org.jmol.symmetry

Class Symmetry

public class Symmetry extends Object implements SymmetryInterface

Field Summary
PointGrouppointGroup
SpaceGroupspaceGroup
SymmetryInfosymmetryInfo
UnitCellunitCell
Constructor Summary
Symmetry()
Method Summary
booleanaddSpaceGroupOperation(String xyz)
booleancreateSpaceGroup(int desiredSpaceGroupIndex, String name, float[] notionalUnitCell, boolean doNormalize)
intdetermineSpaceGroupIndex(String name)
Point3fgetCartesianOffset()
int[]getCellRange()
booleangetCoordinatesAreFractional()
Object[]getEllipsoid(float[] parBorU)
Point3fgetFractionalOffset()
ObjectgetLatticeDesignation()
intgetModelIndex()
float[]getNotionalUnitCell()
ObjectgetPointGroupInfo(int modelIndex, boolean asDraw, boolean asInfo, String type, int index, float scale)
StringgetPointGroupName()
ObjectgetSpaceGroup()
StringgetSpaceGroupInfo(String name, float[] unitCell)
StringgetSpaceGroupName()
Matrix4fgetSpaceGroupOperation(int i)
intgetSpaceGroupOperationCount()
StringgetSpaceGroupXyz(int i, boolean doNormalize)
StringgetSymmetryInfoString()
String[]getSymmetryOperations()
floatgetUnitCellInfo(int infoType)
StringgetUnitCellInfo()
Point3f[]getUnitCellVertices()
StringgetUnitsymmetryInfo()
floatgetUnitsymmetryInfo(int infoType)
booleanhaveSpaceGroup()
booleanhaveUnitCell()
Point3fijkToPoint3f(int nnn)
booleanisPeriodic()
voidnewSpaceGroupPoint(int i, Point3f atom1, Point3f atom2, int transX, int transY, int transZ)
ObjectrotateEllipsoid(int i, Point3f ptTemp, Vector3f[] axes, Point3f ptTemp1, Point3f ptTemp2)
voidsetFinalOperations(Point3f[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize)
voidsetLattice(int latt)
voidsetModelIndex(int i)
voidsetOffset(int nnn)
SymmetryInterfacesetPointGroup(SymmetryInterface siLast, Atom[] atomset, BitSet bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance)
voidsetSpaceGroup(boolean doNormalize)
voidsetSpaceGroup(SymmetryInterface symmetry)
voidsetSymmetryInfo(int modelIndex, Hashtable modelAuxiliaryInfo)
voidsetUnitCell(float[] notionalUnitCell)
voidsetUnitCellOffset(Point3f pt)
voidtoCartesian(Point3f pt)
voidtoFractional(Point3f pt)
voidtoUnitCell(Point3f pt, Point3f offset)

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

addSpaceGroupOperation

public boolean addSpaceGroupOperation(String xyz)

createSpaceGroup

public boolean createSpaceGroup(int desiredSpaceGroupIndex, String name, float[] notionalUnitCell, boolean doNormalize)

determineSpaceGroupIndex

public int determineSpaceGroupIndex(String name)

getCartesianOffset

public Point3f getCartesianOffset()

getCellRange

public int[] getCellRange()

getCoordinatesAreFractional

public boolean getCoordinatesAreFractional()

getEllipsoid

public Object[] getEllipsoid(float[] parBorU)

getFractionalOffset

public Point3f getFractionalOffset()

getLatticeDesignation

public Object getLatticeDesignation()

getModelIndex

public int getModelIndex()

getNotionalUnitCell

public float[] getNotionalUnitCell()

getPointGroupInfo

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

getPointGroupName

public String getPointGroupName()

getSpaceGroup

public Object getSpaceGroup()

getSpaceGroupInfo

public String getSpaceGroupInfo(String name, float[] unitCell)

getSpaceGroupName

public String getSpaceGroupName()

getSpaceGroupOperation

public Matrix4f getSpaceGroupOperation(int i)

getSpaceGroupOperationCount

public int getSpaceGroupOperationCount()

getSpaceGroupXyz

public String getSpaceGroupXyz(int i, boolean doNormalize)

getSymmetryInfoString

public String getSymmetryInfoString()

getSymmetryOperations

public String[] getSymmetryOperations()

getUnitCellInfo

public float getUnitCellInfo(int infoType)

getUnitCellInfo

public String getUnitCellInfo()

getUnitCellVertices

public Point3f[] getUnitCellVertices()

getUnitsymmetryInfo

public String getUnitsymmetryInfo()

getUnitsymmetryInfo

public float getUnitsymmetryInfo(int infoType)

haveSpaceGroup

public boolean haveSpaceGroup()

haveUnitCell

public boolean haveUnitCell()

ijkToPoint3f

public Point3f ijkToPoint3f(int nnn)

isPeriodic

public boolean isPeriodic()

newSpaceGroupPoint

public void newSpaceGroupPoint(int i, Point3f atom1, Point3f atom2, int transX, int transY, int transZ)

rotateEllipsoid

public Object rotateEllipsoid(int i, Point3f ptTemp, Vector3f[] axes, Point3f ptTemp1, Point3f ptTemp2)

setFinalOperations

public void setFinalOperations(Point3f[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize)

setLattice

public void setLattice(int latt)

setModelIndex

public void setModelIndex(int i)

setOffset

public void setOffset(int nnn)

setPointGroup

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

setSpaceGroup

public void setSpaceGroup(boolean doNormalize)

setSpaceGroup

public void setSpaceGroup(SymmetryInterface symmetry)

setSymmetryInfo

public void setSymmetryInfo(int modelIndex, Hashtable modelAuxiliaryInfo)

setUnitCell

public void setUnitCell(float[] notionalUnitCell)

setUnitCellOffset

public void setUnitCellOffset(Point3f pt)

toCartesian

public void toCartesian(Point3f pt)

toFractional

public void toFractional(Point3f pt)

toUnitCell

public void toUnitCell(Point3f pt, Point3f offset)