org.jmol.api
Interface SymmetryInterface

All Known Implementing Classes:
Symmetry

public interface SymmetryInterface


Method Summary
 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()
           
 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 pointGroupPrevious, 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 pt, boolean asAbsolue)
           
 void toFractional(javax.vecmath.Point3f pt, boolean isAbsolute)
           
 void toUnitCell(javax.vecmath.Point3f pt, javax.vecmath.Point3f offset)
           
 

Method Detail

setPointGroup

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

getPointGroupName

java.lang.String getPointGroupName()

getPointGroupInfo

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

setSpaceGroup

void setSpaceGroup(boolean doNormalize)

addSpaceGroupOperation

int addSpaceGroupOperation(java.lang.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

java.lang.String getSpaceGroupName()

getSpaceGroup

java.lang.Object getSpaceGroup()

setSpaceGroup

void setSpaceGroup(SymmetryInterface symmetry)

createSpaceGroup

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

haveSpaceGroup

boolean haveSpaceGroup()

getSpaceGroupInfo

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

getLatticeDesignation

java.lang.Object getLatticeDesignation()

setFinalOperations

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

getSpaceGroupOperationCount

int getSpaceGroupOperationCount()

getSpaceGroupOperation

javax.vecmath.Matrix4f getSpaceGroupOperation(int i)

getSpaceGroupXyz

java.lang.String getSpaceGroupXyz(int i,
                                  boolean doNormalize)

newSpaceGroupPoint

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

rotateEllipsoid

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

setUnitCellAllFractionalRelative

void setUnitCellAllFractionalRelative(boolean TF)

setUnitCell

void setUnitCell(float[] notionalUnitCell)

toCartesian

void toCartesian(javax.vecmath.Point3f pt,
                 boolean asAbsolue)

getEllipsoid

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

getEllipsoid

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

ijkToPoint3f

javax.vecmath.Point3f ijkToPoint3f(int nnn)

toFractional

void toFractional(javax.vecmath.Point3f pt,
                  boolean isAbsolute)

getUnitCellVertices

javax.vecmath.Point3f[] getUnitCellVertices()

getCanonicalCopy

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

getCartesianOffset

javax.vecmath.Point3f getCartesianOffset()

getNotionalUnitCell

float[] getNotionalUnitCell()

getUnitCellAsArray

float[] getUnitCellAsArray(boolean vectorsOnly)

toUnitCell

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

setUnitCellOffset

void setUnitCellOffset(javax.vecmath.Point3f pt)

setOffset

void setOffset(int nnn)

getUnitCellMultiplier

javax.vecmath.Point3f getUnitCellMultiplier()

getUnitCellInfo

float getUnitCellInfo(int infoType)

getCoordinatesAreFractional

boolean getCoordinatesAreFractional()

getCellRange

int[] getCellRange()

getSymmetryInfoString

java.lang.String getSymmetryInfoString()

getSymmetryOperations

java.lang.String[] getSymmetryOperations()

haveUnitCell

boolean haveUnitCell()

getUnitCellInfo

java.lang.String getUnitCellInfo()

isPeriodic

boolean isPeriodic()

setSymmetryInfo

void setSymmetryInfo(int modelIndex,
                     java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo)

getSymmetryOperationDescription

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

isPolymer

boolean isPolymer()

isSlab

boolean isSlab()

addSpaceGroupOperation

void addSpaceGroupOperation(javax.vecmath.Matrix4f mat)

setMinMaxLatticeParameters

void setMinMaxLatticeParameters(javax.vecmath.Point3i minXYZ,
                                javax.vecmath.Point3i maxXYZ)

setUnitCellOrientation

void setUnitCellOrientation(javax.vecmath.Matrix3f matUnitCellOrientation)

getMatrixFromString

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

checkDistance

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

getFractionalOffset

javax.vecmath.Point3f getFractionalOffset()

fcoord

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