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

a class used by ModelLoader only to handle all loading of operations specific to PDB/mmCIF files. By loading only by class name, only loaded if PDB file is called.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	Resolver.BondSorter

Field Summary

Fields

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 Summary

Constructors

Constructor and Description
Resolver()

Method Summary

Methods

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)

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 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

Constructor Detail

Resolver

public Resolver()

Method Detail

getBioModel

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)

Specified by:

getBioModel in interface JmolBioResolver

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

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)

fixPropertyValue

public java.lang.String fixPropertyValue(java.util.BitSet bsAtoms,
                                java.lang.String data)

Specified by:

fixPropertyValue in interface JmolBioResolver