Package org.jmol.adapter.smarter
Class XtalSymmetry
java.lang.Object
org.jmol.adapter.smarter.XtalSymmetry
A class used by AtomSetCollection for building the symmetry of a model and
generating new atoms based on that symmetry.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A class only used by adapter.smarter.XtalSymmetry while building the file-based model. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionaddRotatedTensor
(Atom a, Tensor t, int iSym, boolean reset, XtalSymmetry.FileSymmetry symmetry) void
applySymmetryBio
(Map<String, Object> thisBiomolecule, boolean applySymmetryToBonds, String filter) Get the symmetry that was in place prior to any supercell business.boolean
isWithinCell
(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop) boolean
removePacking
(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop) void
magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes.set
(AtomSetCollectionReader reader) void
setLatticeParameter
(int latt) Shelx and Wien2k readersint
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Constructor Details
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XtalSymmetry
public XtalSymmetry()
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Method Details
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addRotatedTensor
public Tensor addRotatedTensor(Atom a, Tensor t, int iSym, boolean reset, XtalSymmetry.FileSymmetry symmetry) -
applySymmetryBio
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getBaseSymmetry
Get the symmetry that was in place prior to any supercell business.- Returns:
- base symmetry
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getOverallSpan
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getSymmetry
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isWithinCell
public boolean isWithinCell(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop) -
scaleFractionalVibs
public void scaleFractionalVibs()magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes. These have to be "fractionalized" in order to be properly handled by symmetry operations, then, in the end, turned into Cartesians. It is not clear to me at all how this would be handled if there are subsystems. This method must be run PRIOR to applying symmetry and thus prior to creation of modulation sets. -
set
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setLatticeParameter
public void setLatticeParameter(int latt) Shelx and Wien2k readers- Parameters:
latt
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setSpinVectors
public int setSpinVectors() -
removePacking
public boolean removePacking(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop) -
newFileSymmetry
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