org.jmol.modelset

Class BondCollection

public abstract class BondCollection extends AtomCollection

Field Summary
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
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.
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.
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.
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
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)

Field Detail

bondCount

int bondCount

bondGrowthIncrement

private static final int bondGrowthIncrement

bonds

Bond[] bonds

bsAromatic

protected BitSet bsAromatic

bsAromaticDouble

private BitSet bsAromaticDouble

bsAromaticSingle

private BitSet bsAromaticSingle

bsPseudoHBonds

protected BitSet bsPseudoHBonds

defaultCovalentMad

protected short defaultCovalentMad

freeBonds

protected Bond[][][] freeBonds

haveWarned

private boolean haveWarned

hbondMax

private float hbondMax

hbondMin

private float hbondMin

hbondMin2

private float hbondMin2

MAX_BONDS_LENGTH_TO_CACHE

protected static final int MAX_BONDS_LENGTH_TO_CACHE

MAX_NUM_TO_CACHE

protected static final int MAX_NUM_TO_CACHE

numCached

protected int[] numCached

Method Detail

addBondToAtom

private void addBondToAtom(Atom atom, Bond bond)

addHydrogenBond

void addHydrogenBond(Atom atom1, Atom atom2, short order, BitSet bsA, BitSet bsB)

These are not actual hydrogen bonds. They are N-O bonds in proteins and nucleic acids The method is called by AminoPolymer and NucleicPolymer methods, which are indirectly called by this.autoHbond

Parameters: atom1 atom2 order bsA bsB

addToBonds

private Bond[] addToBonds(Bond newBond, Bond[] oldBonds)

assignAromaticBonds

public void assignAromaticBonds()

assignAromaticBonds

protected void assignAromaticBonds(boolean isUserCalculation, BitSet bsBonds)

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

assignAromaticDouble

private boolean assignAromaticDouble(Bond bond)

try to assign AROMATICDOUBLE to this bond. Each atom needs to be have all single bonds except for this one.

Parameters: bond

Returns: true if successful; false otherwise

assignAromaticDouble

private 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.

Parameters: atom

Returns: true if successful, false if not

assignAromaticNandO

private void assignAromaticNandO(BitSet bsSelected)

assignAromaticSingle

private boolean assignAromaticSingle(Bond bond)

try to assign AROMATICSINGLE to this bond. Each atom needs to be able to have one aromatic double bond attached.

Parameters: bond

Returns: true if successful; false otherwise

assignAromaticSingle

private 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.

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)