public class XtalSymmetry
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private boolean |
applySymmetryToBonds |
private AtomSetCollection |
asc |
private int |
bondCount0 |
private boolean |
centroidPacked |
private boolean |
checkAll |
private boolean |
doCentroidUnitCell |
private boolean |
doNormalize |
private boolean |
doPackUnitCell |
private int |
dtype |
private int |
firstSymmetryAtom |
private float[] |
fmatSupercell |
private int[] |
latticeCells |
private boolean |
latticeOnly |
private int |
latticeOp |
private javajs.util.P3i |
maxXYZ |
private javajs.util.P3 |
maxXYZ0 |
private javajs.util.P3i |
minXYZ |
private javajs.util.P3 |
minXYZ0 |
private javajs.util.M3 |
mTemp |
private int |
noSymmetryCount |
private float[] |
notionalUnitCell |
private static int |
PARTICLE_CHAIN |
private static int |
PARTICLE_NONE |
private static int |
PARTICLE_SYMOP |
private javajs.util.P3 |
ptOffset |
private javajs.util.P3 |
ptSupercell |
private javajs.util.P3 |
ptTemp |
private float |
rmaxx |
private float |
rmaxy |
private float |
rmaxz |
private float |
rminx |
private float |
rminy |
private float |
rminz |
private SymmetryInterface |
symmetry |
private float |
symmetryRange |
private javajs.util.P3 |
unitCellOffset |
private javajs.util.V3[] |
unitCellTranslations |
Constructor and Description |
---|
XtalSymmetry() |
Modifier and Type | Method and Description |
---|---|
Tensor |
addRotatedTensor(Atom a,
Tensor t,
int iSym,
boolean reset,
SymmetryInterface symmetry) |
(package private) int |
addSpaceGroupOperation(AtomSetCollectionReader acr,
java.lang.String xyz) |
private void |
appendAtomProperties(int nTimes) |
private void |
applyAllSymmetry(MSInterface ms) |
void |
applySymmetryBio(java.util.Map<java.lang.String,java.lang.Object> thisBiomolecule,
float[] notionalUnitCell,
boolean applySymmetryToBonds,
java.lang.String filter) |
(package private) SymmetryInterface |
applySymmetryFromReader(AtomSetCollectionReader acr,
SymmetryInterface readerSymmetry) |
private void |
applySymmetryLattice(MSInterface ms) |
private void |
finalizeSymmetry(SymmetryInterface symmetry) |
(package private) SymmetryInterface |
getSymmetry() |
private boolean |
isInSymmetryRange(javajs.util.P3 c) |
boolean |
isWithinCell(int dtype,
javajs.util.P3 pt,
float minX,
float maxX,
float minY,
float maxY,
float minZ,
float maxZ,
float slop) |
private void |
reset() |
XtalSymmetry |
set(AtomSetCollection asc) |
(package private) void |
setLatticeCells(AtomSetCollectionReader acr) |
void |
setLatticeParameter(int latt) |
private void |
setNotionalUnitCell(float[] info,
javajs.util.M3 matUnitCellOrientation,
javajs.util.P3 unitCellOffset) |
private void |
setSuperCell(java.lang.String supercell) |
void |
setSupercellFromPoint(javajs.util.P3 pt) |
private javajs.util.P3 |
setSym(int i,
int j,
int k) |
(package private) SymmetryInterface |
setSymmetry(SymmetryInterface symmetry) |
private void |
setSymmetryMinMax(javajs.util.P3 c) |
private void |
setSymmetryOps() |
private void |
setSymmetryRange(float factor) |
(package private) void |
setTensors() |
private int |
symmetryAddAtoms(int transX,
int transY,
int transZ,
int baseCount,
int pt,
int iCellOpPt,
javajs.util.P3[] cartesians,
MSInterface ms) |
private AtomSetCollection asc
private SymmetryInterface symmetry
private float[] notionalUnitCell
private float symmetryRange
private boolean doCentroidUnitCell
private boolean centroidPacked
private boolean applySymmetryToBonds
private int[] latticeCells
private javajs.util.P3 ptSupercell
private float[] fmatSupercell
private boolean doNormalize
private boolean doPackUnitCell
private float rminx
private float rminy
private float rminz
private float rmaxx
private float rmaxy
private float rmaxz
private final javajs.util.P3 ptOffset
private javajs.util.P3 unitCellOffset
private javajs.util.P3i minXYZ
private javajs.util.P3i maxXYZ
private javajs.util.P3 minXYZ0
private javajs.util.P3 maxXYZ0
private boolean checkAll
private int bondCount0
private int dtype
private javajs.util.V3[] unitCellTranslations
private int latticeOp
private boolean latticeOnly
private int noSymmetryCount
private int firstSymmetryAtom
private static final int PARTICLE_NONE
private static final int PARTICLE_CHAIN
private static final int PARTICLE_SYMOP
private javajs.util.P3 ptTemp
private javajs.util.M3 mTemp
public XtalSymmetry set(AtomSetCollection asc)
SymmetryInterface getSymmetry()
SymmetryInterface setSymmetry(SymmetryInterface symmetry)
private void setSymmetryRange(float factor)
void setLatticeCells(AtomSetCollectionReader acr)
public void setSupercellFromPoint(javajs.util.P3 pt)
private void setSuperCell(java.lang.String supercell)
private void setNotionalUnitCell(float[] info, javajs.util.M3 matUnitCellOrientation, javajs.util.P3 unitCellOffset)
int addSpaceGroupOperation(AtomSetCollectionReader acr, java.lang.String xyz)
public void setLatticeParameter(int latt)
SymmetryInterface applySymmetryFromReader(AtomSetCollectionReader acr, SymmetryInterface readerSymmetry) throws java.lang.Exception
java.lang.Exception
private void applySymmetryLattice(MSInterface ms) throws java.lang.Exception
java.lang.Exception
private javajs.util.P3 setSym(int i, int j, int k)
private void setSymmetryMinMax(javajs.util.P3 c)
private boolean isInSymmetryRange(javajs.util.P3 c)
public boolean isWithinCell(int dtype, javajs.util.P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop)
private int symmetryAddAtoms(int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt, javajs.util.P3[] cartesians, MSInterface ms) throws java.lang.Exception
java.lang.Exception
private void applyAllSymmetry(MSInterface ms) throws java.lang.Exception
ms
- modulated structure interfacejava.lang.Exception
private void appendAtomProperties(int nTimes)
private void finalizeSymmetry(SymmetryInterface symmetry)
private void setSymmetryOps()
public void applySymmetryBio(java.util.Map<java.lang.String,java.lang.Object> thisBiomolecule, float[] notionalUnitCell, boolean applySymmetryToBonds, java.lang.String filter)
private void reset()
public Tensor addRotatedTensor(Atom a, Tensor t, int iSym, boolean reset, SymmetryInterface symmetry)
void setTensors()