public final class Resolver extends Object implements JmolBioResolver
Modifier and Type | Class and Description |
---|---|
protected 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 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 javajs.util.P4 |
plane |
private javajs.util.V3 |
vAB |
private javajs.util.V3 |
vAC |
private javajs.util.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,
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,
String group3,
int seqcode,
int firstAtomIndex,
int maxAtomIndex,
int modelIndex,
int[] specialAtomIndexes,
Atom[] atoms) |
void |
finalizeHydrogens() |
private void |
finalizePdbCharges() |
private void |
finalizePdbMultipleBonds() |
String |
fixPropertyValue(BS bsAtoms,
String data) |
Model |
getBioModel(int modelIndex,
int trajectoryBaseIndex,
String jmolData,
Properties modelProperties,
Map<String,Object> modelAuxiliaryInfo) |
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(ModelLoader modelLoader) |
void |
initializeHydrogenAddition() |
void |
iterateOverAllNewStructures(JmolAdapter adapter,
Object atomSetCollection)
Pull in all spans of helix, etc.
|
void |
setHaveHsAlready(boolean b) |
private void |
setHydrogen(int iTo,
int iAtom,
String name,
javajs.util.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 String[] hNames
private int lastSetH
private int maxSerial
private int baseBondIndex
private boolean haveHsAlready
private javajs.util.V3 vAB
private javajs.util.V3 vAC
private javajs.util.V3 vNorm
private javajs.util.P4 plane
private BS bsAssigned
public Model getBioModel(int modelIndex, int trajectoryBaseIndex, String jmolData, Properties modelProperties, Map<String,Object> modelAuxiliaryInfo)
getBioModel
in interface JmolBioResolver
public Group distinguishAndPropagateGroup(Chain chain, 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, 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 addHydrogens()
private void deleteUnneededAtoms()
private void finalizePdbCharges()
private void finalizePdbMultipleBonds()
private void setHydrogen(int iTo, int iAtom, String name, javajs.util.P3 pt)
public String fixPropertyValue(BS bsAtoms, String data)
fixPropertyValue
in interface JmolBioResolver
static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)
public void iterateOverAllNewStructures(JmolAdapter adapter, Object atomSetCollection)
iterateOverAllNewStructures
in interface JmolBioResolver
adapter
- atomSetCollection
- private void setStructure(JmolAdapterStructureIterator iterStructure)
iterStructure
- private void defineStructure(EnumStructure subType, String structureID, int serialID, int strandCount, int startChainID, int startSequenceNumber, char startInsertionCode, int endChainID, int endSequenceNumber, char endInsertionCode, int[] atomRange, int[] modelRange, BS bsAssigned)