Uses of Class
org.jmol.modelset.Bond
Packages that use Bond
Package
Description
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Uses of Bond in org.jmol.api
Method parameters in org.jmol.api with type arguments of type Bond -
Uses of Bond in org.jmol.dssx
Method parameters in org.jmol.dssx with type arguments of type Bond -
Uses of Bond in org.jmol.minimize
Fields in org.jmol.minimize declared as Bond -
Uses of Bond in org.jmol.minimize.forcefield
Methods in org.jmol.minimize.forcefield with parameters of type BondModifier 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 Bond in org.jmol.modelset
Subclasses of Bond in org.jmol.modelsetFields in org.jmol.modelset declared as BondModifier and TypeFieldDescriptionBond[]
BondCollection.bo
Bond[]
Atom.bonds
MAY BE NULLprotected Bond[][][]
BondCollection.freeBonds
Methods in org.jmol.modelset that return BondModifier and TypeMethodDescriptionBondCollection.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) protected Bond
BondCollection.getOrAddBond
(Atom atom, Atom atomOther, int order, short mad, BS bsBonds, float energy, boolean overrideBonding) BondIterator.next()
protected Bond
Methods in org.jmol.modelset with parameters of type BondModifier and TypeMethodDescriptionprotected boolean
BondCollection.allowAromaticBond
(Bond b) static String
LabelToken.formatLabelBond
(Viewer vwr, Bond bond, LabelToken[] tokens, Map<String, Object> values, int[] indices, P3 ptTemp) protected Bond
Method parameters in org.jmol.modelset with type arguments of type Bond -
Uses of Bond in org.jmol.modelsetbio
Method parameters in org.jmol.modelsetbio with type arguments of type BondModifier and TypeMethodDescriptionprotected static int
NucleicPolymer.addHydrogenBond
(Lst<Bond> vAtoms, Atom atom1, Atom atom2) void
BioModelSet.calcAllRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int dsspVersion) only for base models, not trajectoriesvoid
AminoPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
BioPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) void
NucleicPolymer.calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) -
Uses of Bond in org.jmol.shape
Methods in org.jmol.shape with parameters of type Bond -
Uses of Bond in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as Bond -
Uses of Bond in org.jmol.viewer
Methods in org.jmol.viewer with parameters of type Bond