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java.lang.Objectorg.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
public abstract class BondCollection
Nested Class Summary |
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Nested classes/interfaces inherited from class org.jmol.modelset.AtomCollection |
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AtomCollection.AtomSorter |
Field Summary | |
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protected static int |
BOND_GROWTH_INCREMENT
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protected int |
bondCount
|
protected Bond[] |
bonds
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protected java.util.BitSet |
bsAromatic
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private java.util.BitSet |
bsAromaticDouble
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private java.util.BitSet |
bsAromaticSingle
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protected java.util.BitSet |
bsHBondsRasmol
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protected short |
defaultCovalentMad
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protected Bond[][][] |
freeBonds
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protected boolean |
haveHiddenBonds
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private boolean |
haveWarned
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protected static int |
MAX_BONDS_LENGTH_TO_CACHE
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protected static int |
MAX_NUM_TO_CACHE
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protected int |
moleculeCount
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protected JmolMolecule[] |
molecules
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protected int[] |
numCached
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Fields inherited from class org.jmol.modelset.AtomCollection |
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atomCount, atomNames, atoms, atomSerials, atomTypes, bfactor100s, bspf, ellipsoids, g3d, haveStraightness, hydrophobicities, ionicRadii, maxBondingRadius, occupancies, partialCharges, preserveState, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMNO, TAINT_ATOMTYPE, TAINT_COORD, TAINT_ELEMENT, TAINT_FORMALCHARGE, TAINT_HYDROPHOBICITY, TAINT_MAX, tainted, vibrationVectors, viewer |
Constructor Summary | |
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BondCollection()
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Method Summary | |
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private void |
addBondToAtom(Atom atom,
Bond bond)
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protected int |
addHBond(Atom atom1,
Atom atom2,
int order,
float energy)
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private Bond[] |
addToBonds(Bond newBond,
Bond[] oldBonds)
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void |
assignAromaticBonds()
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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,
int order,
short mad,
java.util.BitSet bsBonds,
float energy,
boolean addGroup,
boolean isNew)
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protected Bond |
bondMutually(Atom atom,
Atom atomOther,
int order,
short mad,
float energy)
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protected boolean |
checkValencesAndBond(Atom atomA,
Atom atomB,
int order,
short mad,
java.util.BitSet bsBonds)
|
protected void |
deleteAllBonds()
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void |
deleteBonds(java.util.BitSet bsBond,
boolean isFullModel)
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protected int[] |
deleteConnections(float minDistance,
float maxDistance,
int order,
java.util.BitSet bsA,
java.util.BitSet bsB,
boolean isBonds,
boolean matchNull,
float minDistanceSquared,
float maxDistanceSquared)
|
void |
displayBonds(Bond.BondSet bs,
boolean isDisplay)
|
protected java.util.BitSet |
getAtomBitsMaybeDeleted(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)
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short |
getBondColix1(int i)
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short |
getBondColix2(int i)
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int |
getBondCount()
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protected int |
getBondCountInModel(int modelIndex)
for general use |
BondIterator |
getBondIterator(java.util.BitSet bsSelected)
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BondIterator |
getBondIterator(int bondType,
java.util.BitSet bsSelected)
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int |
getBondModelIndex(int i)
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protected static short |
getBondOrder(float bondingRadiusA,
float bondingRadiusB,
float distance2,
float minBondDistance2,
float bondTolerance)
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int |
getBondOrder(int i)
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float |
getBondRadius(int i)
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Bond[] |
getBonds()
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java.util.BitSet |
getBondsForSelectedAtoms(java.util.BitSet bsAtoms,
boolean bondSelectionModeOr)
|
short |
getDefaultMadFromOrder(int order)
When creating a new bond, determine bond diameter from order |
private Bond |
getOrAddBond(Atom atom,
Atom atomOther,
int order,
short mad,
java.util.BitSet bsBonds,
float energy,
boolean overrideBonding)
|
(package private) void |
getRasmolHydrogenBonds(Model m,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.List<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens)
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protected void |
releaseModelSet()
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protected void |
removeUnnecessaryBonds(Atom atom,
boolean deleteAtom)
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void |
resetAromatic()
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protected void |
resetMolecules()
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protected Bond |
setBond(int index,
Bond bond)
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java.util.BitSet |
setBondOrder(int bondIndex,
char type)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected JmolMolecule[] molecules
protected int moleculeCount
protected Bond[] bonds
protected int bondCount
protected static final int BOND_GROWTH_INCREMENT
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 bsHBondsRasmol
private boolean haveWarned
protected short defaultCovalentMad
private java.util.BitSet bsAromaticSingle
private java.util.BitSet bsAromaticDouble
protected java.util.BitSet bsAromatic
protected boolean haveHiddenBonds
Constructor Detail |
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public BondCollection()
Method Detail |
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protected void releaseModelSet()
releaseModelSet
in class AtomCollection
protected void resetMolecules()
public Bond[] getBonds()
public Bond getBondAt(int bondIndex)
public int getBondCount()
public BondIterator getBondIterator(int 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 int 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, int order, short mad, java.util.BitSet bsBonds, float energy, boolean addGroup, boolean isNew)
private Bond getOrAddBond(Atom atom, Atom atomOther, int order, short mad, java.util.BitSet bsBonds, float energy, boolean overrideBonding)
protected Bond setBond(int index, Bond bond)
protected Bond bondMutually(Atom atom, Atom atomOther, int order, short mad, float energy)
private void addBondToAtom(Atom atom, Bond bond)
private Bond[] addToBonds(Bond newBond, Bond[] oldBonds)
void getRasmolHydrogenBonds(Model m, java.util.BitSet bsA, java.util.BitSet bsB, java.util.List<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens)
protected int addHBond(Atom atom1, Atom atom2, int order, float energy)
protected static short getBondOrder(float bondingRadiusA, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance)
protected boolean checkValencesAndBond(Atom atomA, Atom atomB, int order, short mad, java.util.BitSet bsBonds)
protected void deleteAllBonds()
public short getDefaultMadFromOrder(int order)
order
-
protected int[] deleteConnections(float minDistance, float maxDistance, int order, java.util.BitSet bsA, java.util.BitSet bsB, boolean isBonds, boolean matchNull, float minDistanceSquared, float maxDistanceSquared)
public void deleteBonds(java.util.BitSet bsBond, boolean isFullModel)
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 getAtomBitsMaybeDeleted(int tokType, java.lang.Object specInfo)
AtomCollection
getAtomBitsMaybeDeleted
in class AtomCollection
public java.util.BitSet setBondOrder(int bondIndex, char type)
protected void removeUnnecessaryBonds(Atom atom, boolean deleteAtom)
public void displayBonds(Bond.BondSet bs, boolean isDisplay)
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