Uses of Class
org.jmol.adapter.smarter.Atom
Packages that use Atom
Package
Description
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Uses of Atom in org.jmol.adapter.readers.cif
Methods in org.jmol.adapter.readers.cif that return AtomMethods in org.jmol.adapter.readers.cif with parameters of type AtomModifier and TypeMethodDescriptionprotected boolean
CifReader.addCifAtom
(Atom atom, String id, String componentId, String strChain) protected boolean
CifReader.filterCIFAtom
(Atom atom, String componentId) MSRdr.getAtomSymmetry
(Atom a, XtalSymmetry.FileSymmetry defaultSymmetry) When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.protected boolean
CifReader.processSubclassAtom
(Atom atom, String assemblyId, String strChain) boolean
MMCifReader.processSubclassAtom
(Atom atom, String assemblyId, String strChain) -
Uses of Atom in org.jmol.adapter.readers.molxyz
Methods in org.jmol.adapter.readers.molxyz that return AtomModifier and TypeMethodDescriptionMolReader.addMolAtom
(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z) Methods in org.jmol.adapter.readers.molxyz with parameters of type Atom -
Uses of Atom in org.jmol.adapter.readers.more
Methods in org.jmol.adapter.readers.more with parameters of type AtomModifier and TypeMethodDescriptionprotected boolean
ForceFieldReader.getElementSymbol
(Atom atom, String atomType) -
Uses of Atom in org.jmol.adapter.readers.pdb
Methods in org.jmol.adapter.readers.pdb that return AtomModifier and TypeMethodDescriptionprotected Atom
PdbReader.processAtom
(Atom atom, String name, char altID, String group3, int chainID, int seqNo, char insCode, boolean isHetero, String sym) Methods in org.jmol.adapter.readers.pdb with parameters of type AtomModifier and TypeMethodDescriptionprotected boolean
PdbReader.filterPDBAtom
(Atom atom, int iAtom) protected Atom
PdbReader.processAtom
(Atom atom, String name, char altID, String group3, int chainID, int seqNo, char insCode, boolean isHetero, String sym) protected void
PdbReader.processAtom2
(Atom atom, int serial, float x, float y, float z, int charge) protected void
JmolDataReader.setAdditionalAtomParameters
(Atom atom) protected void
P2nReader.setAdditionalAtomParameters
(Atom atom) protected void
PdbReader.setAdditionalAtomParameters
(Atom atom) adaptable via subclassingprotected void
PqrReader.setAdditionalAtomParameters
(Atom atom) -
Uses of Atom in org.jmol.adapter.readers.pymol
Methods in org.jmol.adapter.readers.pymol with parameters of type AtomModifier and TypeMethodDescriptionprotected void
PyMOLReader.setAdditionalAtomParameters
(Atom atom) -
Uses of Atom in org.jmol.adapter.readers.quantum
Methods in org.jmol.adapter.readers.quantum with parameters of type Atom -
Uses of Atom in org.jmol.adapter.readers.simple
Fields in org.jmol.adapter.readers.simple with type parameters of type AtomMethods in org.jmol.adapter.readers.simple that return AtomMethods in org.jmol.adapter.readers.simple with parameters of type Atom -
Uses of Atom in org.jmol.adapter.readers.xml
Fields in org.jmol.adapter.readers.xml declared as Atom -
Uses of Atom in org.jmol.adapter.readers.xtal
Methods in org.jmol.adapter.readers.xtal with parameters of type AtomModifier and TypeMethodDescriptionvoid
SiestaReader.setAtomCoordXYZ
(Atom atom, float x, float y, float z) -
Uses of Atom in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter declared as AtomFields in org.jmol.adapter.smarter with type parameters of type AtomMethods in org.jmol.adapter.smarter that return AtomModifier and TypeMethodDescriptionAtomSetCollectionReader.addAtomXYZSymName
(String[] tokens, int i, String sym, String name) AtomSetCollection.addNewAtom()
Atom.copyTo
(P3 pt, AtomSetCollection asc) AtomSetCollection.getAtomFromName
(String atomName) Atom.getClone()
AtomSetCollection.newCloneAtom
(Atom atom) AtomSetCollectionReader.setAtomCoordScaled
(Atom atom, String[] tokens, int i, float f) Methods in org.jmol.adapter.smarter with parameters of type AtomModifier and TypeMethodDescriptionvoid
AtomSetCollection.addAtomWithMappedName
(Atom atom) void
AtomSetCollection.addAtomWithMappedSerialNumber
(Atom atom) AtomSetCollection.addNewBondWithOrderA
(Atom atom1, Atom atom2, int order) XtalSymmetry.addRotatedTensor
(Atom a, Tensor t, int iSym, boolean reset, XtalSymmetry.FileSymmetry symmetry) protected boolean
AtomSetCollectionReader.filterAtom
(Atom atom, int iAtom) MSInterface.getAtomSymmetry
(Atom a, XtalSymmetry.FileSymmetry symmetry) AtomSetCollection.newCloneAtom
(Atom atom) void
AtomSetCollection.setAnisoBorU
(Atom atom, float[] data, int type) void
AtomSetCollectionReader.setAtomCoord
(Atom atom) AtomSetCollectionReader.setAtomCoordScaled
(Atom atom, String[] tokens, int i, float f) protected void
AtomSetCollectionReader.setAtomCoordTokens
(Atom atom, String[] tokens, int i) void
AtomSetCollectionReader.setAtomCoordXYZ
(Atom atom, float x, float y, float z) void
AtomSetCollectionReader.setChainID
(Atom atom, String label) protected void
AtomSetCollectionReader.setElementAndIsotope
(Atom atom, String str) allow 13C, 15N, 2H, etc.void