org.jmol.modelsetbio
Class Resolver
java.lang.Object
org.jmol.modelsetbio.Resolver
- All Implemented Interfaces:
- JmolBioResolver
public final class Resolver
- extends java.lang.Object
- implements JmolBioResolver
Method Summary |
void |
addImplicitHydrogenAtoms(JmolAdapter adapter,
int iGroup)
|
Polymer |
buildBioPolymer(Group group,
Group[] groups,
int i,
boolean checkPolymerConnections)
|
void |
clearBioPolymers(Group[] groups,
int groupCount,
java.util.BitSet bsModelsExcluded)
|
private void |
deleteUnneededAtoms()
Delete hydrogen atoms that are still in bsAddedHydrogens,
because they were not actually added. |
Group |
distinguishAndPropagateGroup(Chain chain,
java.lang.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,
java.lang.String group3,
java.lang.Object model)
|
private java.lang.String[][] |
getLigandBondInfo(JmolAdapter adapter,
java.lang.Object model,
java.lang.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,
java.lang.String name,
javax.vecmath.Point3f pt)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
modelLoader
private ModelLoader modelLoader
modelSet
private ModelSet modelSet
bsAddedHydrogens
private java.util.BitSet bsAddedHydrogens
bsAtomsForHs
private java.util.BitSet bsAtomsForHs
htBondMap
private java.util.Map<java.lang.String,java.lang.String> htBondMap
htGroupBonds
private java.util.Map<java.lang.String,java.lang.Boolean> htGroupBonds
hNames
private java.lang.String[] hNames
lastSetH
private int lastSetH
maxSerial
private int maxSerial
baseBondIndex
private int baseBondIndex
haveHsAlready
private boolean haveHsAlready
vAB
private javax.vecmath.Vector3f vAB
vAC
private javax.vecmath.Vector3f vAC
vNorm
private javax.vecmath.Vector3f vNorm
plane
private javax.vecmath.Point4f plane
Resolver
public Resolver()
distinguishAndPropagateGroup
public Group distinguishAndPropagateGroup(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int maxAtomIndex,
int modelIndex,
int[] specialAtomIndexes,
Atom[] atoms)
- Specified by:
distinguishAndPropagateGroup
in interface JmolBioResolver
buildBioPolymer
public Polymer buildBioPolymer(Group group,
Group[] groups,
int i,
boolean checkPolymerConnections)
- Specified by:
buildBioPolymer
in interface JmolBioResolver
clearBioPolymers
public void clearBioPolymers(Group[] groups,
int groupCount,
java.util.BitSet bsModelsExcluded)
- Specified by:
clearBioPolymers
in interface JmolBioResolver
setHaveHsAlready
public void setHaveHsAlready(boolean b)
- Specified by:
setHaveHsAlready
in interface JmolBioResolver
initialize
public void initialize(ModelSet modelSet)
- Specified by:
initialize
in interface JmolBioResolver
initializeHydrogenAddition
public void initializeHydrogenAddition(ModelLoader modelLoader,
int bondCount)
- Specified by:
initializeHydrogenAddition
in interface JmolBioResolver
addImplicitHydrogenAtoms
public void addImplicitHydrogenAtoms(JmolAdapter adapter,
int iGroup)
- Specified by:
addImplicitHydrogenAtoms
in interface JmolBioResolver
getBondInfo
public void getBondInfo(JmolAdapter adapter,
java.lang.String group3,
java.lang.Object model)
getLigandBondInfo
private java.lang.String[][] getLigandBondInfo(JmolAdapter adapter,
java.lang.Object model,
java.lang.String group3)
- reads PDB ligand CIF info and creates a bondInfo object.
- Parameters:
adapter
- model
- group3
-
- Returns:
- [[atom1, atom2, order]...]
finalizeHydrogens
public void finalizeHydrogens()
- Specified by:
finalizeHydrogens
in interface JmolBioResolver
deleteUnneededAtoms
private void deleteUnneededAtoms()
- Delete hydrogen atoms that are still in bsAddedHydrogens,
because they were not actually added.
Also delete ligand hydrogen atoms from CO2- and PO3(2-)
Note that we do this AFTER all atoms have been added. That means that
this operation will not mess up atom indexing
finalizePdbCharges
private void finalizePdbCharges()
finalizePdbMultipleBonds
private void finalizePdbMultipleBonds()
setHydrogen
private void setHydrogen(int iTo,
int iAtom,
java.lang.String name,
javax.vecmath.Point3f pt)