the translational components of this matrix to the values of the Vector3f argument; the other values of this matrix are not modified.final void
Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).final void
Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).Quat.transform2
(T3 pt, T3 ptNew) -
Uses of T3 in org.jmol.adapter.smarter
Subclasses of T3 in org.jmol.adapter.smarterFields in org.jmol.adapter.smarter declared as T3Methods in org.jmol.adapter.smarter that return T3Methods in org.jmol.adapter.smarter with parameters of type T3 -
Uses of T3 in org.jmol.api
Methods in org.jmol.api that return T3Modifier and TypeMethodDescriptionJmolModulationSet.getModPoint
(boolean asEnabled) SymmetryInterface.getUnitCellMultiplier()
T3[]
Methods in org.jmol.api with parameters of type T3Modifier and TypeMethodDescriptionvoid
void
JmolRendererInterface.fillTriangle3i
(P3 screenA, P3 screenB, P3 screenC, T3 ptA, T3 ptB, T3 ptC, boolean doShade) SymmetryInterface.findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) JmolModulationSet.getModulation
(char type, T3 t456, boolean occ100) SymmetryInterface.getUnitCell
(T3[] points, boolean setRelative, String name) void
void
AtomIndexIterator.setModel
(ModelSet modelSet, int modelIndex, int zeroBase, int atomIndex, T3 center, float distance, RadiusData rd) void
void
SymmetryInterface.setOffsetPt
(T3 pt) SymmetryInterface.setPointGroup
(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) void
SymmetryInterface.toCartesian
(T3 pt, boolean ignoreOffset) void
SymmetryInterface.toFractional
(T3 pt, boolean ignoreOffset) boolean
SymmetryInterface.toFromPrimitive
(boolean toPrimitive, char type, T3[] oabc, M3 primitiveToCrystal) void
SymmetryInterface.toUnitCell
(T3 pt, T3 offset) void
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Uses of T3 in org.jmol.atomdata
Methods in org.jmol.atomdata with parameters of type T3Modifier and TypeMethodDescriptionvoid
AtomDataServer.setIteratorForPoint
(AtomIndexIterator iter, int modelIndex, T3 pt, float maxDistance) -
Uses of T3 in org.jmol.bspt
Methods in org.jmol.bspt that return T3Methods in org.jmol.bspt with parameters of type T3Modifier and TypeMethodDescriptionvoid
Iterate through all of your data points, calling addTuplevoid
CubeIterator.initialize
(T3 center, float radius, boolean hemisphereOnly) initialize to return all points within the sphere defined by center and radius -
Uses of T3 in org.jmol.export
Methods in org.jmol.export with parameters of type T3Modifier and TypeMethodDescriptionprotected abstract void
___Exporter.fillTriangle
(short colix, T3 ptA0, T3 ptB0, T3 ptC0, boolean twoSided) protected void
__CartesianExporter.fillTriangle
(short colix, T3 ptA, T3 ptB, T3 ptC, boolean twoSided) void
Export3D.fillTriangle3i
(P3 screenA, P3 screenB, P3 screenC, T3 ptA0, T3 ptB0, T3 ptC0, boolean doShade) protected int
__CartesianExporter.getCoordinateMap
(T3[] vertices, int[] coordMap, BS bsValid) protected int[]
__CartesianExporter.getNormalMap
(T3[] normals, int nNormals, BS bsValid, Lst<String> vNormals) protected String
protected String
protected String
protected void
JSExporter.jsSurface
(Object applet, T3[] vertices, T3[] normals, int[][] indices, int nVertices, int nPolygons, int nFaces, BS bsPolygons, int faceVertexMax, int color, int[] vertexColors, int[] polygonColors) protected abstract void
protected void
protected void
protected void
protected void
protected void
protected void
protected void
protected void
_StlExporter.outputAttrPt
(String attr, T3 pt) protected void
_VrmlExporter.outputAttrPt
(String attr, T3 pt) protected void
_X3dExporter.outputAttrPt
(String attr, T3 pt) 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
___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.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
_IdtfExporter.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
_MayaExporter.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
_ObjExporter.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
_PovrayExporter.outputTriangle
(T3 ptA, T3 ptB, T3 ptC, short colix) protected void
_TachyonExporter.outputTriangle
(T3 ptA, T3 ptB, T3 ptC, short colix) protected void
_VrmlExporter.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
_X3dExporter.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
JSExporter.outputTriangle
(T3 pt1, T3 pt2, T3 pt3, short colix) protected void
___Exporter.outputVertex
(T3 pt, T3 offset) protected void
___Exporter.outputVertices
(T3[] vertices, int nVertices, T3 offset) protected static String
protected void
__CartesianExporter.setSphereMatrix
(T3 center, float rx, float ry, float rz, A4 a, M4 sphereMatrix) protected static void
___Exporter.setTempVertex
(T3 pt, T3 offset, T3 ptTemp) -
Uses of T3 in org.jmol.g3d
Methods in org.jmol.g3d with parameters of type T3 -
Uses of T3 in org.jmol.jvxl.api
Methods in org.jmol.jvxl.api with parameters of type T3Modifier and TypeMethodDescriptionint
VertexDataServer.addVertexCopy
(T3 vertexXYZ, float value, int assocVertex, boolean asCopy) addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.int
VertexDataServer.getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vertexA, int vertexB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn) 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. -
Uses of T3 in org.jmol.jvxl.data
Methods in org.jmol.jvxl.data with parameters of type T3Modifier and TypeMethodDescriptionint
MeshData.addVertexCopy
(T3 vertex, float value, int assocVertex, boolean asCopy) float
VolumeData.distancePointToPlane
(T3 pt) float
VolumeData.distanceToMappingPlane
(T3 pt) float
VolumeData.lookupInterpolatedVoxelValue
(T3 point, boolean getSource) static 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.void
VolumeData.voxelPtToXYZ
(int x, int y, int z, T3 pt) -
Uses of T3 in org.jmol.jvxl.readers
Methods in org.jmol.jvxl.readers with parameters of type T3Modifier and TypeMethodDescriptionprotected int
int
SurfaceReader.addVertexCopy
(T3 vertexXYZ, float value, int assocVertex, boolean asCopy) protected float
SurfaceReader.getSPF
(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn) protected float
JvxlXmlReader.getSurfacePointAndFraction
(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn) protected float
SurfaceReader.getSurfacePointAndFraction
(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn) int
SurfaceReader.getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn) float
SurfaceReader.getValueAtPoint
(T3 pt, boolean getSource) protected void
protected void
SurfaceReader.setVectorAnisotropy
(T3 v) protected void
SurfaceReader.setVertexAnisotropy
(T3 pt) -
Uses of T3 in org.jmol.modelkit
Methods in org.jmol.modelkit with parameters of type T3Modifier and TypeMethodDescriptionvoid
ModelKit.drawUnitCell
(String id, T3 ucLattice, String swidth) boolean
ModelKit.transformAtomsToUnitCell
(SymmetryInterface sym, T3[] oabc, String ucname) Transform the atoms to fractional coordinate, set the unit cell to a new cell, and then transform them back to Cartesians. -
Uses of T3 in org.jmol.modelset
Subclasses of T3 in org.jmol.modelsetMethods in org.jmol.modelset that return T3Methods in org.jmol.modelset with parameters of type T3Modifier and TypeMethodDescriptionModelSet.getAtomsWithin
(float distance, T3 coord, BS bsResult, int modelIndex) AtomCollection.getHybridizationAndAxes
(int atomIndex, int atomicNumber, V3 z, V3 x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ, boolean isQuick, T3 ref) void
ModelSet.setAtomCoordsRelative
(T3 offset, BS bs) void
ModelSet.setBoundBox
(T3 pt1, T3 pt2, boolean byCorner, float scale) void
void
protected void
AtomIteratorWithinModel.setCenter2
(T3 center, float distance) void
ModelSet.setIteratorForPoint
(AtomIndexIterator iterator, int modelIndex, T3 pt, float distance) void
AtomIteratorWithinModel.setModel
(ModelSet modelSet, int modelIndex, int firstModelAtom, int atomIndex, T3 center, float distance, RadiusData rd) ModelSet.setModelCagePts
(int iModel, T3[] originABC, String name) void
AtomCollection.setVibrationVector
(int atomIndex, T3 vib) void
ModelSet.translateModel
(int iModel, T3 pt) move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE -
Uses of T3 in org.jmol.quantum
Fields in org.jmol.quantum declared as T3Methods in org.jmol.quantum with parameters of type T3Modifier and TypeMethodDescriptionvoid
MOCalculation.initialize
(int nX, int nY, int nZ, T3[] points) protected void
QuantumCalculation.initialize
(int nX, int nY, int nZ, T3[] points) protected void
QuantumCalculation.initialize0
(int nX, int nY, int nZ, T3[] points) float
boolean
MOCalculation.setupCalculation
(Map<String, Object> moData, boolean isSlaters, VolumeData volumeData, BS bsSelected, T3[] xyz, Atom[] atoms, int firstAtomOffset, int[][] dfCoefMaps, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, T3[] points) boolean
NciCalculation.setupCalculation
(VolumeData volumeData, BS bsSelected, BS bsExcluded, BS[] bsMolecules, T3[] atomCoordAngstroms, int firstAtomOffset, boolean isReducedDensity, T3[] points, float[] parameters, int testFlags) protected void
QuantumCalculation.setupCoordinates
(float[] originXYZ, float[] stepsXYZ, BS bsSelected, T3[] xyz, Atom[] atoms, T3[] points, boolean renumber) protected void
QuantumCalculation.setXYZBohr
(T3[] points) -
Uses of T3 in org.jmol.render
Fields in org.jmol.render declared as T3Methods in org.jmol.render with parameters of type T3 -
Uses of T3 in org.jmol.script
Methods in org.jmol.script that return T3Modifier and TypeMethodDescriptionNote - this check does not allow a 0 for h, k, or l.ScriptParam.getFractionalPoint
(int i) Could return a P4 for large 1100100100 type indicatorsScriptParam.getPointOrPlane
(int index, int mode) Get the point or plane at an indexMethods in org.jmol.script with parameters of type T3 -
Uses of T3 in org.jmol.shape
Fields in org.jmol.shape declared as T3Methods in org.jmol.shape with parameters of type T3Modifier and TypeMethodDescriptionstatic boolean
Mesh.checkWithin
(T3 pti, Lst<P3> withinPoints, float withinDistance2, boolean isWithinNot) protected int
Shape.coordinateInRange
(int x, int y, T3 vertex, int dmin2, P3i ptXY) V3[]
Mesh.getNormals
(T3[] vertices, P4 plane) MeshCollection.getPickedPoint
(T3 v, int modelIndex) void
Mesh.initialize
(int lighting, T3[] vertices, P4 plane) void
Mesh.rotateTranslate
(Quat q, T3 offset, boolean isAbsolute) protected void
MeshCollection.setStatusPicked
(int flag, T3 v, Map<String, Object> map) protected void
Mesh.sumVertexNormals
(T3[] vertices, V3[] normals) protected static void
Mesh.sumVertexNormals2
(Mesh m, T3[] vertices, V3[] normals) -
Uses of T3 in org.jmol.shapecgo
Methods in org.jmol.shapecgo with parameters of type T3 -
Uses of T3 in org.jmol.shapespecial
Methods in org.jmol.shapespecial with parameters of type T3 -
Uses of T3 in org.jmol.shapesurface
Methods in org.jmol.shapesurface that return T3Methods in org.jmol.shapesurface with parameters of type T3Modifier 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) int
Isosurface.addVertexCopy
(T3 vertexXYZ, float value, int assocVertex, boolean asCopy) int
Isosurface.getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn) protected void
IsosurfaceMesh.sumVertexNormals
(T3[] vertices, V3[] vectorSums) -
Uses of T3 in org.jmol.smiles
Subclasses of T3 in org.jmol.smilesModifier and TypeClassDescriptionclass
This class represents an atom in aSmilesMolecule
.Methods in org.jmol.smiles with parameters of type T3Modifier and TypeMethodDescriptionstatic float
SmilesMeasure.setTorsionData
(T3 pt1a, T3 pt1, T3 pt2, T3 pt2a, org.jmol.smiles.VTemp v, boolean withDihedral) calculate temporary points -
Uses of T3 in org.jmol.symmetry
Methods in org.jmol.symmetry that return T3Modifier and TypeMethodDescriptionT3[]
UnitCell.getConventionalUnitCell
(String latticeType, M3 primitiveToCrystal) return a conventional lattice from a primitivestatic T3[]
UnitCell.getMatrixAndUnitCell
(SimpleUnitCell uc, Object def, M4 retMatrix) Symmetry.getUnitCellMultiplier()
T3[]
Methods in org.jmol.symmetry with parameters of type T3Modifier and TypeMethodDescriptionstatic String
Get string version of fractionSymmetry.findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) static UnitCell
A special constructor for spacially defined unit cells.static char
SymmetryOperation.getGlideFromTrans
(T3 ftrans, T3 ax1) Symmetry.getUnitCell
(T3[] oabc, boolean setRelative, String name) SymmetryOperation.getxyzTrans
(T3 t) void
void
UnitCellIterator.setModel
(ModelSet modelSet, int modelIndex, int zeroBase, int atomIndex, T3 center, float distance, RadiusData rd) void
Symmetry.setOffsetPt
(T3 pt) Symmetry.setPointGroup
(Viewer vwr, SymmetryInterface siLast, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) void
Symmetry.toCartesian
(T3 pt, boolean ignoreOffset) void
Symmetry.toFractional
(T3 pt, boolean ignoreOffset) boolean
Symmetry.toFromPrimitive
(boolean toPrimitive, char type, T3[] oabc, M3 primitiveToCrystal) void
Symmetry.toUnitCell
(T3 pt, T3 offset) final void
UnitCell.toUnitCellRnd
(T3 pt, T3 offset) when offset is null, use the current cell, otherwise use the original unit cellvoid
-
Uses of T3 in org.jmol.util
Subclasses of T3 in org.jmol.utilModifier and TypeClassDescriptionclass
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 occupancyclass
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)class
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.Fields in org.jmol.util declared as T3Modifier and TypeFieldDescriptionT3[]
MeshSurface.altVertices
T3[]
MeshSurface.normals
T3[]
MeshSurface.vs
verticesMethods in org.jmol.util that return T3Modifier and TypeMethodDescriptionModulationSet.getModPoint
(boolean asEnabled) static T3[]
SimpleUnitCell.getReciprocal
(T3[] abc, T3[] ret, float scale) Generate the reciprocal unit cell, scaled as desiredT3[]
MeshSurface.getVertices()
static T3[]
set cell vectors by string.static T3[]
SimpleUnitCell.setAbcFromParams
(float[] params, T3[] ucnew) ModulationSet.setCalcPoint
(T3 pt, T3 t456, float vibScale, float scale) get updated value for offset vector and for occupancyVibration.setCalcPoint
(T3 pt, T3 t456, float scale, float modulationScale) Methods in org.jmol.util with parameters of type T3Modifier and TypeMethodDescriptionvoid
BoxInfo.addBoundBoxPoint
(T3 pt) static void
void
int
int
Calculate r_I internal d-space coordinate of an atom.static String
static String
must be its own, because of the possibility of being nullstatic Object
Escape.escapeHelical
(String id, int tokType, P3 a, P3 b, T3[] pts) Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxisstatic String
SimpleUnitCell.escapeMultiplier
(T3 pt) 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}static int
SimpleUnitCell.getCellRange
(T3 fset, P3[] cellRange) static void
GData.getHermiteList
(int tension, T3 p0, T3 p1, T3 p2, T3 p3, T3 p4, T3[] list, int index0, int n, boolean isPt) Used by Navigator, BioShapeRenderer, and DrawRendererModulationSet.getModulation
(char type, T3 tuv, boolean occ100) static T3[]
SimpleUnitCell.getReciprocal
(T3[] abc, T3[] ret, float scale) Generate the reciprocal unit cell, scaled as desiredstatic final P3[]
BoxInfo.getVerticesFromOABC
(T3[] oabc) Triangulator.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.static MeshSurface
MeshSurface.newMesh
(boolean isAlt, T3[] vertices, int vertexCount, int[][] polygonIndexes, T3[] normals, int nNormals) static P4
Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}static T3[]
set cell vectors by string.static T3[]
SimpleUnitCell.setAbcFromParams
(float[] params, T3[] ucnew) void
BoxInfo.setBoundBox
(T3 pt1, T3 pt2, boolean byCorner, float scale) void
BoxInfo.setBoundBoxFromOABC
(T3[] points) ModulationSet.setCalcPoint
(T3 pt, T3 t456, float vibScale, float scale) get updated value for offset vector and for occupancyVibration.setCalcPoint
(T3 pt, T3 t456, float scale, float modulationScale) Tensor.setFromEigenVectors
(T3[] eigenVectors, float[] eigenValues, String type, String id, Tensor t) Standard constructor for charge and iso.void
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.void
void
final void
SimpleUnitCell.toCartesian
(T3 pt, boolean ignoreOffset) final void
SimpleUnitCell.toFractional
(T3 pt, boolean ignoreOffset) static final P3[]
Delivers [center a b c] for generation of unit cells from a boundboxvoid
SimpleUnitCell.unitizeDim
(int dimension, T3 pt) Used for just about everything; via UnitCell including SpaceGroup.getSiteMultiplicity, Symmetry.getInvariantSymops, Symmetry.removeDuplicates, Symmetry.unitize, Symmetry.toUnitCell, SymmetryDesc.getTransform.static void
SimpleUnitCell.unitizeDimRnd
(int dimension, T3 pt, float slop) Only used for getting equivalent points and checking for duplicates. -
Uses of T3 in org.jmol.viewer
Methods in org.jmol.viewer that return T3Modifier and TypeMethodDescriptionT3[]
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c.TransformManager.getVibrationPoint
(Vibration v, T3 pt, float scale) returnMethods in org.jmol.viewer with parameters of type T3Modifier and TypeMethodDescriptionViewer.findSpaceGroup
(SymmetryInterface sym, BS bsAtoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) protected void
TransformManager.getScreenTemp
(T3 ptXYZ) protected void
TransformManager4D.getScreenTemp
(T3 ptXYZ) TransformManager.getVibrationPoint
(Vibration v, T3 pt, float scale) returnvoid
Hover over an arbitrary point.void
TransformManager.rotatePoint
(T3 pt, T3 ptRot) void
Viewer.setAtomCoordsRelative
(T3 offset, BS bs) void
Viewer.setIteratorForPoint
(AtomIndexIterator iterator, int modelIndex, T3 pt, float distance) void
Viewer.startSpinningAxis
(T3 pt1, T3 pt2, boolean isClockwise) void
Viewer.toCartesian
(T3 pt, boolean ignoreOffset) absolute or relative to origin of UNITCELL {x y z}void
Viewer.toCartesianUC
(SymmetryInterface unitCell, T3 pt, boolean ignoreOffset) void
Viewer.toFractional
(T3 pt, boolean ignoreOffset) void
Viewer.toFractionalUC
(SymmetryInterface unitCell, T3 pt, boolean ignoreOffset) TransformManager.transformPt
(T3 ptXYZ) CAUTION! returns a POINTER TO A TEMPORARY VARIABLETransformManager.transformPt2D
(T3 ptXyp) void
TransformManager.transformPt2Df
(T3 v, P3 pt) void
TransformManager.transformPt3f
(T3 ptXYZ, P3 screen) void
TransformManager.transformPtNoClip
(T3 ptXYZ, T3 pointScreen) void
TransformManager.transformPtScr
(T3 ptXYZ, P3i pointScreen) void
TransformManager.transformPtScrT3
(T3 ptXYZ, T3 pointScreen) void
TransformManager.transformPtScrT32D
(T3 v, P3 pt) void
TransformManager.unTransformPoint
(T3 screenPt, T3 coordPt) boolean
TransformManager.xyzIsSlabbedInternal
(T3 ptRef)