org.jmol.modelset
public abstract class BondCollection extends AtomCollection
Field Summary | |
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int | bondCount |
static int | bondGrowthIncrement |
Bond[] | bonds |
protected BitSet | bsAromatic |
BitSet | bsAromaticDouble |
BitSet | bsAromaticSingle |
protected BitSet | bsPseudoHBonds |
protected short | defaultCovalentMad |
protected Bond[][][] | freeBonds |
boolean | haveWarned |
float | hbondMax |
float | hbondMin |
float | hbondMin2 |
protected static int | MAX_BONDS_LENGTH_TO_CACHE |
protected static int | MAX_NUM_TO_CACHE |
protected int[] | numCached |
Method Summary | |
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void | addBondToAtom(Atom atom, Bond bond) |
void | addHydrogenBond(Atom atom1, Atom atom2, short order, BitSet bsA, BitSet bsB)
These are not actual hydrogen bonds. |
Bond[] | addToBonds(Bond newBond, Bond[] oldBonds) |
void | assignAromaticBonds() |
protected void | assignAromaticBonds(boolean isUserCalculation, BitSet bsBonds)
algorithm discussed above.
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boolean | assignAromaticDouble(Bond bond)
try to assign AROMATICDOUBLE to this bond. |
boolean | assignAromaticDouble(Atom atom)
N atoms with 3 bonds cannot also have a double bond;
other atoms need one and only one double bond;
the rest must be single bonds.
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void | assignAromaticNandO(BitSet bsSelected) |
boolean | assignAromaticSingle(Bond bond)
try to assign AROMATICSINGLE to this bond. |
boolean | assignAromaticSingle(Atom atom, int notBondIndex)
N atoms with 3 bonds cannot also have a double bond;
other atoms needs all single bonds,
because the bond leading up to it is double.
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boolean | assignAromaticSingleHetero(Atom atom) |
protected int | autoHbond(BitSet bsA, BitSet bsB, BitSet bsBonds) |
Bond | bondAtoms(Atom atom1, Atom atom2, short order, short mad, BitSet bsBonds) |
protected Bond | bondMutually(Atom atom, Atom atomOther, short order, short mad) |
boolean | checkValencesAndBond(Atom atomA, Atom atomB, short order, short mad, BitSet bsBonds) |
protected void | deleteAllBonds() |
protected void | deleteBonds(BitSet bs) |
protected int[] | deleteConnections(float minDistance, float maxDistance, short order, BitSet bsA, BitSet bsB, boolean isBonds, boolean matchNull, float minDistanceSquared, float maxDistanceSquared) |
protected BitSet | getAtomBits(int tokType, Object specInfo) |
Bond | getBondAt(int bondIndex) |
Atom | getBondAtom1(int i) |
Atom | getBondAtom2(int i) |
short | getBondColix1(int i) |
short | getBondColix2(int i) |
int | getBondCount() |
protected int | getBondCountInModel(int modelIndex)
for general use
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BondIterator | getBondIterator(short bondType, BitSet bsSelected) |
BondIterator | getBondIterator(BitSet bsSelected) |
int | getBondModelIndex(int i) |
short | getBondOrder(int i) |
protected short | getBondOrder(Atom atomA, float bondingRadiusA, Atom atomB, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance) |
float | getBondRadius(int i) |
Bond[] | getBonds() |
BitSet | getBondsForSelectedAtoms(BitSet bsAtoms) |
protected BitSet | getBondsForSelectedAtoms(BitSet bsAtoms, boolean bondSelectionModeOr) |
protected short | getDefaultMadFromOrder(short order)
When creating a new bond, determine bond diameter from order |
Bond | getOrAddBond(Atom atom, Atom atomOther, short order, short mad, BitSet bsBonds) |
void | merge(ModelSet modelSet) |
protected void | releaseModelSet() |
void | resetAromatic() |
protected Bond | setBond(int index, Bond bond) |
Parameters: atom1 atom2 order bsA bsB
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
Parameters: bond
Returns: true if successful; false otherwise
Parameters: atom
Returns: true if successful, false if not
Parameters: bond
Returns: true if successful; false otherwise
Parameters: atom notBondIndex that index of the bond leading to this atom --- to be ignored
Returns: true if successful, false if not
Parameters: modelIndex the model of interest or -1 for all
Returns: the actual number of connections
Parameters: order
Returns: if hydrogen bond, default to 1; otherwise 0 (general default)