org.jmol.adapter.readers.cifpdb

Class PdbReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.cifpdb.PdbReader

Direct Known Subclasses:

PqrReader

public class PdbReader
extends AtomSetCollectionReader

PDB file reader.

http://www.rcsb.org

Author:

Miguel, Egon, and Bob (hansonr@stolaf.edu) symmetry added by Bob Hanson: setFractionalCoordinates() setSpaceGroupName() setUnitCell() initializeCartesianToFractional(); setUnitCellItem() setAtomCoord() applySymmetryAndSetTrajectory()

Field Summary

Fields

Modifier and Type	Field and Description
private int	atomCount
private java.util.List	biomolecules
private java.util.List	biomts
private int[]	chainAtomCounts
(package private) java.lang.String	compnd
private int	configurationPtr
private int	conformationIndex
private java.util.Hashtable	currentCompnd
private java.lang.String	currentGroup3
private java.lang.String	currentKey
private int	currentResno
private boolean	haveMappedSerials
private java.util.Hashtable	htElementsInCurrentGroup
private java.util.Hashtable	htFormul
private java.util.Hashtable	htHetero
private java.util.Hashtable	htMolIds
private java.util.Hashtable	htSites
private int	iAtom
private boolean	isMultiModel
private char	lastAltLoc
private java.lang.String	lastAtomData
private int	lastAtomIndex
private int	lastGroup
private char	lastInsertion
private int	lineLength
private static java.lang.String	lineOptions
private int	maxSerial
private int	nRes
private int	nUNK
private java.lang.StringBuffer	pdbHeader
private boolean	resetKey
private java.lang.StringBuffer	sbConect
(package private) java.lang.StringBuffer	sbIgnored
(package private) java.lang.StringBuffer	sbSelected
private int	serial
private java.util.List	vCompnds

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
PdbReader()

Method Summary

Methods

Modifier and Type	Method and Description
private void	anisou()
void	applySymmetryAndSetTrajectory()
private void	atom(int serial)
protected boolean	checkLine()
private void	checkNotPDB()
private void	compndOld()
private void	compndSource(boolean isSource)
private void	conect()
private void	cryst1()
private java.lang.String	deduceElementSymbol(boolean isHetero)
private void	expdta()
protected boolean	filterAtom(Atom atom, int iAtom)
protected void	finalizeReader()
private void	formul()
private float	getFloat(int ich, int cch)
private int	getModelNumber()
private void	header()
private void	het()
private void	hetnam()
protected void	initializeReader()
private void	model(int modelNumber)
protected float	readBFactor()
protected int	readOccupancy()
protected float	readPartialCharge()
protected float	readRadius()
private void	remark290()
private void	remark350()
private void	scale(int n)
private void	setBiomoleculeAtomCounts()
private void	site()
private void	structure()

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem

Methods inherited from class java.lang.Object

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

Field Detail

lineLength

private int lineLength

htFormul

private final java.util.Hashtable htFormul

htHetero

private java.util.Hashtable htHetero

htSites

private java.util.Hashtable htSites

currentGroup3

private java.lang.String currentGroup3

currentResno

private int currentResno

htElementsInCurrentGroup

private java.util.Hashtable htElementsInCurrentGroup

maxSerial

private int maxSerial

chainAtomCounts

private int[] chainAtomCounts

nUNK

private int nUNK

nRes

private int nRes

isMultiModel

private boolean isMultiModel

lineOptions

private static final java.lang.String lineOptions

See Also:

Constant Field Values

serial

private int serial

pdbHeader

private java.lang.StringBuffer pdbHeader

configurationPtr

private int configurationPtr

vCompnds

private java.util.List vCompnds

currentCompnd

private java.util.Hashtable currentCompnd

currentKey

private java.lang.String currentKey

htMolIds

private java.util.Hashtable htMolIds

resetKey

private boolean resetKey

compnd

java.lang.String compnd

biomolecules

private java.util.List biomolecules

biomts

private java.util.List biomts

atomCount

private int atomCount

lastAtomData

private java.lang.String lastAtomData

lastAtomIndex

private int lastAtomIndex

iAtom

private int iAtom

lastGroup

private int lastGroup

lastInsertion

private char lastInsertion

lastAltLoc

private char lastAltLoc

conformationIndex

private int conformationIndex

sbIgnored

java.lang.StringBuffer sbIgnored

sbSelected

java.lang.StringBuffer sbSelected

sbConect

private java.lang.StringBuffer sbConect

haveMappedSerials

private boolean haveMappedSerials

Constructor Detail

PdbReader

public PdbReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

applySymmetryAndSetTrajectory

public void applySymmetryAndSetTrajectory()
                                   throws java.lang.Exception

Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

Throws:

java.lang.Exception

header

private void header()

compndOld

private void compndOld()

compndSource

private void compndSource(boolean isSource)

setBiomoleculeAtomCounts

private void setBiomoleculeAtomCounts()

remark350

private void remark350()
                throws java.lang.Exception

Throws:

java.lang.Exception

remark290

private void remark290()
                throws java.lang.Exception

Throws:

java.lang.Exception

atom

private void atom(int serial)

filterAtom

protected boolean filterAtom(Atom atom,
                 int iAtom)

Overrides:

filterAtom in class AtomSetCollectionReader

Returns:

true if we want this atom

readOccupancy

protected int readOccupancy()

readBFactor

protected float readBFactor()

readPartialCharge

protected float readPartialCharge()

readRadius

protected float readRadius()

deduceElementSymbol

private java.lang.String deduceElementSymbol(boolean isHetero)

conect

private void conect()

structure

private void structure()

getModelNumber

private int getModelNumber()

model

private void model(int modelNumber)

checkNotPDB

private void checkNotPDB()

cryst1

private void cryst1()
             throws java.lang.Exception

Throws:

java.lang.Exception

getFloat

private float getFloat(int ich,
             int cch)
                throws java.lang.Exception

Throws:

java.lang.Exception

scale

private void scale(int n)
            throws java.lang.Exception

Throws:

java.lang.Exception

expdta

private void expdta()

formul

private void formul()

het

private void het()

hetnam

private void hetnam()

anisou

private void anisou()

site

private void site()