no.uio.labmed.pdb
Class PDBparser

java.lang.Object
  |
  +--no.uio.labmed.pdb.DataFileReader
        |
        +--no.uio.labmed.pdb.AbstractPDBparser
              |
              +--no.uio.labmed.pdb.PDBparser
Direct Known Subclasses:
PDBinterpreter, ReadPDB, TestParser

public class PDBparser
extends AbstractPDBparser

PDB parser.


Nested Class Summary
 
Nested classes inherited from class no.uio.labmed.pdb.AbstractPDBparser
AbstractPDBparser.AtomicData, AbstractPDBparser.SecondaryStructureData
 
Field Summary
 java.util.ArrayList exceptionList
           
 java.io.PrintStream exceptionPrintStream
           
 AbstractPDBparser.AtomicData nullAtomicData
           
 
Fields inherited from class no.uio.labmed.pdb.AbstractPDBparser
forgetAtomicData, forgetSecondaryStructureData, keywordsRecognized, TYPE_HELIX, TYPE_SHEET, TYPE_TURN
 
Constructor Summary
PDBparser()
           
 
Method Summary
 void addException(java.lang.Exception e)
           
 void addParseException(java.lang.String s)
           
 void addParseException(java.lang.String s, java.lang.Exception e)
           
 void addParseException(java.lang.String s, java.lang.String line)
           
 java.lang.String getChainId()
           
 int getResidueID()
           
 void parse()
           
 void printException(java.lang.Exception e)
           
 java.lang.String readLine()
           
 void setExceptionPrintStream(java.io.PrintStream ps)
           
 
Methods inherited from class no.uio.labmed.pdb.AbstractPDBparser
alternateAtom, beginConnectivityAnnotationSection, beginConnectivitySection, beginCoordinateSection, beginCoordinateTransformationSection, beginHeterogenSection, beginMiscellaneousFeaturesSection, beginParse, beginPrimaryStructureSection, beginSecondaryStructureSection, beginTitleSection, endAtomChain, endAtomResidue, endConnectivityAnnotationSection, endConnectivitySection, endCoordinateSection, endCoordinateTransformationSection, endHeterogenSection, endMiscellaneousFeaturesSection, endModel, endParse, endPrimaryStructureSection, endSecondaryStructureSection, endTitleSection, keywordRecognized, lineHasKnownKey, newAnisou, newAtom, newAtomChain, newAtomResidue, newAuthor, newCaveat, newCispep, newCompnd, newConect, newCryst1, newDbref, newExpdta, newFormul, newHeader, newHelix, newHet, newHetatm, newHetnam, newHetsyn, newHydbnd, newJrnl, newKeywds, newLink, newMaster, newModel, newModres, newMtrix, newObslte, newOrigx, newRemark, newResidue, newRevdat, newScale, newSecondaryStructure, newSeqadv, newSeqresChain, newSheet, newSigatm, newSiguij, newSite, newSltbrg, newSource, newSprsde, newSSbond, newTitle, newTurn, newTvect, terChain
 
Methods inherited from class no.uio.labmed.pdb.DataFileReader
checkKey, close, getInt, getInt, getInt, getInt, getNum, getNum, getNum, getNum, getValue, hasKey, hasValue, line, nextLine, open, open, pos, rest, skip, sub, sub
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

nullAtomicData

public AbstractPDBparser.AtomicData nullAtomicData

exceptionPrintStream

public java.io.PrintStream exceptionPrintStream

exceptionList

public java.util.ArrayList exceptionList
Constructor Detail

PDBparser

public PDBparser()
Method Detail

readLine

public java.lang.String readLine()
Overrides:
readLine in class DataFileReader

addException

public void addException(java.lang.Exception e)

addParseException

public void addParseException(java.lang.String s,
                              java.lang.Exception e)

addParseException

public void addParseException(java.lang.String s,
                              java.lang.String line)

addParseException

public void addParseException(java.lang.String s)

printException

public void printException(java.lang.Exception e)

setExceptionPrintStream

public void setExceptionPrintStream(java.io.PrintStream ps)

parse

public void parse()
Specified by:
parse in class AbstractPDBparser

getResidueID

public int getResidueID()

getChainId

public java.lang.String getChainId()