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java.lang.Objectorg.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
public abstract class BondCollection
Field Summary | |
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protected int |
bondCount
|
private static int |
bondGrowthIncrement
|
protected Bond[] |
bonds
|
protected java.util.BitSet |
bsAromatic
|
private java.util.BitSet |
bsAromaticDouble
|
private java.util.BitSet |
bsAromaticSingle
|
protected java.util.BitSet |
bsPseudoHBonds
|
protected short |
defaultCovalentMad
|
protected Bond[][][] |
freeBonds
|
private boolean |
haveWarned
|
protected static int |
MAX_BONDS_LENGTH_TO_CACHE
|
protected static int |
MAX_NUM_TO_CACHE
|
protected int[] |
numCached
|
protected static boolean |
showRebondTimes
|
Fields inherited from class org.jmol.modelset.AtomCollection |
---|
atomCount, atomNames, atoms, atomSerials, atomTypes, bfactor100s, bspf, clientAtomReferences, ellipsoids, g3d, haveStraightness, maxBondingRadius, occupancies, partialCharges, specialAtomIDs, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMTYPE, TAINT_COORD, TAINT_MAX, tainted, vibrationVectors, viewer |
Constructor Summary | |
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BondCollection()
|
Method Summary | |
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private void |
addBondToAtom(Atom atom,
Bond bond)
|
(package private) void |
addHydrogenBond(Atom atom1,
Atom atom2,
short order,
java.util.BitSet bsA,
java.util.BitSet bsB,
float energy)
These are not actual hydrogen bonds. |
private Bond[] |
addToBonds(Bond newBond,
Bond[] oldBonds)
|
void |
assignAromaticBonds()
|
protected void |
assignAromaticBonds(boolean isUserCalculation,
java.util.BitSet bsBonds)
algorithm discussed above. |
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. |
private boolean |
assignAromaticDouble(Bond bond)
try to assign AROMATICDOUBLE to this bond. |
private void |
assignAromaticNandO(java.util.BitSet bsSelected)
|
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. |
private boolean |
assignAromaticSingle(Bond bond)
try to assign AROMATICSINGLE to this bond. |
private boolean |
assignAromaticSingleHetero(Atom atom)
|
Bond |
bondAtoms(Atom atom1,
Atom atom2,
short order,
short mad,
java.util.BitSet bsBonds)
|
protected Bond |
bondMutually(Atom atom,
Atom atomOther,
short order,
short mad)
|
protected boolean |
checkValencesAndBond(Atom atomA,
Atom atomB,
short order,
short mad,
java.util.BitSet bsBonds)
|
protected void |
deleteAllBonds()
|
protected void |
deleteBonds(java.util.BitSet bs)
|
protected int[] |
deleteConnections(float minDistance,
float maxDistance,
short order,
java.util.BitSet bsA,
java.util.BitSet bsB,
boolean isBonds,
boolean matchNull,
float minDistanceSquared,
float maxDistanceSquared)
|
protected java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general unqualified lookup of atom set type |
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(java.util.BitSet bsSelected)
|
BondIterator |
getBondIterator(short bondType,
java.util.BitSet bsSelected)
|
int |
getBondModelIndex(int i)
|
protected short |
getBondOrder(Atom atomA,
float bondingRadiusA,
Atom atomB,
float bondingRadiusB,
float distance2,
float minBondDistance2,
float bondTolerance)
|
short |
getBondOrder(int i)
|
float |
getBondRadius(int i)
|
Bond[] |
getBonds()
|
java.util.BitSet |
getBondsForSelectedAtoms(java.util.BitSet bsAtoms,
boolean bondSelectionModeOr)
|
protected short |
getDefaultMadFromOrder(short order)
When creating a new bond, determine bond diameter from order |
protected Bond |
getOrAddBond(Atom atom,
Atom atomOther,
short order,
short mad,
java.util.BitSet bsBonds)
|
private Bond |
getOrAddHBond(Atom atom,
Atom atomOther,
short order,
short mad,
java.util.BitSet bsBonds,
float energy)
|
protected Bond |
hBondMutually(Atom atom,
Atom atomOther,
short order,
short mad,
float energy)
|
protected void |
merge(ModelSet modelSet)
|
protected void |
releaseModelSet()
|
void |
resetAromatic()
|
protected Bond |
setBond(int index,
Bond bond)
|
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected Bond[] bonds
protected int bondCount
protected static final boolean showRebondTimes
private static final int bondGrowthIncrement
protected static final int MAX_BONDS_LENGTH_TO_CACHE
protected static final int MAX_NUM_TO_CACHE
protected int[] numCached
protected Bond[][][] freeBonds
protected java.util.BitSet bsPseudoHBonds
private boolean haveWarned
protected short defaultCovalentMad
private java.util.BitSet bsAromaticSingle
private java.util.BitSet bsAromaticDouble
protected java.util.BitSet bsAromatic
Constructor Detail |
---|
public BondCollection()
Method Detail |
---|
protected void releaseModelSet()
releaseModelSet
in class AtomCollection
protected void merge(ModelSet modelSet)
public Bond[] getBonds()
public Bond getBondAt(int bondIndex)
public int getBondCount()
public BondIterator getBondIterator(short bondType, java.util.BitSet bsSelected)
public BondIterator getBondIterator(java.util.BitSet bsSelected)
public Atom getBondAtom1(int i)
public Atom getBondAtom2(int i)
public float getBondRadius(int i)
public short getBondOrder(int i)
public short getBondColix1(int i)
public short getBondColix2(int i)
public int getBondModelIndex(int i)
protected int getBondCountInModel(int modelIndex)
modelIndex
- the model of interest or -1 for all
public java.util.BitSet getBondsForSelectedAtoms(java.util.BitSet bsAtoms, boolean bondSelectionModeOr)
public Bond bondAtoms(Atom atom1, Atom atom2, short order, short mad, java.util.BitSet bsBonds)
protected Bond getOrAddBond(Atom atom, Atom atomOther, short order, short mad, java.util.BitSet bsBonds)
private Bond getOrAddHBond(Atom atom, Atom atomOther, short order, short mad, java.util.BitSet bsBonds, float energy)
protected Bond setBond(int index, Bond bond)
protected Bond hBondMutually(Atom atom, Atom atomOther, short order, short mad, float energy)
protected Bond bondMutually(Atom atom, Atom atomOther, short order, short mad)
private void addBondToAtom(Atom atom, Bond bond)
private Bond[] addToBonds(Bond newBond, Bond[] oldBonds)
void addHydrogenBond(Atom atom1, Atom atom2, short order, java.util.BitSet bsA, java.util.BitSet bsB, float energy)
atom1
- atom2
- order
- bsA
- bsB
- energy
- protected short getBondOrder(Atom atomA, float bondingRadiusA, Atom atomB, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance)
protected boolean checkValencesAndBond(Atom atomA, Atom atomB, short order, short mad, java.util.BitSet bsBonds)
protected void deleteAllBonds()
protected short getDefaultMadFromOrder(short order)
order
-
protected int[] deleteConnections(float minDistance, float maxDistance, short order, java.util.BitSet bsA, java.util.BitSet bsB, boolean isBonds, boolean matchNull, float minDistanceSquared, float maxDistanceSquared)
protected void deleteBonds(java.util.BitSet bs)
public void resetAromatic()
public void assignAromaticBonds()
protected void assignAromaticBonds(boolean isUserCalculation, java.util.BitSet bsBonds)
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 routineprivate boolean assignAromaticDouble(Bond bond)
bond
-
private boolean assignAromaticSingle(Bond bond)
bond
-
private boolean assignAromaticSingle(Atom atom, int notBondIndex)
atom
- notBondIndex
- that index of the bond leading to this atom --- to be ignored
private boolean assignAromaticDouble(Atom atom)
atom
-
private boolean assignAromaticSingleHetero(Atom atom)
private void assignAromaticNandO(java.util.BitSet bsSelected)
protected java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
AtomCollection
getAtomBits
in class AtomCollection
|
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