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.adapter.writers
Fields in org.jmol.adapter.writers declared as Atom -
Uses of Atom in org.jmol.api
Methods in org.jmol.api that return AtomMethods in org.jmol.api with parameters of type AtomModifier and TypeMethodDescriptionvoidJmolAnnotationParser.getAtomValidation(Viewer vwr, String type, Atom atom) floatJmolNMRInterface.getChemicalShift(Atom atom) If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shieldingSymmetryInterface.getConstrainableEquivAtom(Atom a) floatJmolNMRInterface.getDipolarConstantHz(Atom a1, Atom a2) floatJmolNMRInterface.getDipolarCouplingHz(Atom a1, Atom a2, V3 vField) floatJmolNMRInterface.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) floatJmolNMRInterface.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 MMFF94booleanForceFieldMMFF.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.atBond.atom1Bond.atom2protected final Atom[]ModelSet.closestMethods 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 TypeMethodDescriptionvoidBondCollection.addConnectedHAtoms(Atom atom, BS bsAtoms) intBondCollection.bondAtoms(Atom atom1, Atom atom2, int order, short mad, BS bsBonds, float energy, boolean addGroup, boolean isNew) protected BondBondCollection.bondMutually(Atom atom, Atom atomOther, int order, short mad, float energy) intprotected voidAtomCollection.findNearest2(int x, int y, Atom[] closest, BS bsNot, int min) LabelToken.formatLabel(Viewer vwr, Atom atom, String strFormat, P3 ptTemp) static StringLabelToken.formatLabelAtomArray(Viewer vwr, Atom atom, LabelToken[] tokens, char chAtom, int[] indices, P3 ptTemp) returns a formatted string based on the precompiled label tokensintModelSet.getAtomCIPChiralityCode(Atom atom) Determine the Cahn-Ingold-Prelog R/S chirality of an atomvoidTrajectory.getFractional(Atom a, P3 ptTemp) Group.getLeadAtomOr(Atom atom) voidintAtomCollection.getMissingHydrogenCount(Atom atom, boolean allowNegative) protected BondBondCollection.getOrAddBond(Atom atom, Atom atomOther, int order, short mad, BS bsBonds, float energy, boolean overrideBonding) Bond.getOtherAtom(Atom thisAtom) voidModelSet.getPointTransf(int i, Atom a, Quat q, P3 pTemp) pick up the appropriate value for this atomGroup.getQuaternionFrame(Atom[] atoms) protected floatAtomCollection.getRadiusVdwJmol(Atom atom) booleanbooleanMeasurement.isConnected(Atom[] atoms, int count) booleanAtom.isCovalentlyBonded(Atom atomOther) protected booleanGroup.isCursorOnTopOf(Atom atom, int x, int y, int radius, Atom champ) static booleanprotected booleanBondCollection.isInRange(Atom atom1, Atom atom2, float minD, float maxD, boolean minFrac, boolean maxfrac, boolean isFractional) Consider the min/max option for CONNECTbooleanMeasurement.isIntramolecular(Atom[] atoms, int count) voidBondCollection.removeUnnecessaryBonds(Atom atom, boolean deleteAtom) voidAtomCollection.setElement(Atom atom, int atomicNumber, boolean doTaint) voidMethod 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 AtomAlphaMonomer.getAtom(byte specialAtomID) protected final AtomMonomer.getAtomFromOffsetIndex(int offsetIndex) NucleicMonomer.getC1P()AminoMonomer.getCarbonylCarbonAtom()AminoMonomer.getCarbonylOxygenAtom()AminoMonomer.getExplicitNH()final AtomMonomer.getLeadAtom()NucleicMonomer.getN0()NucleicMonomer.getN3()AminoMonomer.getNitrogenAtom()protected final AtomMonomer.getSpecialAtom(byte[] interestingIDs, byte specialAtomID) final AtomMonomer.getWingAtom()Methods in org.jmol.modelsetbio with parameters of type AtomModifier and TypeMethodDescriptionprotected static intNucleicPolymer.addHydrogenBond(Lst<Bond> vAtoms, Atom atom1, Atom atom2) BioResolver.distinguishAndPropagateGroup(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) voidBioPolymer.findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BS bsNot) voidNucleicMonomer.findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd) Get a unitID.protected booleanMonomer.updateOffsetsForAlternativeLocations(Atom[] atoms, BS bsSelected) -
Uses of Atom in org.jmol.quantum
Methods in org.jmol.quantum with parameters of type AtomModifier and TypeMethodDescriptionvoidMepCalculation.assignPotentials(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, String data) voidMlpCalculation.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[]voidMepCalculation.calculate(VolumeData volumeData, BS bsSelected, P3[] xyz, Atom[] atoms, float[] potentials, int calcType) static intNMRCalculation.getCalcType(Atom[] atoms, String[] elementsToFill, int mode) floatNMRCalculation.getChemicalShift(Atom atom) floatNMRCalculation.getDipolarConstantHz(Atom a1, Atom a2) floatNMRCalculation.getDipolarCouplingHz(Atom a1, Atom a2, V3 vField) floatNMRCalculation.getIsoOrAnisoHz(boolean isIso, Atom a1, Atom a2, String units, Tensor isc) floatNMRCalculation.getJCouplingHz(Atom a1, Atom a2, String type, Tensor isc) floatNMRCalculation.getMagneticShielding(Atom atom) double[]NMRCalculation.getNOEorJHH(Atom[] atoms, int mode) protected floatMepCalculation.getTabulatedPotential(Atom atom) booleanMOCalculation.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 voidQuantumCalculation.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 TypeMethodDescriptionvoidShape.findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BS bsNot) static shortshortprotected short -
Uses of Atom in org.jmol.shapebio
Methods in org.jmol.shapebio with parameters of type AtomModifier and TypeMethodDescriptionvoidBackbone.addDisplayedBackbone(Atom a, boolean isVisible) voidBioShape.findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BS bsNot) voidBioShapeCollection.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 EllipsoidEllipsoid.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 that return AtomModifier and TypeMethodDescriptionSymmetry.getConstrainableEquivAtom(Atom a) This atom is usually the atom being moved, but in some cases we need to switch to a different atom in order to avoid the special case where a screw axis (SG 224 Wyckoff i) or glide (plane group 12 Wyckoff c) creates a stationary point.Methods in org.jmol.symmetry with parameters of type AtomModifier and TypeMethodDescriptionSymmetry.getConstrainableEquivAtom(Atom a) This atom is usually the atom being moved, but in some cases we need to switch to a different atom in order to avoid the special case where a screw axis (SG 224 Wyckoff i) or glide (plane group 12 Wyckoff c) creates a stationary point.Symmetry.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 that return AtomMethods in org.jmol.util with parameters of type AtomModifier and TypeMethodDescriptionstatic BSJmolMolecule.getBitSetForMF(Atom[] at, BS bsAtoms, String mf) voidVibration.rotateSpin(M3 matInv, M3 rot, M3 dRot, Atom a) 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 TypeMethodDescriptionvoidShapeManager.findNearestShapeAtomIndex(int x, int y, Atom[] closest, BS bsNot) Viewer.getAtomValidation(String type, Atom atom) shortColorManager.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 TypeMethodDescriptionvoiddouble[]NmrMolecule.calcCouple(Atom[] atoms) protected org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCoupleNmrMolecule.getDihedralCouple(Atom[] atoms) intNMR_Viewer.indexInFrame(Atom atom)