Uses of Class
org.jmol.modelset.Atom
Packages that use Atom
Package
Description
Provides a software implementation of complete 3D graphics engine
for rendering molecules and associated shapes.
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
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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.api
Methods in org.jmol.api with parameters of type AtomModifier and TypeMethodDescriptionvoid
JmolAnnotationParser.getAtomValidation
(Viewer vwr, String type, Atom atom) float
JmolNMRInterface.getChemicalShift
(Atom atom) If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shieldingfloat
JmolNMRInterface.getDipolarConstantHz
(Atom a1, Atom a2) float
JmolNMRInterface.getDipolarCouplingHz
(Atom a1, Atom a2, V3 vField) float
JmolNMRInterface.getIsoOrAnisoHz
(boolean isIso, Atom a1, Atom a2, String type, Tensor t) If t is null, then a1, a2, and type are used to find the appropriate tensor.SymmetryInterface.getIterator
(Viewer vwr, Atom atom, BS bstoms, float radius) float
JmolNMRInterface.getMagneticShielding
(Atom atom) int[][]
SmilesMatcherInterface.getMapForJME
(String jme, Atom[] at, BS bsAtoms) double[]
JmolNMRInterface.getNOEorJHH
(Atom[] atoms, int mode) Method parameters in org.jmol.api with type arguments of type Atom -
Uses of Atom in org.jmol.atomdata
Fields in org.jmol.atomdata declared as Atom -
Uses of Atom in org.jmol.c
Methods in org.jmol.c with parameters of type Atom -
Uses of Atom in org.jmol.dssx
Methods in org.jmol.dssx with parameters of type Atom -
Uses of Atom in org.jmol.export
Methods in org.jmol.export with parameters of type Atom -
Uses of Atom in org.jmol.g3d
Methods in org.jmol.g3d with parameters of type Atom -
Uses of Atom in org.jmol.minimize
Fields in org.jmol.minimize declared as Atom -
Uses of Atom in org.jmol.minimize.forcefield
Methods in org.jmol.minimize.forcefield with parameters of type AtomModifier and TypeMethodDescriptionfloat[]
ForceFieldMMFF.calculatePartialCharges
(Bond[] bonds, int[] bTypes, Atom[] atoms, int[] aTypes, BS bsAtoms, boolean doRound) assign partial charges ala MMFF94boolean
ForceFieldMMFF.setArrays
(Atom[] atoms, BS bsAtoms, Bond[] bonds, int rawBondCount, boolean doRound, boolean allowUnknowns) -
Uses of Atom in org.jmol.modelkit
Methods in org.jmol.modelkit that return Atom -
Uses of Atom in org.jmol.modelset
Fields in org.jmol.modelset declared as AtomModifier and TypeFieldDescriptionAtom[]
AtomCollection.at
Bond.atom1
Bond.atom2
protected final Atom[]
ModelSet.closest
Methods in org.jmol.modelset that return AtomModifier and TypeMethodDescriptionModelSet.addAtom
(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, boolean isNegDisorder, byte specialAtomID, BS atomSymmetry, float bondRadius) Atom.findAromaticNeighbor
(int notAtomIndex) AtomCollection.getAtom
(int iatom) ModelSet.getBasisAtom
(int iatom, boolean doCheck) Group.getCarbonylOxygenAtom()
Group.getLeadAtom()
Group.getLeadAtomOr
(Atom atom) Group.getNitrogenAtom()
Bond.getOtherAtom
(Atom thisAtom) Atom.setAtom
(int modelIndex, int atomIndex, P3 xyz, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, boolean isNegDisorder) Methods in org.jmol.modelset with parameters of type AtomModifier and TypeMethodDescriptionvoid
BondCollection.addConnectedHAtoms
(Atom atom, BS bsAtoms) int
BondCollection.bondAtoms
(Atom atom1, Atom atom2, int order, short mad, BS bsBonds, float energy, boolean addGroup, boolean isNew) protected Bond
BondCollection.bondMutually
(Atom atom, Atom atomOther, int order, short mad, float energy) int
protected void
AtomCollection.findNearest2
(int x, int y, Atom[] closest, BS bsNot, int min) LabelToken.formatLabel
(Viewer vwr, Atom atom, String strFormat, P3 ptTemp) static String
LabelToken.formatLabelAtomArray
(Viewer vwr, Atom atom, LabelToken[] tokens, char chAtom, int[] indices, P3 ptTemp) returns a formatted string based on the precompiled label tokensint
ModelSet.getAtomCIPChiralityCode
(Atom atom) Determine the Cahn-Ingold-Prelog R/S chirality of an atomvoid
Trajectory.getFractional
(Atom a, P3 ptTemp) Group.getLeadAtomOr
(Atom atom) void
int
AtomCollection.getMissingHydrogenCount
(Atom atom, boolean allowNegative) protected Bond
BondCollection.getOrAddBond
(Atom atom, Atom atomOther, int order, short mad, BS bsBonds, float energy, boolean overrideBonding) Bond.getOtherAtom
(Atom thisAtom) void
ModelSet.getPointTransf
(int i, Atom a, Quat q, P3 pTemp) pick up the appropriate value for this atomGroup.getQuaternionFrame
(Atom[] atoms) protected float
AtomCollection.getRadiusVdwJmol
(Atom atom) boolean
boolean
Measurement.isConnected
(Atom[] atoms, int count) boolean
Atom.isCovalentlyBonded
(Atom atomOther) protected boolean
Group.isCursorOnTopOf
(Atom atom, int x, int y, int radius, Atom champ) static boolean
protected boolean
BondCollection.isInRange
(Atom atom1, Atom atom2, float minD, float maxD, boolean minFrac, boolean maxfrac, boolean isFractional) Consider the min/max option for CONNECTboolean
Measurement.isIntramolecular
(Atom[] atoms, int count) void
BondCollection.removeUnnecessaryBonds
(Atom atom, boolean deleteAtom) void
AtomCollection.setElement
(Atom atom, int atomicNumber, boolean doTaint) void
Method parameters in org.jmol.modelset with type arguments of type AtomModifier and TypeMethodDescriptionModelSet.addHydrogens
(Lst<Atom> vConnections, P3[] pts) these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEWP3[][]
AtomCollection.calculateHydrogens
(BS bs, int[] nTotal, Lst<Atom> vConnect, int flags) get a list of potential H atom positions based on elemental valence and formal chargeConstructors in org.jmol.modelset with parameters of type Atom -
Uses of Atom in org.jmol.modelsetbio
Methods in org.jmol.modelsetbio that return AtomModifier and TypeMethodDescriptionfinal Atom
AlphaMonomer.getAtom
(byte specialAtomID) protected final Atom
Monomer.getAtomFromOffsetIndex
(int offsetIndex) NucleicMonomer.getC1P()
AminoMonomer.getCarbonylCarbonAtom()
AminoMonomer.getCarbonylOxygenAtom()
AminoMonomer.getExplicitNH()
final Atom
Monomer.getLeadAtom()
NucleicMonomer.getN0()
NucleicMonomer.getN3()
AminoMonomer.getNitrogenAtom()
protected final Atom
Monomer.getSpecialAtom
(byte[] interestingIDs, byte specialAtomID) final Atom
Monomer.getWingAtom()
Methods in org.jmol.modelsetbio with parameters of type AtomModifier and TypeMethodDescriptionprotected static int
NucleicPolymer.addHydrogenBond
(Lst<Bond> vAtoms, Atom atom1, Atom atom2) BioResolver.distinguishAndPropagateGroup
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) void
BioPolymer.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BS bsNot) void
NucleicMonomer.findNearestAtomIndex
(int x, int y, Atom[] closest, short madBegin, short madEnd) Get a unitID. -
Uses of Atom in org.jmol.quantum
Methods in org.jmol.quantum with parameters of type AtomModifier and TypeMethodDescriptionvoid
MepCalculation.assignPotentials
(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, String data) void
MlpCalculation.assignPotentials
(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, String data) static double[]
NMRCalculation.calc2or3JorNOE
(Viewer viewer, Atom[] atoms, String CHEquation, int mode) Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;static double[]
void
MepCalculation.calculate
(VolumeData volumeData, BS bsSelected, P3[] xyz, Atom[] atoms, float[] potentials, int calcType) static int
NMRCalculation.getCalcType
(Atom[] atoms, String[] elementsToFill, int mode) float
NMRCalculation.getChemicalShift
(Atom atom) float
NMRCalculation.getDipolarConstantHz
(Atom a1, Atom a2) float
NMRCalculation.getDipolarCouplingHz
(Atom a1, Atom a2, V3 vField) float
NMRCalculation.getIsoOrAnisoHz
(boolean isIso, Atom a1, Atom a2, String units, Tensor isc) float
NMRCalculation.getJCouplingHz
(Atom a1, Atom a2, String type, Tensor isc) float
NMRCalculation.getMagneticShielding
(Atom atom) double[]
NMRCalculation.getNOEorJHH
(Atom[] atoms, int mode) protected float
MepCalculation.getTabulatedPotential
(Atom atom) boolean
MOCalculation.setupCalculation
(Map<String, Object> moData, boolean isSlaters, VolumeData volumeData, BS bsSelected, T3[] xyz, Atom[] atoms, int firstAtomOffset, int[][] dfCoefMaps, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, T3[] points) protected void
QuantumCalculation.setupCoordinates
(float[] originXYZ, float[] stepsXYZ, BS bsSelected, T3[] xyz, Atom[] atoms, T3[] points, boolean renumber) -
Uses of Atom in org.jmol.render
Methods in org.jmol.render with parameters of type Atom -
Uses of Atom in org.jmol.script
Method parameters in org.jmol.script with type arguments of type Atom -
Uses of Atom in org.jmol.shape
Methods in org.jmol.shape with parameters of type AtomModifier and TypeMethodDescriptionvoid
Shape.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, BS bsNot) static short
short
protected short
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Uses of Atom in org.jmol.shapebio
Methods in org.jmol.shapebio with parameters of type AtomModifier and TypeMethodDescriptionvoid
Backbone.addDisplayedBackbone
(Atom a, boolean isVisible) void
BioShape.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, BS bsNot) void
BioShapeCollection.findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, BS bsNot) -
Uses of Atom in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as AtomMethods in org.jmol.shapespecial with parameters of type AtomModifier and TypeMethodDescriptionstatic Ellipsoid
Ellipsoid.getEllipsoidForAtomTensor
(Tensor t, Atom center) -
Uses of Atom in org.jmol.shapesurface
Fields in org.jmol.shapesurface declared as Atom -
Uses of Atom in org.jmol.smiles
Methods in org.jmol.smiles with parameters of type AtomModifier and TypeMethodDescriptionint[][]
SmilesMatcher.getMapForJME
(String jme, Atom[] at, BS bsAtoms) -
Uses of Atom in org.jmol.symmetry
Methods in org.jmol.symmetry with parameters of type AtomModifier and TypeMethodDescriptionSymmetry.getIterator
(Viewer vwr, Atom atom, BS bsAtoms, float radius) UnitCellIterator.set
(SymmetryInterface unitCell, Atom atom, Atom[] atoms, BS bsAtoms, float distance) -
Uses of Atom in org.jmol.util
Fields in org.jmol.util declared as AtomMethods in org.jmol.util with parameters of type AtomModifier and TypeMethodDescriptionstatic BS
JmolMolecule.getBitSetForMF
(Atom[] at, BS bsAtoms, String mf) Constructors in org.jmol.util with parameters of type AtomModifierConstructorDescriptionContactPair
(Atom[] atoms, int i1, int i2, float R, float r, float vdwA, float vdwB) -
Uses of Atom in org.jmol.viewer
Methods in org.jmol.viewer with parameters of type AtomModifier and TypeMethodDescriptionvoid
ShapeManager.findNearestShapeAtomIndex
(int x, int y, Atom[] closest, BS bsNot) Viewer.getAtomValidation
(String type, Atom atom) short
ColorManager.getColixAtomPalette
(Atom atom, byte pid) ChimeMessenger.getInfoXYZ
(Atom a) called when an atom is pickedJmolChimeMessenger.getInfoXYZ
(Atom a) Viewer.getNBOAtomLabel
(Atom atom) Method parameters in org.jmol.viewer with type arguments of type Atom -
Uses of Atom in org.openscience.jmol.app.janocchio
Methods in org.openscience.jmol.app.janocchio that return AtomMethods in org.openscience.jmol.app.janocchio with parameters of type AtomModifier and TypeMethodDescriptionvoid
double[]
NmrMolecule.calcCouple
(Atom[] atoms) protected org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple
NmrMolecule.getDihedralCouple
(Atom[] atoms) int
NMR_Viewer.indexInFrame
(Atom atom)