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 BS |
bsAddedHydrogens |
private BS |
bsAssigned |
private BS |
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 P4 |
plane |
private V3 |
vAB |
private V3 |
vAC |
private V3 |
vNorm |
Constructor and Description |
---|
Resolver() |
Modifier and Type | Method and Description |
---|---|
private void |
addHydrogens() |
void |
addImplicitHydrogenAtoms(JmolAdapter adapter,
int iGroup,
int nH) |
(package private) static BioPolymer |
allocateBioPolymer(Group[] groups,
int firstGroupIndex,
boolean checkConnections) |
private void |
defineStructure(EnumStructure subType,
java.lang.String structureID,
int serialID,
int strandCount,
int startChainID,
int startSequenceNumber,
char startInsertionCode,
int endChainID,
int endSequenceNumber,
char endInsertionCode,
int[] atomRange,
int[] modelRange,
BS bsAssigned) |
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(BS bsAtoms,
java.lang.String data) |
Model |
getBioModel(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(ModelLoader modelLoader) |
void |
initializeHydrogenAddition() |
void |
iterateOverAllNewStructures(JmolAdapter adapter,
java.lang.Object atomSetCollection)
Pull in all spans of helix, etc.
|
void |
setHaveHsAlready(boolean b) |
private void |
setHydrogen(int iTo,
int iAtom,
java.lang.String name,
P3 pt) |
private void |
setStructure(JmolAdapterStructureIterator iterStructure)
note that istart and iend will be adjusted.
|
private ModelLoader modelLoader
private ModelSet modelSet
private BS bsAddedHydrogens
private BS 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 V3 vAB
private V3 vAC
private V3 vNorm
private P4 plane
private BS bsAssigned
public Model getBioModel(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(ModelLoader modelLoader)
initialize
in interface JmolBioResolver
public void initializeHydrogenAddition()
initializeHydrogenAddition
in interface JmolBioResolver
public void addImplicitHydrogenAtoms(JmolAdapter adapter, int iGroup, int nH)
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 addHydrogens()
private void deleteUnneededAtoms()
private void finalizePdbCharges()
private void finalizePdbMultipleBonds()
private void setHydrogen(int iTo, int iAtom, java.lang.String name, P3 pt)
public java.lang.String fixPropertyValue(BS bsAtoms, java.lang.String data)
fixPropertyValue
in interface JmolBioResolver
static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)
public void iterateOverAllNewStructures(JmolAdapter adapter, java.lang.Object atomSetCollection)
iterateOverAllNewStructures
in interface JmolBioResolver
adapter
- atomSetCollection
- private void setStructure(JmolAdapterStructureIterator iterStructure)
iterStructure
- private void defineStructure(EnumStructure subType, java.lang.String structureID, int serialID, int strandCount, int startChainID, int startSequenceNumber, char startInsertionCode, int endChainID, int endSequenceNumber, char endInsertionCode, int[] atomRange, int[] modelRange, BS bsAssigned)