org.jmol.modelsetbio
public final class Resolver extends Object implements JmolBioResolver
Modifier and Type | Class and Description |
---|---|
(package private) class |
Resolver.BondSorter |
Modifier and Type | Field and Description |
---|---|
private int |
baseBondIndex |
private BitSet |
bsAddedHydrogens |
private BitSet |
bsAtomsForHs |
private boolean |
haveHsAlready |
private String[] |
hNames |
private Map<String,String> |
htBondMap |
private Map<String,Boolean> |
htGroupBonds |
private int |
lastSetH |
private int |
maxSerial |
private ModelLoader |
modelLoader |
private ModelSet |
modelSet |
private Point4f |
plane |
private Vector3f |
vAB |
private Vector3f |
vAC |
private Vector3f |
vNorm |
Constructor and Description |
---|
Resolver() |
Modifier and Type | Method and Description |
---|---|
void |
addImplicitHydrogenAtoms(JmolAdapter adapter,
int iGroup) |
Polymer |
buildBioPolymer(Group group,
Group[] groups,
int i,
boolean checkPolymerConnections) |
void |
clearBioPolymers(Group[] groups,
int groupCount,
BitSet bsModelsExcluded) |
private void |
deleteUnneededAtoms()
Delete hydrogen atoms that are still in bsAddedHydrogens,
because they were not actually added.
|
Group |
distinguishAndPropagateGroup(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int maxAtomIndex,
int modelIndex,
int[] specialAtomIndexes,
Atom[] atoms) |
void |
finalizeHydrogens() |
private void |
finalizePdbCharges() |
private void |
finalizePdbMultipleBonds() |
void |
getBondInfo(JmolAdapter adapter,
String group3,
Object model) |
private String[][] |
getLigandBondInfo(JmolAdapter adapter,
Object model,
String group3)
reads PDB ligand CIF info and creates a bondInfo object.
|
void |
initialize(ModelSet modelSet) |
void |
initializeHydrogenAddition(ModelLoader modelLoader,
int bondCount) |
void |
setHaveHsAlready(boolean b) |
private void |
setHydrogen(int iTo,
int iAtom,
String name,
Point3f pt) |
private ModelLoader modelLoader
private ModelSet modelSet
private BitSet bsAddedHydrogens
private BitSet bsAtomsForHs
private String[] hNames
private int lastSetH
private int maxSerial
private int baseBondIndex
private boolean haveHsAlready
private Vector3f vAB
private Vector3f vAC
private Vector3f vNorm
private Point4f plane
public Group distinguishAndPropagateGroup(Chain chain, String group3, int seqcode, int firstAtomIndex, int maxAtomIndex, int modelIndex, int[] specialAtomIndexes, Atom[] atoms)
distinguishAndPropagateGroup
in interface JmolBioResolver
public Polymer buildBioPolymer(Group group, Group[] groups, int i, boolean checkPolymerConnections)
buildBioPolymer
in interface JmolBioResolver
public void clearBioPolymers(Group[] groups, int groupCount, BitSet bsModelsExcluded)
clearBioPolymers
in interface JmolBioResolver
public void setHaveHsAlready(boolean b)
setHaveHsAlready
in interface JmolBioResolver
public void initialize(ModelSet modelSet)
initialize
in interface JmolBioResolver
public void initializeHydrogenAddition(ModelLoader modelLoader, int bondCount)
initializeHydrogenAddition
in interface JmolBioResolver
public void addImplicitHydrogenAtoms(JmolAdapter adapter, int iGroup)
addImplicitHydrogenAtoms
in interface JmolBioResolver
public void getBondInfo(JmolAdapter adapter, String group3, Object model)
private String[][] getLigandBondInfo(JmolAdapter adapter, Object model, String group3)
adapter
- model
- group3
- public void finalizeHydrogens()
finalizeHydrogens
in interface JmolBioResolver
private void deleteUnneededAtoms()
private void finalizePdbCharges()
private void finalizePdbMultipleBonds()