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 createSpaceGroup(int desiredSpaceGroupIndex, String name, float[] notionalUnitCell, boolean doNormalize)
           
 Point3f[] getCanonicalCopy(float scale)
           
 Point3f getCartesianOffset()
           
 int[] getCellRange()
           
 boolean getCoordinatesAreFractional()
           
 Object[] getEllipsoid(float[] parBorU)
           
 Point3f getFractionalOffset()
           
 Object getLatticeDesignation()
           
 int getModelIndex()
           
 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()
           
 float getUnitCellAsArray(int infoType)
           
 String getUnitCellInfo()
           
 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 setModelIndex(int i)
           
 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, Hashtable 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,
                         boolean doNormalize)

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)

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()

toUnitCell

void toUnitCell(Point3f pt,
                Point3f offset)

setUnitCellOffset

void setUnitCellOffset(Point3f pt)

setOffset

void setOffset(int nnn)

getFractionalOffset

Point3f getFractionalOffset()

getUnitCellAsArray

float getUnitCellAsArray(int infoType)

getModelIndex

int getModelIndex()

setModelIndex

void setModelIndex(int i)

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,
                     Hashtable 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)