org.jmol.api
Interface SymmetryInterface

All Known Implementing Classes:

Symmetry

public interface SymmetryInterface

Method Summary

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

Method Detail

setPointGroup

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

getPointGroupName

String getPointGroupName()

getPointGroupInfo

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

setSpaceGroup

void setSpaceGroup(boolean doNormalize)

addSpaceGroupOperation

int addSpaceGroupOperation(String xyz,
                           int opId)

setLattice

void setLattice(int latt)

set symmetry lattice type using Hall rotations

Parameters:

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

getSpaceGroupName

String getSpaceGroupName()

getSpaceGroup

Object getSpaceGroup()

setSpaceGroup

void setSpaceGroup(SymmetryInterface symmetry)

createSpaceGroup

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

haveSpaceGroup

boolean haveSpaceGroup()

getSpaceGroupInfo

String getSpaceGroupInfo(String name,
                         SymmetryInterface cellInfo)

getLatticeDesignation

Object getLatticeDesignation()

setFinalOperations

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

getSpaceGroupOperationCount

int getSpaceGroupOperationCount()

getSpaceGroupOperation

Matrix4f getSpaceGroupOperation(int i)

getSpaceGroupXyz

String getSpaceGroupXyz(int i,
                        boolean doNormalize)

newSpaceGroupPoint

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

rotateEllipsoid

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

setUnitCellAllFractionalRelative

void setUnitCellAllFractionalRelative(boolean TF)

setUnitCell

void setUnitCell(float[] notionalUnitCell)

toCartesian

void toCartesian(Point3f pt,
                 boolean asAbsolue)

getEllipsoid

Object[] getEllipsoid(float[] parBorU)

getEllipsoid

Object[] getEllipsoid(Vector3f[] vectors,
                      float a,
                      float b,
                      float c)

ijkToPoint3f

Point3f ijkToPoint3f(int nnn)

toFractional

void toFractional(Point3f pt,
                  boolean isAbsolute)

getUnitCellVertices

Point3f[] getUnitCellVertices()

getCanonicalCopy

Point3f[] getCanonicalCopy(float scale)

getCartesianOffset

Point3f getCartesianOffset()

getNotionalUnitCell

float[] getNotionalUnitCell()

getUnitCellAsArray

float[] getUnitCellAsArray(boolean vectorsOnly)

toUnitCell

void toUnitCell(Point3f pt,
                Point3f offset)

setUnitCellOffset

void setUnitCellOffset(Point3f pt)

setOffset

void setOffset(int nnn)

getUnitCellMultiplier

Point3f getUnitCellMultiplier()

getUnitCellInfo

float getUnitCellInfo(int infoType)

getCoordinatesAreFractional

boolean getCoordinatesAreFractional()

getCellRange

int[] getCellRange()

getSymmetryInfoString

String getSymmetryInfoString()

getSymmetryOperations

String[] getSymmetryOperations()

haveUnitCell

boolean haveUnitCell()

getUnitCellInfo

String getUnitCellInfo()

isPeriodic

boolean isPeriodic()

setSymmetryInfo

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

getSymmetryOperationDescription

Object[] getSymmetryOperationDescription(int iSym,
                                         SymmetryInterface cellInfo,
                                         Point3f pt1,
                                         Point3f pt2,
                                         String id)

isPolymer

boolean isPolymer()

isSlab

boolean isSlab()

addSpaceGroupOperation

void addSpaceGroupOperation(Matrix4f mat)

setMinMaxLatticeParameters

void setMinMaxLatticeParameters(Point3i minXYZ,
                                Point3i maxXYZ)

setUnitCellOrientation

void setUnitCellOrientation(Matrix3f matUnitCellOrientation)

getMatrixFromString

String getMatrixFromString(String xyz,
                           float[] temp,
                           boolean allowScaling)

checkDistance

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

getFractionalOffset

Point3f getFractionalOffset()

fcoord

String fcoord(Tuple3f p)