Package org.jmol.modelset
Class BondCollection
java.lang.Object
org.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
- Direct Known Subclasses:
ModelSet
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.modelset.AtomCollection
AtomCollection.AtomSorter
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Field Summary
FieldsModifier and TypeFieldDescriptionBond[]
protected static final int
int
protected BS
protected short
protected Bond[][][]
protected boolean
boolean
protected static final int
protected static final int
protected int
protected JmolMolecule[]
protected int[]
protected V3
protected V3
Fields inherited from class org.jmol.modelset.AtomCollection
ac, at, atomTensorList, atomTensors, bioModelset, bsClickable, bsModulated, bsPartialCharges, bspf, bsVisible, CALC_H_ALLOW_H, CALC_H_DOALL, CALC_H_HAVEH, CALC_H_IGNORE_H, CALC_H_JUSTC, CALC_H_QUICK, canSkipLoad, g3d, haveChirality, haveStraightness, maxBondingRadius, occupancies, pointGroup, preserveState, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMNO, TAINT_ATOMTYPE, TAINT_BONDINGRADIUS, TAINT_CHAIN, TAINT_COORD, TAINT_ELEMENT, TAINT_FORMALCHARGE, TAINT_HYDROPHOBICITY, TAINT_MAX, TAINT_OCCUPANCY, TAINT_PARTIALCHARGE, TAINT_RESNO, TAINT_SEQID, TAINT_SITE, TAINT_TEMPERATURE, TAINT_VALENCE, TAINT_VANDERWAALS, TAINT_VIBRATION, tainted, trajectory, userSettableValues, vibrations, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addConnectedHAtoms
(Atom atom, BS bsAtoms) int
protected boolean
void
assignAromaticBondsBs
(boolean isUserCalculation, BS bsBonds) algorithm discussed above.bondAtoms
(Atom atom1, Atom atom2, int order, short mad, BS bsBonds, float energy, boolean addGroup, boolean isNew) protected Bond
bondMutually
(Atom atom, Atom atomOther, int order, short mad, float energy) protected void
protected void
protected int[]
deleteConnections
(float minD, float maxD, int order, BS bsA, BS bsB, boolean isBonds, boolean matchNull) void
displayBonds
(BondSet bs, boolean isDisplay) protected float
fixD
(float d, boolean isF) protected BS
getAtomBitsMDb
(int tokType, Object specInfo) getAtomsConnected
(float min, float max, int intType, BS bs) short
getBondColix1
(int i) short
getBondColix2
(int i) protected int
getBondCountInModel
(int modelIndex) for general usegetBondIterator
(BS bsBonds) getBondIteratorForType
(int bondType, BS bsAtoms) getBondsForSelectedAtoms
(BS bsAtoms, boolean bondSelectionModeOr) short
getDefaultMadFromOrder
(int order) When creating a new bond, determine bond diameter from orderprotected Bond
getOrAddBond
(Atom atom, Atom atomOther, int order, short mad, BS bsBonds, float energy, boolean overrideBonding) protected boolean
isInRange
(Atom atom1, Atom atom2, float minD, float maxD, boolean minFrac, boolean maxfrac, boolean isFractional) Consider the min/max option for CONNECTprotected void
void
removeUnnecessaryBonds
(Atom atom, boolean deleteAtom) void
protected Bond
protected void
setupBC()
Methods inherited from class org.jmol.modelset.AtomCollection
addTensor, calculateHydrogens, calculateSurface, calculateVolume, chainToUpper, clearBfactorRange, clearVisibleSets, deleteModelAtoms, fillADa, findMaxRadii, findNearest2, fixFormalCharges, generateCrystalClass, getAllAtomTensors, getAtom, getAtomBitsMDa, getAtomicCharges, getAtomIdentityInfo, getAtomIndices, getAtomInfo, getAtomPointVector, getAtomsFromAtomNumberInFrame, getAtomsInFrame, getAtomsNearPlane, getAtomTensor, getAtomTensorList, getAtomTypes, getBfactor100Hi, getBfactor100Lo, getBFactors, getBondingRadii, getChainBits, getClickableSet, getElementName, getFirstAtomIndexFromAtomNumber, getHybridizationAndAxes, getHydrophobicity, getLabeler, getMaxVanderwaalsRadius, getMissingHydrogenCount, getModulation, getOccupancyFloat, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSpecNameOrNull, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibCoord, getVibration, getVisibleSet, isAtomHidden, isDeleted, isModulated, mergeAtomArrays, modelSetHasVibrationVectors, releaseModelSetAC, scaleVectorsToMax, setAPa, setAtomCoord, setAtomCoord2, setAtomCoordRelative, setAtomData, setAtomName, setAtomNumber, setAtomsCoordRelative, setAtomTensors, setBFactor, setBondingRadius, setBsHidden, setElement, setFormalCharges, setOccupancy, setPartialCharge, setPreserveState, setSite, setTaintedAtoms, setupAC, setVibrationVector, taintAtom, taintAtoms, unTaintAtoms, validateBspf
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Field Details
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bo
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bondCount
public int bondCount -
numCached
protected int[] numCached -
freeBonds
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molecules
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moleculeCount
protected int moleculeCount -
defaultCovalentMad
protected short defaultCovalentMad -
bsAromatic
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haveHiddenBonds
public boolean haveHiddenBonds -
v1
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v2
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BOND_GROWTH_INCREMENT
protected static final int BOND_GROWTH_INCREMENT- See Also:
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MAX_BONDS_LENGTH_TO_CACHE
protected static final int MAX_BONDS_LENGTH_TO_CACHE- See Also:
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MAX_NUM_TO_CACHE
protected static final int MAX_NUM_TO_CACHE- See Also:
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haveAtropicBonds
protected boolean haveAtropicBonds
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Constructor Details
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BondCollection
public BondCollection()
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Method Details
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setupBC
protected void setupBC() -
releaseModelSetBC
protected void releaseModelSetBC() -
getBondIteratorForType
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getBondIterator
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getBondColix1
public short getBondColix1(int i) -
getBondColix2
public short getBondColix2(int i) -
getBondCountInModel
protected int getBondCountInModel(int modelIndex) for general use- Parameters:
modelIndex
- the model of interest or -1 for all- Returns:
- the actual number of connections
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getBondsForSelectedAtoms
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bondAtoms
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getOrAddBond
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setBond
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bondMutually
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addHBond
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deleteAllBonds2
protected void deleteAllBonds2() -
getDefaultMadFromOrder
public short getDefaultMadFromOrder(int order) When creating a new bond, determine bond diameter from order- Parameters:
order
-- Returns:
- if hydrogen bond, default to 1; otherwise 0 (general default)
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deleteConnections
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fixD
protected float fixD(float d, boolean isF) -
isInRange
protected boolean isInRange(Atom atom1, Atom atom2, float minD, float maxD, boolean minFrac, boolean maxfrac, boolean isFractional) Consider the min/max option for CONNECT- Parameters:
atom1
-atom2
-minD
-maxD
-minFrac
-maxfrac
-isFractional
-- Returns:
- true if in range
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dBb
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resetAromatic
public void resetAromatic() -
assignAromaticBondsBs
algorithm discussed above.- Parameters:
isUserCalculation
- if set, don't reset the base aromatic bitset and do report changes to STICKS as though this were a bondOrder command.bsBonds
- passed to us by autoBond routine
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allowAromaticBond
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getAtomBitsMDb
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removeUnnecessaryBonds
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displayBonds
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getAtomsConnected
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addConnectedHAtoms
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