public interface SymmetryInterface
Modifier and Type | Method and Description |
---|---|
int |
addBioMoleculeOperation(javajs.util.M4 mat,
boolean isReverse) |
void |
addLatticeVectors(javajs.util.List<float[]> lattvecs) |
String |
addOp(javajs.util.Matrix rs,
javajs.util.Matrix vs) |
int |
addSpaceGroupOperation(String xyz,
int opId) |
boolean |
checkDistance(javajs.util.P3 f1,
javajs.util.P3 f2,
float distance,
float dx,
int iRange,
int jRange,
int kRange,
javajs.util.P3 ptOffset) |
boolean |
checkUnitCell(SymmetryInterface uc,
javajs.util.P3 cell,
javajs.util.P3 ptTemp,
boolean isAbsolute) |
boolean |
createSpaceGroup(int desiredSpaceGroupIndex,
String name,
Object object) |
String |
fcoord(javajs.util.T3 p) |
javajs.util.P3[] |
getCanonicalCopy(float scale,
boolean withOffset) |
javajs.util.P3 |
getCartesianOffset() |
int[] |
getCellRange() |
boolean |
getCoordinatesAreFractional() |
javajs.util.P3 |
getFractionalOffset() |
Object |
getLatticeDesignation() |
int |
getLatticeOp() |
String |
getMatrixFromString(String xyz,
float[] temp,
boolean allowScaling,
int modDim) |
float[] |
getNotionalUnitCell() |
javajs.util.Matrix |
getOperationRsVs(int iop) |
Object |
getPointGroupInfo(int modelIndex,
boolean asDraw,
boolean asInfo,
String type,
int index,
float scale) |
String |
getPointGroupName() |
int |
getSiteMultiplicity(javajs.util.P3 a) |
Object |
getSpaceGroup() |
Map<String,Object> |
getSpaceGroupInfo(ModelSet modelSet,
int modelIndex,
String spaceGroup,
int symOp,
javajs.util.P3 pt1,
javajs.util.P3 pt2,
String drawID) |
String |
getSpaceGroupInfo(String name,
SymmetryInterface cellInfo) |
String |
getSpaceGroupName() |
javajs.util.M4 |
getSpaceGroupOperation(int i) |
int |
getSpaceGroupOperationCount() |
String |
getSpaceGroupXyz(int i,
boolean doNormalize) |
Object |
getSymmetryInfo(ModelSet modelSet,
int iModel,
int iAtom,
SymmetryInterface uc,
String xyz,
int op,
javajs.util.P3 pt,
javajs.util.P3 pt2,
String id,
int type) |
String |
getSymmetryInfoString() |
String |
getSymmetryInfoString(Map<String,Object> sginfo,
int symOp,
String drawID,
boolean labelOnly) |
String[] |
getSymmetryOperations() |
Tensor |
getTensor(float[] parBorU) |
SymmetryInterface |
getUnitCell(javajs.util.T3[] points,
boolean setRelative) |
float[] |
getUnitCellAsArray(boolean vectorsOnly) |
String |
getUnitCellInfo() |
float |
getUnitCellInfoType(int infoType) |
javajs.util.P3 |
getUnitCellMultiplier() |
String |
getUnitCellState() |
javajs.util.V3[] |
getUnitCellVectors() |
javajs.util.P3[] |
getUnitCellVertices() |
boolean |
haveUnitCell() |
boolean |
isBio() |
boolean |
isPeriodic() |
boolean |
isPolymer() |
boolean |
isSlab() |
boolean |
isSupercell() |
void |
newSpaceGroupPoint(int i,
javajs.util.P3 atom1,
javajs.util.P3 atom2,
int transX,
int transY,
int transZ) |
BS |
notInCentroid(ModelSet modelSet,
BS bsAtoms,
int[] minmax) |
javajs.util.V3[] |
rotateAxes(int iop,
javajs.util.V3[] axes,
javajs.util.P3 ptTemp,
javajs.util.M3 mTemp) |
void |
setCartesianOffset(javajs.util.T3 origin) |
void |
setFinalOperations(String name,
javajs.util.P3[] atoms,
int iAtomFirst,
int noSymmetryCount,
boolean doNormalize) |
void |
setLattice(int latt)
set symmetry lattice type using Hall rotations
|
void |
setMinMaxLatticeParameters(javajs.util.P3i minXYZ,
javajs.util.P3i maxXYZ) |
void |
setOffset(int nnn) |
void |
setOffsetPt(javajs.util.P3 pt) |
SymmetryInterface |
setPointGroup(SymmetryInterface pointGroupPrevious,
Atom[] atomset,
BS bsAtoms,
boolean haveVibration,
float distanceTolerance,
float linearTolerance) |
void |
setSpaceGroup(boolean doNormalize) |
void |
setSpaceGroupS(SymmetryInterface symmetry) |
void |
setSymmetryInfo(int modelIndex,
Map<String,Object> modelAuxiliaryInfo) |
void |
setUnitCell(float[] notionalUnitCell) |
void |
setUnitCellAllFractionalRelative(boolean TF) |
void |
setUnitCellOrientation(javajs.util.M3 matUnitCellOrientation) |
void |
toCartesian(javajs.util.T3 pt,
boolean asAbsolue) |
void |
toFractional(javajs.util.T3 pt,
boolean isAbsolute) |
javajs.util.P3 |
toSupercell(javajs.util.P3 fpt) |
void |
toUnitCell(javajs.util.P3 pt,
javajs.util.P3 offset) |
boolean |
unitCellEquals(SymmetryInterface uc2) |
void |
unitize(javajs.util.P3 ptFrac) |
SymmetryInterface setPointGroup(SymmetryInterface pointGroupPrevious, Atom[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance)
String getPointGroupName()
Object getPointGroupInfo(int modelIndex, boolean asDraw, boolean asInfo, String type, int index, float scale)
void setSpaceGroup(boolean doNormalize)
int addSpaceGroupOperation(String xyz, int opId)
void setLattice(int latt)
latt
- SHELX index or character lattice character P I R F A B C S T or \0String getSpaceGroupName()
Object getSpaceGroup()
void setSpaceGroupS(SymmetryInterface symmetry)
String getSpaceGroupInfo(String name, SymmetryInterface cellInfo)
Object getLatticeDesignation()
void setFinalOperations(String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize)
int getSpaceGroupOperationCount()
javajs.util.M4 getSpaceGroupOperation(int i)
String getSpaceGroupXyz(int i, boolean doNormalize)
void newSpaceGroupPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ)
javajs.util.V3[] rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
void setUnitCellAllFractionalRelative(boolean TF)
void setUnitCell(float[] notionalUnitCell)
void toCartesian(javajs.util.T3 pt, boolean asAbsolue)
Tensor getTensor(float[] parBorU)
void toFractional(javajs.util.T3 pt, boolean isAbsolute)
javajs.util.P3[] getUnitCellVertices()
javajs.util.P3[] getCanonicalCopy(float scale, boolean withOffset)
javajs.util.P3 getCartesianOffset()
float[] getNotionalUnitCell()
float[] getUnitCellAsArray(boolean vectorsOnly)
void toUnitCell(javajs.util.P3 pt, javajs.util.P3 offset)
void setOffsetPt(javajs.util.P3 pt)
void setOffset(int nnn)
javajs.util.P3 getUnitCellMultiplier()
float getUnitCellInfoType(int infoType)
boolean getCoordinatesAreFractional()
int[] getCellRange()
String getSymmetryInfoString()
String[] getSymmetryOperations()
boolean haveUnitCell()
String getUnitCellInfo()
boolean isPeriodic()
boolean isBio()
boolean isPolymer()
boolean isSlab()
int addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)
void setMinMaxLatticeParameters(javajs.util.P3i minXYZ, javajs.util.P3i maxXYZ)
void setUnitCellOrientation(javajs.util.M3 matUnitCellOrientation)
String getMatrixFromString(String xyz, float[] temp, boolean allowScaling, int modDim)
boolean checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)
javajs.util.P3 getFractionalOffset()
String fcoord(javajs.util.T3 p)
void setCartesianOffset(javajs.util.T3 origin)
javajs.util.V3[] getUnitCellVectors()
SymmetryInterface getUnitCell(javajs.util.T3[] points, boolean setRelative)
javajs.util.P3 toSupercell(javajs.util.P3 fpt)
boolean isSupercell()
String getSymmetryInfoString(Map<String,Object> sginfo, int symOp, String drawID, boolean labelOnly)
Map<String,Object> getSpaceGroupInfo(ModelSet modelSet, int modelIndex, String spaceGroup, int symOp, javajs.util.P3 pt1, javajs.util.P3 pt2, String drawID)
Object getSymmetryInfo(ModelSet modelSet, int iModel, int iAtom, SymmetryInterface uc, String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type)
boolean checkUnitCell(SymmetryInterface uc, javajs.util.P3 cell, javajs.util.P3 ptTemp, boolean isAbsolute)
boolean unitCellEquals(SymmetryInterface uc2)
void unitize(javajs.util.P3 ptFrac)
void addLatticeVectors(javajs.util.List<float[]> lattvecs)
int getLatticeOp()
javajs.util.Matrix getOperationRsVs(int iop)
int getSiteMultiplicity(javajs.util.P3 a)
String addOp(javajs.util.Matrix rs, javajs.util.Matrix vs)
String getUnitCellState()