Symmetry
public interface SymmetryInterface
Modifier and Type | Method | 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) |
|
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) |
|
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() |
|
boolean |
getCoordinatesAreFractional() |
|
javajs.util.P3 |
getFractionalOffset() |
|
javajs.util.T3 |
getFractionalOrigin() |
|
java.lang.String |
getIntTableNumber() |
|
AtomIndexIterator |
getIterator(Viewer vwr,
Atom atom,
Atom[] atoms,
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) |
|
java.lang.String |
getSpaceGroupInfoStr(java.lang.String name,
SymmetryInterface cellInfo) |
|
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) |
|
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() |
|
float |
getUnitCellInfoType(int infoType) |
|
javajs.util.P3 |
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) |
|
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 |
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 |
setMinMaxLatticeParameters(javajs.util.P3i minXYZ,
javajs.util.P3i maxXYZ) |
|
void |
setOffset(int nnn) |
|
void |
setOffsetPt(javajs.util.T3 pt) |
|
SymmetryInterface |
setPointGroup(SymmetryInterface pointGroupPrevious,
javajs.util.T3 center,
javajs.util.T3[] atomset,
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) |
|
void |
setTimeReversal(int op,
int val) |
|
void |
setUnitCell(float[] params,
boolean setRelative) |
|
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.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)
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)
java.lang.String getSpaceGroupInfoStr(java.lang.String name, SymmetryInterface cellInfo)
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)
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.P3 getUnitCellMultiplier()
java.lang.String getUnitCellState()
javajs.util.P3[] getUnitCellVectors()
javajs.util.P3[] getUnitCellVerticesNoOffset()
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.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 setMinMaxLatticeParameters(javajs.util.P3i minXYZ, javajs.util.P3i maxXYZ)
void setOffset(int nnn)
void setOffsetPt(javajs.util.T3 pt)
SymmetryInterface setPointGroup(SymmetryInterface pointGroupPrevious, javajs.util.T3 center, javajs.util.T3[] atomset, 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)
ms
- iatom
- xyz
- op
- pt
- pt2
- id
- 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
- TODOvoid 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, BS bstoms, float radius)
boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc)
java.lang.String getLatticeType()
java.lang.String getIntTableNumber()
javajs.util.Lst<javajs.util.P3> generateCrystalClass(javajs.util.P3 pt0)
void toFractionalM(javajs.util.M4 m)