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 PointGroup	pointGroup
private SpaceGroup	spaceGroup
private SymmetryInfo	symmetryInfo
private UnitCell	unitCell

Constructor Summary

Constructors

Constructor and Description
Symmetry()

Method Summary

Methods

Modifier and Type	Method and Description
void	addSpaceGroupOperation(javax.vecmath.Matrix4f mat)
int	addSpaceGroupOperation(java.lang.String xyz, int opId)
boolean	checkDistance(javax.vecmath.Point3f f1, javax.vecmath.Point3f f2, float distance, float dx, int iRange, int jRange, int kRange, javax.vecmath.Point3f ptOffset)
boolean	createSpaceGroup(int desiredSpaceGroupIndex, java.lang.String name, float[] notionalUnitCell)
java.lang.String	fcoord(javax.vecmath.Tuple3f p)
javax.vecmath.Point3f[]	getCanonicalCopy(float scale)
javax.vecmath.Point3f	getCartesianOffset()
int[]	getCellRange()
boolean	getCoordinatesAreFractional()
java.lang.Object[]	getEllipsoid(float[] parBorU)
java.lang.Object[]	getEllipsoid(javax.vecmath.Vector3f[] vectors, float a, float b, float c)
javax.vecmath.Point3f	getFractionalOffset()
java.lang.Object	getLatticeDesignation()
java.lang.String	getMatrixFromString(java.lang.String xyz, float[] temp, boolean allowScaling)
float[]	getNotionalUnitCell()
java.lang.Object	getPointGroupInfo(int modelIndex, boolean asDraw, boolean asInfo, java.lang.String type, int index, float scale)
java.lang.String	getPointGroupName()
java.lang.Object	getSpaceGroup()
java.lang.String	getSpaceGroupInfo(java.lang.String name, SymmetryInterface cellInfo)
java.lang.String	getSpaceGroupName()
javax.vecmath.Matrix4f	getSpaceGroupOperation(int i)
int	getSpaceGroupOperationCount()
java.lang.String	getSpaceGroupXyz(int i, boolean doNormalize)
java.lang.String	getSymmetryInfoString()
java.lang.Object[]	getSymmetryOperationDescription(int isym, SymmetryInterface cellInfo, javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, java.lang.String id)
java.lang.String[]	getSymmetryOperations()
float[]	getUnitCellAsArray(boolean vectorsOnly)
java.lang.String	getUnitCellInfo()
float	getUnitCellInfo(int infoType)
javax.vecmath.Point3f	getUnitCellMultiplier()
javax.vecmath.Point3f[]	getUnitCellVertices()
java.lang.String	getUnitsymmetryInfo()
float	getUnitsymmetryInfo(int infoType)
boolean	haveSpaceGroup()
boolean	haveUnitCell()
javax.vecmath.Point3f	ijkToPoint3f(int nnn)
boolean	isPeriodic()
boolean	isPolymer()
boolean	isSlab()
void	newSpaceGroupPoint(int i, javax.vecmath.Point3f atom1, javax.vecmath.Point3f atom2, int transX, int transY, int transZ)
java.lang.Object	rotateEllipsoid(int i, javax.vecmath.Point3f ptTemp, javax.vecmath.Vector3f[] axes, javax.vecmath.Point3f ptTemp1, javax.vecmath.Point3f ptTemp2)
void	setFinalOperations(javax.vecmath.Point3f[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize)
void	setLattice(int latt) set symmetry lattice type using Hall rotations
void	setMinMaxLatticeParameters(javax.vecmath.Point3i minXYZ, javax.vecmath.Point3i maxXYZ)
void	setOffset(int nnn)
SymmetryInterface	setPointGroup(SymmetryInterface siLast, Atom[] atomset, java.util.BitSet bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance)
void	setSpaceGroup(boolean doNormalize)
void	setSpaceGroup(SymmetryInterface symmetry)
void	setSymmetryInfo(int modelIndex, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo)
void	setUnitCell(float[] notionalUnitCell)
void	setUnitCellAllFractionalRelative(boolean TF)
void	setUnitCellOffset(javax.vecmath.Point3f pt)
void	setUnitCellOrientation(javax.vecmath.Matrix3f matUnitCellOrientation)
void	toCartesian(javax.vecmath.Point3f fpt, boolean isAbsolute)
void	toFractional(javax.vecmath.Point3f pt, boolean isAbsolute)
void	toUnitCell(javax.vecmath.Point3f pt, javax.vecmath.Point3f offset)

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

Constructor Detail

Symmetry

public Symmetry()

Method Detail

setPointGroup

public SymmetryInterface setPointGroup(SymmetryInterface siLast,
                              Atom[] atomset,
                              java.util.BitSet 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

addSpaceGroupOperation

public void addSpaceGroupOperation(javax.vecmath.Matrix4f mat)

Specified by:

addSpaceGroupOperation 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 java.lang.String getSpaceGroupName()

Specified by:

getSpaceGroupName in interface SymmetryInterface

getSpaceGroup

public java.lang.Object getSpaceGroup()

Specified by:

getSpaceGroup in interface SymmetryInterface

setSpaceGroup

public void setSpaceGroup(SymmetryInterface symmetry)

Specified by:

setSpaceGroup in interface SymmetryInterface

createSpaceGroup

public boolean createSpaceGroup(int desiredSpaceGroupIndex,
                       java.lang.String name,
                       float[] notionalUnitCell)

Specified by:

createSpaceGroup in interface SymmetryInterface

haveSpaceGroup

public boolean haveSpaceGroup()

Specified by:

haveSpaceGroup in interface SymmetryInterface

getSpaceGroupInfo

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

Specified by:

getSpaceGroupInfo in interface SymmetryInterface

getLatticeDesignation

public java.lang.Object getLatticeDesignation()

Specified by:

getLatticeDesignation in interface SymmetryInterface

setFinalOperations

public void setFinalOperations(javax.vecmath.Point3f[] 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 javax.vecmath.Matrix4f 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,
                      javax.vecmath.Point3f atom1,
                      javax.vecmath.Point3f atom2,
                      int transX,
                      int transY,
                      int transZ)

Specified by:

newSpaceGroupPoint in interface SymmetryInterface

rotateEllipsoid

public java.lang.Object rotateEllipsoid(int i,
                               javax.vecmath.Point3f ptTemp,
                               javax.vecmath.Vector3f[] axes,
                               javax.vecmath.Point3f ptTemp1,
                               javax.vecmath.Point3f ptTemp2)

Specified by:

rotateEllipsoid in interface SymmetryInterface

getSymmetryOperationDescription

public java.lang.Object[] getSymmetryOperationDescription(int isym,
                                                 SymmetryInterface cellInfo,
                                                 javax.vecmath.Point3f pt1,
                                                 javax.vecmath.Point3f pt2,
                                                 java.lang.String id)

Specified by:

getSymmetryOperationDescription in interface SymmetryInterface

fcoord

public java.lang.String fcoord(javax.vecmath.Tuple3f p)

Specified by:

fcoord in interface SymmetryInterface

getMatrixFromString

public java.lang.String getMatrixFromString(java.lang.String xyz,
                                   float[] temp,
                                   boolean allowScaling)

Specified by:

getMatrixFromString in interface SymmetryInterface

ijkToPoint3f

public javax.vecmath.Point3f ijkToPoint3f(int nnn)

Specified by:

ijkToPoint3f 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 java.lang.String getSymmetryInfoString()

Specified by:

getSymmetryInfoString in interface SymmetryInterface

getSymmetryOperations

public java.lang.String[] 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)

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 java.lang.String getUnitsymmetryInfo()

setUnitCellOrientation

public void setUnitCellOrientation(javax.vecmath.Matrix3f matUnitCellOrientation)

Specified by:

setUnitCellOrientation in interface SymmetryInterface

toUnitCell

public void toUnitCell(javax.vecmath.Point3f pt,
              javax.vecmath.Point3f offset)

Specified by:

toUnitCell in interface SymmetryInterface

toCartesian

public void toCartesian(javax.vecmath.Point3f fpt,
               boolean isAbsolute)

Specified by:

toCartesian in interface SymmetryInterface

toFractional

public void toFractional(javax.vecmath.Point3f 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

getEllipsoid

public java.lang.Object[] getEllipsoid(float[] parBorU)

Specified by:

getEllipsoid in interface SymmetryInterface

getEllipsoid

public java.lang.Object[] getEllipsoid(javax.vecmath.Vector3f[] vectors,
                              float a,
                              float b,
                              float c)

Specified by:

getEllipsoid in interface SymmetryInterface

getUnitCellVertices

public javax.vecmath.Point3f[] getUnitCellVertices()

Specified by:

getUnitCellVertices in interface SymmetryInterface

getCartesianOffset

public javax.vecmath.Point3f getCartesianOffset()

Specified by:

getCartesianOffset in interface SymmetryInterface

getFractionalOffset

public javax.vecmath.Point3f getFractionalOffset()

Specified by:

getFractionalOffset in interface SymmetryInterface

setUnitCellOffset

public void setUnitCellOffset(javax.vecmath.Point3f pt)

Specified by:

setUnitCellOffset in interface SymmetryInterface

setOffset

public void setOffset(int nnn)

Specified by:

setOffset in interface SymmetryInterface

getUnitCellMultiplier

public javax.vecmath.Point3f getUnitCellMultiplier()

Specified by:

getUnitCellMultiplier in interface SymmetryInterface

getCanonicalCopy

public javax.vecmath.Point3f[] getCanonicalCopy(float scale)

Specified by:

getCanonicalCopy in interface SymmetryInterface

getUnitsymmetryInfo

public float getUnitsymmetryInfo(int infoType)

getUnitCellInfo

public float getUnitCellInfo(int infoType)

Specified by:

getUnitCellInfo 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(javax.vecmath.Point3i minXYZ,
                              javax.vecmath.Point3i maxXYZ)

Specified by:

setMinMaxLatticeParameters in interface SymmetryInterface

setUnitCellAllFractionalRelative

public void setUnitCellAllFractionalRelative(boolean TF)

Specified by:

setUnitCellAllFractionalRelative in interface SymmetryInterface

checkDistance

public boolean checkDistance(javax.vecmath.Point3f f1,
                    javax.vecmath.Point3f f2,
                    float distance,
                    float dx,
                    int iRange,
                    int jRange,
                    int kRange,
                    javax.vecmath.Point3f ptOffset)

Specified by:

checkDistance in interface SymmetryInterface