public interface SymmetryInterface
Modifier and Type | Method and Description |
---|---|
int |
addBioMoleculeOperation(javajs.util.M4 mat,
boolean isReverse) |
boolean |
addLatticeVectors(javajs.util.Lst<float[]> lattvecs) |
java.lang.String |
addOp(java.lang.String code,
javajs.util.Matrix rs,
javajs.util.Matrix vs,
javajs.util.Matrix sigma) |
int |
addSpaceGroupOperation(java.lang.String xyz,
int opId) |
void |
calculateCIPChiralityForAtoms(Viewer vwr,
javajs.util.BS bsAtoms) |
java.lang.String[] |
calculateCIPChiralityForSmiles(Viewer vwr,
java.lang.String smiles) |
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,
java.lang.String name,
java.lang.Object data,
int modDim) |
java.lang.String |
fcoord(javajs.util.T3 p) |
javajs.util.Lst<javajs.util.P3> |
generateCrystalClass(javajs.util.P3 pt0) |
javajs.util.P3[] |
getCanonicalCopy(float scale,
boolean withOffset) |
javajs.util.P3 |
getCartesianOffset() |
int[] |
getCellRange() |
javajs.util.T3[] |
getConventionalUnitCell(java.lang.String latticeType,
javajs.util.M3 primitiveToCryst) |
boolean |
getCoordinatesAreFractional() |
javajs.util.P3 |
getFractionalOffset() |
javajs.util.T3 |
getFractionalOrigin() |
java.lang.String |
getIntTableNumber() |
AtomIndexIterator |
getIterator(Viewer vwr,
Atom atom,
Atom[] atoms,
javajs.util.BS bstoms,
float radius) |
java.lang.Object |
getLatticeDesignation() |
int |
getLatticeOp() |
java.lang.String |
getLatticeType() |
java.lang.String |
getMatrixFromString(java.lang.String xyz,
float[] temp,
boolean allowScaling,
int modDim) |
javajs.util.Lst<java.lang.String> |
getMoreInfo() |
javajs.util.Matrix |
getOperationRsVs(int op) |
java.lang.Object |
getPointGroupInfo(int modelIndex,
java.lang.String drawID,
boolean asInfo,
java.lang.String type,
int index,
float scale) |
java.lang.String |
getPointGroupName() |
javajs.util.Quat |
getQuaternionRotation(java.lang.String abc) |
int |
getSiteMultiplicity(javajs.util.P3 a) |
java.lang.Object |
getSpaceGroup() |
java.util.Map<java.lang.String,java.lang.Object> |
getSpaceGroupInfo(ModelSet modelSet,
java.lang.String spaceGroup,
int modelIndex,
boolean isFull,
float[] cellParams) |
java.lang.Object |
getSpaceGroupInfoObj(java.lang.String name,
SymmetryInterface cellInfo,
boolean isFull) |
java.lang.String |
getSpaceGroupName() |
javajs.util.M4 |
getSpaceGroupOperation(int i) |
java.lang.String |
getSpaceGroupOperationCode(int op) |
int |
getSpaceGroupOperationCount() |
java.lang.String |
getSpaceGroupXyz(int i,
boolean doNormalize) |
float |
getSpinOp(int op) |
boolean |
getState(javajs.util.SB commands) |
java.lang.Object |
getSymmetryInfoAtom(ModelSet ms,
int iatom,
java.lang.String xyz,
int op,
javajs.util.P3 pt,
javajs.util.P3 pt2,
java.lang.String id,
int type,
float scaleFactor,
int nth,
int options) |
java.lang.String |
getSymmetryInfoStr() |
javajs.util.M4[] |
getSymmetryOperations() |
Tensor |
getTensor(Viewer vwr,
float[] anisoBorU) |
SymmetryInterface |
getUnitCell(javajs.util.T3[] points,
boolean setRelative,
java.lang.String name) |
float[] |
getUnitCellAsArray(boolean vectorsOnly) |
java.lang.String |
getUnitCellInfo() |
java.util.Map<java.lang.String,java.lang.Object> |
getUnitCellInfoMap() |
float |
getUnitCellInfoType(int infoType) |
javajs.util.T3 |
getUnitCellMultiplier() |
float[] |
getUnitCellParams() |
java.lang.String |
getUnitCellState() |
javajs.util.P3[] |
getUnitCellVectors() |
javajs.util.P3[] |
getUnitCellVerticesNoOffset() |
javajs.util.T3[] |
getV0abc(java.lang.Object def) |
boolean |
haveUnitCell() |
void |
initializeOrientation(javajs.util.M3 matUnitCellOrientation) |
boolean |
isBio() |
boolean |
isPolymer() |
boolean |
isSimple() |
boolean |
isSlab() |
boolean |
isSupercell() |
void |
newSpaceGroupPoint(int i,
javajs.util.P3 atom1,
javajs.util.P3 atom2,
int transX,
int transY,
int transZ,
javajs.util.M4 o) |
javajs.util.BS |
notInCentroid(ModelSet modelSet,
javajs.util.BS bsAtoms,
int[] minmax) |
javajs.util.V3[] |
rotateAxes(int iop,
javajs.util.V3[] axes,
javajs.util.P3 ptTemp,
javajs.util.M3 mTemp) |
void |
setFinalOperations(java.lang.String name,
javajs.util.P3[] atoms,
int iAtomFirst,
int noSymmetryCount,
boolean doNormalize,
java.lang.String filterSymop) |
void |
setLattice(int latt)
set symmetry lattice type using Hall rotations
|
void |
setLatticeType(java.lang.String type) |
void |
setOffset(int nnn) |
void |
setOffsetPt(javajs.util.T3 pt) |
SymmetryInterface |
setPointGroup(SymmetryInterface pointGroupPrevious,
javajs.util.T3 center,
javajs.util.T3[] atomset,
javajs.util.BS bsAtoms,
boolean haveVibration,
float distanceTolerance,
float linearTolerance,
boolean localEnvOnly) |
void |
setSpaceGroup(boolean doNormalize) |
void |
setSpaceGroupFrom(SymmetryInterface symmetry) |
void |
setSpaceGroupName(java.lang.String name) |
SymmetryInterface |
setSymmetryInfo(int modelIndex,
java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo,
float[] notionalCell) |
void |
setTimeReversal(int op,
int val) |
void |
setUnitCell(float[] params,
boolean setRelative) |
void |
setUnitCell(Symmetry uc) |
void |
toCartesian(javajs.util.T3 pt,
boolean asAbsolute) |
void |
toFractional(javajs.util.T3 pt,
boolean asAbsolute) |
void |
toFractionalM(javajs.util.M4 m) |
boolean |
toFromPrimitive(boolean toPrimitive,
char type,
javajs.util.T3[] oabc,
javajs.util.M3 primitiveToCrystal) |
javajs.util.P3 |
toSupercell(javajs.util.P3 fpt) |
void |
toUnitCell(javajs.util.T3 pt,
javajs.util.T3 offset) |
boolean |
unitCellEquals(SymmetryInterface uc2) |
void |
unitize(javajs.util.T3 ptFrac) |
int addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)
boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
java.lang.String addOp(java.lang.String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)
int addSpaceGroupOperation(java.lang.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, java.lang.String name, java.lang.Object data, int modDim)
java.lang.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()
java.lang.Object getLatticeDesignation()
int getLatticeOp()
java.lang.String getMatrixFromString(java.lang.String xyz, float[] temp, boolean allowScaling, int modDim)
javajs.util.Lst<java.lang.String> getMoreInfo()
float[] getUnitCellParams()
javajs.util.Matrix getOperationRsVs(int op)
java.lang.Object getPointGroupInfo(int modelIndex, java.lang.String drawID, boolean asInfo, java.lang.String type, int index, float scale)
java.lang.String getPointGroupName()
int getSiteMultiplicity(javajs.util.P3 a)
java.lang.Object getSpaceGroup()
java.util.Map<java.lang.String,java.lang.Object> getSpaceGroupInfo(ModelSet modelSet, java.lang.String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)
java.lang.Object getSpaceGroupInfoObj(java.lang.String name, SymmetryInterface cellInfo, boolean isFull)
java.lang.String getSpaceGroupName()
void setSpaceGroupName(java.lang.String name)
javajs.util.M4 getSpaceGroupOperation(int i)
java.lang.String getSpaceGroupOperationCode(int op)
int getSpaceGroupOperationCount()
java.lang.String getSpaceGroupXyz(int i, boolean doNormalize)
java.lang.String getSymmetryInfoStr()
javajs.util.M4[] getSymmetryOperations()
float getSpinOp(int op)
SymmetryInterface getUnitCell(javajs.util.T3[] points, boolean setRelative, java.lang.String name)
float[] getUnitCellAsArray(boolean vectorsOnly)
java.lang.String getUnitCellInfo()
float getUnitCellInfoType(int infoType)
javajs.util.T3 getUnitCellMultiplier()
java.lang.String getUnitCellState()
javajs.util.P3[] getUnitCellVectors()
javajs.util.P3[] getUnitCellVerticesNoOffset()
java.util.Map<java.lang.String,java.lang.Object> getUnitCellInfoMap()
boolean haveUnitCell()
boolean isBio()
boolean isSimple()
boolean isPolymer()
boolean isSlab()
boolean isSupercell()
void newSpaceGroupPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ, javajs.util.M4 o)
javajs.util.BS notInCentroid(ModelSet modelSet, javajs.util.BS bsAtoms, int[] minmax)
javajs.util.V3[] rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
void setFinalOperations(java.lang.String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, java.lang.String filterSymop)
void setLattice(int latt)
latt
- SHELX index or character lattice character P I R F A B C S T or \0void setOffset(int nnn)
void setOffsetPt(javajs.util.T3 pt)
SymmetryInterface setPointGroup(SymmetryInterface pointGroupPrevious, javajs.util.T3 center, javajs.util.T3[] atomset, javajs.util.BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, boolean localEnvOnly)
void setSpaceGroup(boolean doNormalize)
void setSpaceGroupFrom(SymmetryInterface symmetry)
SymmetryInterface setSymmetryInfo(int modelIndex, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo, float[] notionalCell)
java.lang.Object getSymmetryInfoAtom(ModelSet ms, int iatom, java.lang.String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, java.lang.String id, int type, float scaleFactor, int nth, int options)
ms
- iatom
- xyz
- op
- pt
- pt2
- a second point or an offsetid
- type
- T.point, T.lattice, or T.draw, T.matrix4f, T.label, T.list, T.info, T.translation, T.axis, T.plane, T.angle, T.centerscaleFactor
- nth
- TODOoptions
- could be T.offsetvoid setTimeReversal(int op, int val)
void setUnitCell(float[] params, boolean setRelative)
void initializeOrientation(javajs.util.M3 matUnitCellOrientation)
void toCartesian(javajs.util.T3 pt, boolean asAbsolute)
void toFractional(javajs.util.T3 pt, boolean asAbsolute)
javajs.util.P3 toSupercell(javajs.util.P3 fpt)
void toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)
boolean unitCellEquals(SymmetryInterface uc2)
void unitize(javajs.util.T3 ptFrac)
javajs.util.T3[] getV0abc(java.lang.Object def)
javajs.util.Quat getQuaternionRotation(java.lang.String abc)
javajs.util.T3 getFractionalOrigin()
boolean getState(javajs.util.SB commands)
AtomIndexIterator getIterator(Viewer vwr, Atom atom, Atom[] atoms, javajs.util.BS bstoms, float radius)
boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc, javajs.util.M3 primitiveToCrystal)
java.lang.String getLatticeType()
void setLatticeType(java.lang.String type)
java.lang.String getIntTableNumber()
javajs.util.Lst<javajs.util.P3> generateCrystalClass(javajs.util.P3 pt0)
void toFractionalM(javajs.util.M4 m)
void calculateCIPChiralityForAtoms(Viewer vwr, javajs.util.BS bsAtoms)
java.lang.String[] calculateCIPChiralityForSmiles(Viewer vwr, java.lang.String smiles) throws java.lang.Exception
java.lang.Exception
javajs.util.T3[] getConventionalUnitCell(java.lang.String latticeType, javajs.util.M3 primitiveToCryst)
void setUnitCell(Symmetry uc)