org.jmol.symmetry

Class Symmetry

java.lang.Object

org.jmol.symmetry.Symmetry

All Implemented Interfaces:

SymmetryInterface

public class Symmetry
extends Object
implements SymmetryInterface

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	isBio
private PointGroup	pointGroup
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)
void	addLatticeVectors(javajs.util.List<float[]> lattvecs)
String	addOp(javajs.util.Matrix rs, javajs.util.Matrix vs)
int	addSpaceGroupOperation(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, String name, Object object)
String	fcoord(javajs.util.T3 p)
javajs.util.P3[]	getCanonicalCopy(float scale, boolean withOffset)
javajs.util.P3	getCartesianOffset()
int[]	getCellRange()
boolean	getCoordinatesAreFractional()
javajs.util.P3	getFractionalOffset()
Object	getLatticeDesignation()
int	getLatticeOp()
String	getMatrixFromString(String xyz, float[] rotTransMatrix, boolean allowScaling, int modDim)
float[]	getNotionalUnitCell()
javajs.util.Matrix	getOperationRsVs(int iop)
Object	getPointGroupInfo(int modelIndex, boolean asDraw, boolean asInfo, String type, int index, float scale)
String	getPointGroupName()
int	getSiteMultiplicity(javajs.util.P3 pt)
Object	getSpaceGroup()
Map<String,Object>	getSpaceGroupInfo(ModelSet modelSet, int modelIndex, String spaceGroup, int symOp, javajs.util.P3 pt1, javajs.util.P3 pt2, String drawID)
String	getSpaceGroupInfo(String name, SymmetryInterface cellInfo)
String	getSpaceGroupName()
javajs.util.M4	getSpaceGroupOperation(int i)
int	getSpaceGroupOperationCount()
String	getSpaceGroupXyz(int i, boolean doNormalize)
Object	getSymmetryInfo(ModelSet modelSet, int iModel, int iAtom, SymmetryInterface uc, String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type)
String	getSymmetryInfoString()
String	getSymmetryInfoString(Map<String,Object> sginfo, int symOp, String drawID, boolean labelOnly)
Object[]	getSymmetryOperationDescription(ModelSet modelSet, int isym, SymmetryInterface cellInfo, javajs.util.P3 pt1, javajs.util.P3 pt2, String id)
String[]	getSymmetryOperations()
Tensor	getTensor(float[] parBorU)
SymmetryInterface	getUnitCell(javajs.util.T3[] points, boolean setRelative)
float[]	getUnitCellAsArray(boolean vectorsOnly)
String	getUnitCellInfo()
float	getUnitCellInfoType(int infoType)
javajs.util.P3	getUnitCellMultiplier()
String	getUnitCellState()
javajs.util.V3[]	getUnitCellVectors()
javajs.util.P3[]	getUnitCellVertices()
String	getUnitsymmetryInfo()
boolean	haveUnitCell()
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	setCartesianOffset(javajs.util.T3 origin)
void	setFinalOperations(String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize)
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.P3 pt)
SymmetryInterface	setPointGroup(SymmetryInterface siLast, Atom[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance)
void	setSpaceGroup(boolean doNormalize)
void	setSpaceGroupS(SymmetryInterface symmetry)
void	setSymmetryInfo(int modelIndex, Map<String,Object> modelAuxiliaryInfo)
void	setUnitCell(float[] notionalUnitCell)
void	setUnitCellAllFractionalRelative(boolean TF)
void	setUnitCellOrientation(javajs.util.M3 matUnitCellOrientation)
void	toCartesian(javajs.util.T3 fpt, boolean isAbsolute)
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

private SpaceGroup spaceGroup

symmetryInfo

private SymmetryInfo symmetryInfo

unitCell

private UnitCell unitCell

isBio

private boolean isBio

Constructor Detail

Symmetry

public Symmetry()

Method Detail

setPointGroup

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

Specified by:

setPointGroup in interface SymmetryInterface

getPointGroupName

public String getPointGroupName()

Specified by:

getPointGroupName in interface SymmetryInterface

getPointGroupInfo

public Object getPointGroupInfo(int modelIndex,
                                boolean asDraw,
                                boolean asInfo,
                                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(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

getSpaceGroupName

public String getSpaceGroupName()

Specified by:

getSpaceGroupName in interface SymmetryInterface

getSpaceGroup

public Object getSpaceGroup()

Specified by:

getSpaceGroup in interface SymmetryInterface

setSpaceGroupS

public void setSpaceGroupS(SymmetryInterface symmetry)

Specified by:

setSpaceGroupS in interface SymmetryInterface

createSpaceGroup

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

Specified by:

createSpaceGroup in interface SymmetryInterface

getSpaceGroupInfo

public String getSpaceGroupInfo(String name,
                                SymmetryInterface cellInfo)

Specified by:

getSpaceGroupInfo in interface SymmetryInterface

getLatticeDesignation

public Object getLatticeDesignation()

Specified by:

getLatticeDesignation in interface SymmetryInterface

setFinalOperations

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

Specified by:

setFinalOperations in interface SymmetryInterface

getSpaceGroupOperationCount

public int getSpaceGroupOperationCount()

Specified by:

getSpaceGroupOperationCount in interface SymmetryInterface

getSpaceGroupOperation

public javajs.util.M4 getSpaceGroupOperation(int i)

Specified by:

getSpaceGroupOperation in interface SymmetryInterface

getSpaceGroupXyz

public 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

getSymmetryOperationDescription

public Object[] getSymmetryOperationDescription(ModelSet modelSet,
                                                int isym,
                                                SymmetryInterface cellInfo,
                                                javajs.util.P3 pt1,
                                                javajs.util.P3 pt2,
                                                String id)

fcoord

public String fcoord(javajs.util.T3 p)

Specified by:

fcoord in interface SymmetryInterface

getMatrixFromString

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

Specified by:

getMatrixFromString in interface SymmetryInterface

getCoordinatesAreFractional

public boolean getCoordinatesAreFractional()

Specified by:

getCoordinatesAreFractional in interface SymmetryInterface

getCellRange

public int[] getCellRange()

Specified by:

getCellRange in interface SymmetryInterface

getSymmetryInfoString

public String getSymmetryInfoString()

Specified by:

getSymmetryInfoString in interface SymmetryInterface

getSymmetryOperations

public String[] getSymmetryOperations()

Specified by:

getSymmetryOperations in interface SymmetryInterface

isPeriodic

public boolean isPeriodic()

Specified by:

isPeriodic in interface SymmetryInterface

setSymmetryInfo

public void setSymmetryInfo(int modelIndex,
                            Map<String,Object> modelAuxiliaryInfo)

Specified by:

setSymmetryInfo in interface SymmetryInterface

setUnitCell

public void setUnitCell(float[] notionalUnitCell)

Specified by:

setUnitCell in interface SymmetryInterface

haveUnitCell

public boolean haveUnitCell()

Specified by:

haveUnitCell in interface SymmetryInterface

getUnitsymmetryInfo

public String getUnitsymmetryInfo()

setUnitCellOrientation

public void setUnitCellOrientation(javajs.util.M3 matUnitCellOrientation)

Specified by:

setUnitCellOrientation 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 isAbsolute)

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(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

setCartesianOffset

public void setCartesianOffset(javajs.util.T3 origin)

Specified by:

setCartesianOffset in interface SymmetryInterface

getFractionalOffset

public javajs.util.P3 getFractionalOffset()

Specified by:

getFractionalOffset in interface SymmetryInterface

setOffsetPt

public void setOffsetPt(javajs.util.P3 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 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

setUnitCellAllFractionalRelative

public void setUnitCellAllFractionalRelative(boolean TF)

Specified by:

setUnitCellAllFractionalRelative 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)

Specified by:

getUnitCell in interface SymmetryInterface

isSupercell

public boolean isSupercell()

Specified by:

isSupercell in interface SymmetryInterface

getSymmetryInfoString

public String getSymmetryInfoString(Map<String,Object> sginfo,
                                    int symOp,
                                    String drawID,
                                    boolean labelOnly)

Specified by:

getSymmetryInfoString in interface SymmetryInterface

getSpaceGroupInfo

public Map<String,Object> getSpaceGroupInfo(ModelSet modelSet,
                                            int modelIndex,
                                            String spaceGroup,
                                            int symOp,
                                            javajs.util.P3 pt1,
                                            javajs.util.P3 pt2,
                                            String drawID)

Specified by:

getSpaceGroupInfo in interface SymmetryInterface

getSymmetryInfo

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

Specified by:

getSymmetryInfo 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)

checkUnitCell

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

Specified by:

checkUnitCell in interface SymmetryInterface

unitCellEquals

public boolean unitCellEquals(SymmetryInterface uc2)

Specified by:

unitCellEquals in interface SymmetryInterface

addLatticeVectors

public void addLatticeVectors(javajs.util.List<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

isBio

public boolean isBio()

Specified by:

isBio in interface SymmetryInterface

addOp

public String addOp(javajs.util.Matrix rs,
                    javajs.util.Matrix vs)

Specified by:

addOp in interface SymmetryInterface

getUnitCellState

public String getUnitCellState()

Specified by:

getUnitCellState in interface SymmetryInterface