org.jmol.adapter.readers.cifpdb

Class PdbReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.cifpdb.PdbReader

Direct Known Subclasses:

P2nReader, 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 boolean	applySymmetry
private int	atomCount
private java.util.List<java.util.Map<java.lang.String,java.lang.Object>>	biomolecules
private java.util.List<javax.vecmath.Matrix4f>	biomts
private int[]	chainAtomCounts
private java.lang.String	compnd
private int	configurationPtr
private int	conformationIndex
private java.util.Map<java.lang.String,java.lang.String>	currentCompnd
private java.lang.String	currentGroup3
private java.lang.String	currentKey
private int	currentResno
private boolean	haveDoubleBonds
private boolean	haveMappedSerials
private java.util.Map<java.lang.String,java.lang.Boolean>	htElementsInCurrentGroup
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Boolean>>	htFormul
private java.util.Map<java.lang.String,java.lang.String>	htHetero
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>>	htMolIds
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>>	htSites
private int	iAtom
private boolean	isConnectStateBug
private boolean	isMultiModel
private char	lastAltLoc
private java.lang.String	lastAtomData
private int	lastAtomIndex
private int	lastGroup
private char	lastInsertion
private int	lastSourceSerial
private int	lastTargetSerial
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	sb
private java.lang.StringBuffer	sbConect
private java.lang.StringBuffer	sbIgnored
private java.lang.StringBuffer	sbSelected
private int	serial
private java.util.List<java.util.Map<java.lang.String,java.lang.String>>	vCompnds

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

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

Constructor Summary

Constructors

Constructor and Description
PdbReader()

Method Summary

Methods

Modifier and Type	Method and Description
private void	anisou()
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) The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
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)
private void	remark290()
private void	remark350()
private void	scale(int n)
protected void	setAdditionalAtomParameters(Atom atom) adaptable via subclassing
private void	setBiomoleculeAtomCounts()
private void	site()
private void	structure()
private void	title()

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Boolean>> htFormul

htHetero

private java.util.Map<java.lang.String,java.lang.String> htHetero

htSites

private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> htSites

currentGroup3

private java.lang.String currentGroup3

currentResno

private int currentResno

htElementsInCurrentGroup

private java.util.Map<java.lang.String,java.lang.Boolean> 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

applySymmetry

private boolean applySymmetry

isConnectStateBug

private boolean isConnectStateBug

vCompnds

private java.util.List<java.util.Map<java.lang.String,java.lang.String>> vCompnds

currentCompnd

private java.util.Map<java.lang.String,java.lang.String> currentCompnd

currentKey

private java.lang.String currentKey

htMolIds

private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> htMolIds

resetKey

private boolean resetKey

compnd

private java.lang.String compnd

biomolecules

private java.util.List<java.util.Map<java.lang.String,java.lang.Object>> biomolecules

biomts

private java.util.List<javax.vecmath.Matrix4f> 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

private java.lang.StringBuffer sbIgnored

sbSelected

private java.lang.StringBuffer sbSelected

sbConect

private java.lang.StringBuffer sbConect

sb

private java.lang.StringBuffer sb

lastSourceSerial

private int lastSourceSerial

lastTargetSerial

private int lastTargetSerial

haveDoubleBonds

private boolean haveDoubleBonds

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

header

private void header()

title

private void title()

compndSource

private void compndSource(boolean isSource)

compndOld

private void compndOld()

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

setAdditionalAtomParameters

protected void setAdditionalAtomParameters(Atom atom)

adaptable via subclassing

Parameters:

atom -

deduceElementSymbol

private java.lang.String deduceElementSymbol(boolean isHetero)

The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed. The actual rules are as follows (using 1-based numbering: 1) Chemical symbols may be in columns 77 and 78 for total disambiguity. 2) Only valid chemical symbols should be in columns 13 and 14 These are the first two characters of a four-character field. 3) Four-character atom names for hydrogen necessarily start in column 13, so when that is the case, if the four-letter name starts with "H" then it is hydrogen regardless of what letter comes next. For example, "HG3 " is mercury (and should be in a HETATM record, not an ATOM record, anyway), but "HG33" is hydrogen, presumably. This leave open the ambiguity of a four-letter H name in a heteroatom set where the symbol is really H, not Hg or Ha, or Ho or Hf, etc.

Parameters:

isHetero -

Returns:

an atom symbol

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()