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()
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 |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, 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 |
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
PdbReader
public PdbReader()
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()