org.jmol.symmetry

Class Symmetry

java.lang.Object

org.jmol.symmetry.Symmetry

All Implemented Interfaces:

SymmetryInterface

public class Symmetry
extends java.lang.Object
implements SymmetryInterface

Field Summary

Fields

Modifier and Type	Field and Description
private SymmetryDesc	desc
private boolean	isBio
private PointGroup	pointGroup
(package private) SpaceGroup	spaceGroup
private SymmetryInfo	symmetryInfo
private UnitCell	unitCell

Constructor Summary

Constructors

Constructor and Description
Symmetry()

Method Summary

Modifier and Type	Method and Description
int	addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)
boolean	addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
java.lang.String	addOp(java.lang.String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)
int	addSpaceGroupOperation(java.lang.String xyz, int opId)
boolean	checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)
boolean	checkUnitCell(SymmetryInterface uc, javajs.util.P3 cell, javajs.util.P3 ptTemp, boolean isAbsolute)
boolean	createSpaceGroup(int desiredSpaceGroupIndex, java.lang.String name, java.lang.Object object)
java.lang.String	fcoord(javajs.util.T3 p)
javajs.util.P3[]	getCanonicalCopy(float scale, boolean withOffset)
javajs.util.P3	getCartesianOffset()
int[]	getCellRange()
boolean	getCoordinatesAreFractional()
private SymmetryDesc	getDesc(ModelSet modelSet)
javajs.util.P3	getFractionalOffset()
javajs.util.T3	getFractionalOrigin()
java.lang.Object	getLatticeDesignation()
int	getLatticeOp()
java.lang.String	getMatrixFromString(java.lang.String xyz, float[] rotTransMatrix, boolean allowScaling, int modDim)
javajs.util.Lst<java.lang.String>	getMoreInfo()
float[]	getNotionalUnitCell()
javajs.util.Matrix	getOperationRsVs(int iop)
java.lang.Object	getPointGroupInfo(int modelIndex, boolean asDraw, boolean asInfo, java.lang.String type, int index, float scale)
java.lang.String	getPointGroupName()
javajs.util.Quat	getQuaternionRotation(java.lang.String abc)
int	getSiteMultiplicity(javajs.util.P3 pt)
java.lang.Object	getSpaceGroup()
java.util.Map<java.lang.String,java.lang.Object>	getSpaceGroupInfo(ModelSet modelSet, java.lang.String sgName)
java.lang.String	getSpaceGroupInfoStr(java.lang.String name, SymmetryInterface cellInfo)
java.lang.String	getSpaceGroupName()
javajs.util.M4	getSpaceGroupOperation(int i)
java.lang.String	getSpaceGroupOperationCode(int iOp)
int	getSpaceGroupOperationCount()
java.lang.String	getSpaceGroupXyz(int i, boolean doNormalize)
float	getSpinOp(int op)
java.lang.Object	getSymmetryInfo(ModelSet modelSet, int iModel, int iAtom, SymmetryInterface uc, java.lang.String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, java.lang.String id, int type)
java.lang.Object	getSymmetryInfoAtom(ModelSet modelSet, BS bsAtoms, java.lang.String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, java.lang.String id, int type)
java.lang.String	getSymmetryInfoStr()
java.lang.String	getSymmetryInfoString(ModelSet modelSet, int modelIndex, int symOp, javajs.util.P3 pt1, javajs.util.P3 pt2, java.lang.String drawID, java.lang.String type)
javajs.util.M4[]	getSymmetryOperations()
Tensor	getTensor(Viewer vwr, float[] parBorU)
SymmetryInterface	getUnitCell(javajs.util.T3[] points, boolean setRelative, java.lang.String name)
float[]	getUnitCellAsArray(boolean vectorsOnly)
java.lang.String	getUnitCellInfo()
float	getUnitCellInfoType(int infoType)
javajs.util.P3	getUnitCellMultiplier()
java.lang.String	getUnitCellState()
javajs.util.V3[]	getUnitCellVectors()
javajs.util.P3[]	getUnitCellVertices()
java.lang.String	getUnitsymmetryInfo()
javajs.util.T3[]	getV0abc(java.lang.Object def) Accepts a string, a 3x3 matrix, or a 4x4 matrix.
boolean	haveUnitCell()
void	initializeOrientation(javajs.util.M3 mat)
boolean	isBio()
private boolean	isNotCentroid(javajs.util.P3 center, int n, int[] minmax, boolean centroidPacked)
boolean	isPeriodic()
boolean	isPolymer()
boolean	isSlab()
boolean	isSupercell()
void	newSpaceGroupPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ)
BS	notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax)
javajs.util.V3[]	rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
void	setFinalOperations(java.lang.String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, java.lang.String filterSymop)
void	setLattice(int latt) set symmetry lattice type using Hall rotations
void	setMinMaxLatticeParameters(javajs.util.P3i minXYZ, javajs.util.P3i maxXYZ)
void	setOffset(int nnn)
void	setOffsetPt(javajs.util.T3 pt)
SymmetryInterface	setPointGroup(SymmetryInterface siLast, Atom[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance)
void	setSpaceGroup(boolean doNormalize)
void	setSpaceGroupFrom(SymmetryInterface symmetry)
void	setSymmetryInfo(int modelIndex, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo, float[] notionalCell) Set the symmetry in the
void	setTimeReversal(int op, int val)
void	setUnitCell(float[] notionalUnitCell, boolean setRelative)
void	toCartesian(javajs.util.T3 fpt, boolean ignoreOffset)
void	toFractional(javajs.util.T3 pt, boolean isAbsolute)
javajs.util.P3	toSupercell(javajs.util.P3 fpt)
void	toUnitCell(javajs.util.P3 pt, javajs.util.P3 offset)
boolean	unitCellEquals(SymmetryInterface uc2)
void	unitize(javajs.util.P3 ptFrac)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

pointGroup

private PointGroup pointGroup

spaceGroup

SpaceGroup spaceGroup

symmetryInfo

private SymmetryInfo symmetryInfo

unitCell

private UnitCell unitCell

isBio

private boolean isBio

desc

private SymmetryDesc desc

Constructor Detail

Symmetry

public Symmetry()

Method Detail

isBio

public boolean isBio()

Specified by:

isBio in interface SymmetryInterface

setPointGroup

public SymmetryInterface setPointGroup(SymmetryInterface siLast,
                                       Atom[] atomset,
                                       BS bsAtoms,
                                       boolean haveVibration,
                                       float distanceTolerance,
                                       float linearTolerance)

Specified by:

setPointGroup in interface SymmetryInterface

getPointGroupName

public java.lang.String getPointGroupName()

Specified by:

getPointGroupName in interface SymmetryInterface

getPointGroupInfo

public java.lang.Object getPointGroupInfo(int modelIndex,
                                          boolean asDraw,
                                          boolean asInfo,
                                          java.lang.String type,
                                          int index,
                                          float scale)

Specified by:

getPointGroupInfo in interface SymmetryInterface

setSpaceGroup

public void setSpaceGroup(boolean doNormalize)

Specified by:

setSpaceGroup in interface SymmetryInterface

addSpaceGroupOperation

public int addSpaceGroupOperation(java.lang.String xyz,
                                  int opId)

Specified by:

addSpaceGroupOperation in interface SymmetryInterface

addBioMoleculeOperation

public int addBioMoleculeOperation(javajs.util.M4 mat,
                                   boolean isReverse)

Specified by:

addBioMoleculeOperation in interface SymmetryInterface

setLattice

public void setLattice(int latt)

Description copied from interface: SymmetryInterface

set symmetry lattice type using Hall rotations

Specified by:

setLattice in interface SymmetryInterface

Parameters:

latt - SHELX index or character lattice character P I R F A B C S T or \0

getSpaceGroup

public java.lang.Object getSpaceGroup()

Specified by:

getSpaceGroup in interface SymmetryInterface

setSpaceGroupFrom

public void setSpaceGroupFrom(SymmetryInterface symmetry)

Specified by:

setSpaceGroupFrom in interface SymmetryInterface

createSpaceGroup

public boolean createSpaceGroup(int desiredSpaceGroupIndex,
                                java.lang.String name,
                                java.lang.Object object)

Specified by:

createSpaceGroup in interface SymmetryInterface

getSpaceGroupInfoStr

public java.lang.String getSpaceGroupInfoStr(java.lang.String name,
                                             SymmetryInterface cellInfo)

Specified by:

getSpaceGroupInfoStr in interface SymmetryInterface

getLatticeDesignation

public java.lang.Object getLatticeDesignation()

Specified by:

getLatticeDesignation in interface SymmetryInterface

setFinalOperations

public void setFinalOperations(java.lang.String name,
                               javajs.util.P3[] atoms,
                               int iAtomFirst,
                               int noSymmetryCount,
                               boolean doNormalize,
                               java.lang.String filterSymop)

Specified by:

setFinalOperations in interface SymmetryInterface

getSpaceGroupOperation

public javajs.util.M4 getSpaceGroupOperation(int i)

Specified by:

getSpaceGroupOperation in interface SymmetryInterface

getSpaceGroupXyz

public java.lang.String getSpaceGroupXyz(int i,
                                         boolean doNormalize)

Specified by:

getSpaceGroupXyz in interface SymmetryInterface

newSpaceGroupPoint

public void newSpaceGroupPoint(int i,
                               javajs.util.P3 atom1,
                               javajs.util.P3 atom2,
                               int transX,
                               int transY,
                               int transZ)

Specified by:

newSpaceGroupPoint in interface SymmetryInterface

rotateAxes

public javajs.util.V3[] rotateAxes(int iop,
                                   javajs.util.V3[] axes,
                                   javajs.util.P3 ptTemp,
                                   javajs.util.M3 mTemp)

Specified by:

rotateAxes in interface SymmetryInterface

getSpaceGroupOperationCode

public java.lang.String getSpaceGroupOperationCode(int iOp)

Specified by:

getSpaceGroupOperationCode in interface SymmetryInterface

setTimeReversal

public void setTimeReversal(int op,
                            int val)

Specified by:

setTimeReversal in interface SymmetryInterface

getSpinOp

public float getSpinOp(int op)

Specified by:

getSpinOp in interface SymmetryInterface

addLatticeVectors

public boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)

Specified by:

addLatticeVectors in interface SymmetryInterface

getLatticeOp

public int getLatticeOp()

Specified by:

getLatticeOp in interface SymmetryInterface

getOperationRsVs

public javajs.util.Matrix getOperationRsVs(int iop)

Specified by:

getOperationRsVs in interface SymmetryInterface

getSiteMultiplicity

public int getSiteMultiplicity(javajs.util.P3 pt)

Specified by:

getSiteMultiplicity in interface SymmetryInterface

addOp

public java.lang.String addOp(java.lang.String code,
                              javajs.util.Matrix rs,
                              javajs.util.Matrix vs,
                              javajs.util.Matrix sigma)

Specified by:

addOp in interface SymmetryInterface

getMatrixFromString

public java.lang.String getMatrixFromString(java.lang.String xyz,
                                            float[] rotTransMatrix,
                                            boolean allowScaling,
                                            int modDim)

Specified by:

getMatrixFromString in interface SymmetryInterface

getSpaceGroupName

public java.lang.String getSpaceGroupName()

Specified by:

getSpaceGroupName in interface SymmetryInterface

getSpaceGroupOperationCount

public int getSpaceGroupOperationCount()

Specified by:

getSpaceGroupOperationCount in interface SymmetryInterface

getCoordinatesAreFractional

public boolean getCoordinatesAreFractional()

Specified by:

getCoordinatesAreFractional in interface SymmetryInterface

getCellRange

public int[] getCellRange()

Specified by:

getCellRange in interface SymmetryInterface

getSymmetryInfoStr

public java.lang.String getSymmetryInfoStr()

Specified by:

getSymmetryInfoStr in interface SymmetryInterface

getSymmetryOperations

public javajs.util.M4[] getSymmetryOperations()

Specified by:

getSymmetryOperations in interface SymmetryInterface

isPeriodic

public boolean isPeriodic()

Specified by:

isPeriodic in interface SymmetryInterface

setSymmetryInfo

public void setSymmetryInfo(int modelIndex,
                            java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo,
                            float[] notionalCell)

Set the symmetry in the

Specified by:

setSymmetryInfo in interface SymmetryInterface

haveUnitCell

public boolean haveUnitCell()

Specified by:

haveUnitCell in interface SymmetryInterface

checkUnitCell

public boolean checkUnitCell(SymmetryInterface uc,
                             javajs.util.P3 cell,
                             javajs.util.P3 ptTemp,
                             boolean isAbsolute)

Specified by:

checkUnitCell in interface SymmetryInterface

setUnitCell

public void setUnitCell(float[] notionalUnitCell,
                        boolean setRelative)

Specified by:

setUnitCell in interface SymmetryInterface

unitCellEquals

public boolean unitCellEquals(SymmetryInterface uc2)

Specified by:

unitCellEquals in interface SymmetryInterface

getUnitCellState

public java.lang.String getUnitCellState()

Specified by:

getUnitCellState in interface SymmetryInterface

getMoreInfo

public javajs.util.Lst<java.lang.String> getMoreInfo()

Specified by:

getMoreInfo in interface SymmetryInterface

getUnitsymmetryInfo

public java.lang.String getUnitsymmetryInfo()

initializeOrientation

public void initializeOrientation(javajs.util.M3 mat)

Specified by:

initializeOrientation in interface SymmetryInterface

unitize

public void unitize(javajs.util.P3 ptFrac)

Specified by:

unitize in interface SymmetryInterface

toUnitCell

public void toUnitCell(javajs.util.P3 pt,
                       javajs.util.P3 offset)

Specified by:

toUnitCell in interface SymmetryInterface

toCartesian

public void toCartesian(javajs.util.T3 fpt,
                        boolean ignoreOffset)

Specified by:

toCartesian in interface SymmetryInterface

toSupercell

public javajs.util.P3 toSupercell(javajs.util.P3 fpt)

Specified by:

toSupercell in interface SymmetryInterface

toFractional

public void toFractional(javajs.util.T3 pt,
                         boolean isAbsolute)

Specified by:

toFractional in interface SymmetryInterface

getNotionalUnitCell

public float[] getNotionalUnitCell()

Specified by:

getNotionalUnitCell in interface SymmetryInterface

getUnitCellAsArray

public float[] getUnitCellAsArray(boolean vectorsOnly)

Specified by:

getUnitCellAsArray in interface SymmetryInterface

getTensor

public Tensor getTensor(Viewer vwr,
                        float[] parBorU)

Specified by:

getTensor in interface SymmetryInterface

getUnitCellVertices

public javajs.util.P3[] getUnitCellVertices()

Specified by:

getUnitCellVertices in interface SymmetryInterface

getCartesianOffset

public javajs.util.P3 getCartesianOffset()

Specified by:

getCartesianOffset in interface SymmetryInterface

getFractionalOffset

public javajs.util.P3 getFractionalOffset()

Specified by:

getFractionalOffset in interface SymmetryInterface

setOffsetPt

public void setOffsetPt(javajs.util.T3 pt)

Specified by:

setOffsetPt in interface SymmetryInterface

setOffset

public void setOffset(int nnn)

Specified by:

setOffset in interface SymmetryInterface

getUnitCellMultiplier

public javajs.util.P3 getUnitCellMultiplier()

Specified by:

getUnitCellMultiplier in interface SymmetryInterface

getCanonicalCopy

public javajs.util.P3[] getCanonicalCopy(float scale,
                                         boolean withOffset)

Specified by:

getCanonicalCopy in interface SymmetryInterface

getUnitCellInfoType

public float getUnitCellInfoType(int infoType)

Specified by:

getUnitCellInfoType in interface SymmetryInterface

getUnitCellInfo

public java.lang.String getUnitCellInfo()

Specified by:

getUnitCellInfo in interface SymmetryInterface

isSlab

public boolean isSlab()

Specified by:

isSlab in interface SymmetryInterface

isPolymer

public boolean isPolymer()

Specified by:

isPolymer in interface SymmetryInterface

setMinMaxLatticeParameters

public void setMinMaxLatticeParameters(javajs.util.P3i minXYZ,
                                       javajs.util.P3i maxXYZ)

Specified by:

setMinMaxLatticeParameters in interface SymmetryInterface

checkDistance

public boolean checkDistance(javajs.util.P3 f1,
                             javajs.util.P3 f2,
                             float distance,
                             float dx,
                             int iRange,
                             int jRange,
                             int kRange,
                             javajs.util.P3 ptOffset)

Specified by:

checkDistance in interface SymmetryInterface

getUnitCellVectors

public javajs.util.V3[] getUnitCellVectors()

Specified by:

getUnitCellVectors in interface SymmetryInterface

getUnitCell

public SymmetryInterface getUnitCell(javajs.util.T3[] points,
                                     boolean setRelative,
                                     java.lang.String name)

Specified by:

getUnitCell in interface SymmetryInterface

isSupercell

public boolean isSupercell()

Specified by:

isSupercell in interface SymmetryInterface

notInCentroid

public BS notInCentroid(ModelSet modelSet,
                        BS bsAtoms,
                        int[] minmax)

Specified by:

notInCentroid in interface SymmetryInterface

isNotCentroid

private boolean isNotCentroid(javajs.util.P3 center,
                              int n,
                              int[] minmax,
                              boolean centroidPacked)

getDesc

private SymmetryDesc getDesc(ModelSet modelSet)

getSymmetryInfoAtom

public java.lang.Object getSymmetryInfoAtom(ModelSet modelSet,
                                            BS bsAtoms,
                                            java.lang.String xyz,
                                            int op,
                                            javajs.util.P3 pt,
                                            javajs.util.P3 pt2,
                                            java.lang.String id,
                                            int type)

Specified by:

getSymmetryInfoAtom in interface SymmetryInterface

getSymmetryInfoString

public java.lang.String getSymmetryInfoString(ModelSet modelSet,
                                              int modelIndex,
                                              int symOp,
                                              javajs.util.P3 pt1,
                                              javajs.util.P3 pt2,
                                              java.lang.String drawID,
                                              java.lang.String type)

Specified by:

getSymmetryInfoString in interface SymmetryInterface

getSpaceGroupInfo

public java.util.Map<java.lang.String,java.lang.Object> getSpaceGroupInfo(ModelSet modelSet,
                                                                          java.lang.String sgName)

Specified by:

getSpaceGroupInfo in interface SymmetryInterface

getSymmetryInfo

public java.lang.Object getSymmetryInfo(ModelSet modelSet,
                                        int iModel,
                                        int iAtom,
                                        SymmetryInterface uc,
                                        java.lang.String xyz,
                                        int op,
                                        javajs.util.P3 pt,
                                        javajs.util.P3 pt2,
                                        java.lang.String id,
                                        int type)

Specified by:

getSymmetryInfo in interface SymmetryInterface

fcoord

public java.lang.String fcoord(javajs.util.T3 p)

Specified by:

fcoord in interface SymmetryInterface

getV0abc

public javajs.util.T3[] getV0abc(java.lang.Object def)

Accepts a string, a 3x3 matrix, or a 4x4 matrix. Returns a set of four values as a P3 array consisting of an origin and three unit cell vectors a, b, and c.

Specified by:

getV0abc in interface SymmetryInterface

getQuaternionRotation

public javajs.util.Quat getQuaternionRotation(java.lang.String abc)

Specified by:

getQuaternionRotation in interface SymmetryInterface

getFractionalOrigin

public javajs.util.T3 getFractionalOrigin()

Specified by:

getFractionalOrigin in interface SymmetryInterface