org.jmol.modelsetbio
Class Resolver

java.lang.Object
  org.jmol.modelsetbio.Resolver

All Implemented Interfaces:

JmolBioResolver

public final class Resolver
extends Object
implements JmolBioResolver

Nested Class Summary

(package private) class

Resolver.BondSorter

Field Summary

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 Summary

Resolver()

Method Summary

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

modelLoader

private ModelLoader modelLoader

modelSet

private ModelSet modelSet

bsAddedHydrogens

private BitSet bsAddedHydrogens

bsAtomsForHs

private BitSet bsAtomsForHs

htBondMap

private Map<String,String> htBondMap

htGroupBonds

private Map<String,Boolean> htGroupBonds

hNames

private String[] hNames

lastSetH

private int lastSetH

maxSerial

private int maxSerial

baseBondIndex

private int baseBondIndex

haveHsAlready

private boolean haveHsAlready

vAB

private Vector3f vAB

vAC

private Vector3f vAC

vNorm

private Vector3f vNorm

plane

private Point4f plane

Constructor Detail

Resolver

public Resolver()

Method Detail

distinguishAndPropagateGroup

public Group distinguishAndPropagateGroup(Chain chain,
                                          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,
                             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,
                        String group3,
                        Object model)

getLigandBondInfo

private String[][] getLigandBondInfo(JmolAdapter adapter,
                                     Object model,
                                     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,
                         String name,
                         Point3f pt)