public final class Resolver extends java.lang.Object implements JmolBioResolver
Modifier and Type | Class and Description |
---|---|
(package private) class |
Resolver.BondSorter |
Modifier and Type | Field and Description |
---|---|
private int |
baseBondIndex |
private java.util.BitSet |
bsAddedHydrogens |
private java.util.BitSet |
bsAtomsForHs |
private boolean |
haveHsAlready |
private java.lang.String[] |
hNames |
private java.util.Map<java.lang.String,java.lang.String> |
htBondMap |
private java.util.Map<java.lang.String,java.lang.Boolean> |
htGroupBonds |
private int |
lastSetH |
private int |
maxSerial |
private ModelLoader |
modelLoader |
private ModelSet |
modelSet |
private javax.vecmath.Point4f |
plane |
private javax.vecmath.Vector3f |
vAB |
private javax.vecmath.Vector3f |
vAC |
private javax.vecmath.Vector3f |
vNorm |
Constructor and Description |
---|
Resolver() |
Modifier and Type | Method and Description |
---|---|
void |
addImplicitHydrogenAtoms(JmolAdapter adapter,
int iGroup) |
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() |
java.lang.String |
fixPropertyValue(java.util.BitSet bsAtoms,
java.lang.String data) |
Model |
getBioModel(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
java.lang.String jmolData,
java.util.Properties modelProperties,
java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo) |
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) |
private ModelLoader modelLoader
private ModelSet modelSet
private java.util.BitSet bsAddedHydrogens
private java.util.BitSet bsAtomsForHs
private java.util.Map<java.lang.String,java.lang.String> htBondMap
private java.util.Map<java.lang.String,java.lang.Boolean> htGroupBonds
private java.lang.String[] hNames
private int lastSetH
private int maxSerial
private int baseBondIndex
private boolean haveHsAlready
private javax.vecmath.Vector3f vAB
private javax.vecmath.Vector3f vAC
private javax.vecmath.Vector3f vNorm
private javax.vecmath.Point4f plane
public Model getBioModel(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, java.lang.String jmolData, java.util.Properties modelProperties, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo)
getBioModel
in interface JmolBioResolver
public Group distinguishAndPropagateGroup(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int maxAtomIndex, int modelIndex, int[] specialAtomIndexes, Atom[] atoms)
distinguishAndPropagateGroup
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, java.lang.String group3, java.lang.Object model)
private java.lang.String[][] getLigandBondInfo(JmolAdapter adapter, java.lang.Object model, java.lang.String group3)
adapter
- model
- group3
- public void finalizeHydrogens()
finalizeHydrogens
in interface JmolBioResolver
private void deleteUnneededAtoms()
private void finalizePdbCharges()
private void finalizePdbMultipleBonds()
private void setHydrogen(int iTo, int iAtom, java.lang.String name, javax.vecmath.Point3f pt)
public java.lang.String fixPropertyValue(java.util.BitSet bsAtoms, java.lang.String data)
fixPropertyValue
in interface JmolBioResolver