no.uio.labmed.molecule
Class ReadPDB

java.lang.Object
  |
  +--no.uio.labmed.pdb.DataFileReader
        |
        +--no.uio.labmed.pdb.AbstractPDBparser
              |
              +--no.uio.labmed.pdb.PDBparser
                    |
                    +--no.uio.labmed.molecule.ReadPDB

public class ReadPDB
extends PDBparser


Nested Class Summary
 class ReadPDB.AtomData
           
 
Nested classes inherited from class no.uio.labmed.pdb.AbstractPDBparser
AbstractPDBparser.SecondaryStructureData
 
Field Summary
 java.util.ArrayList modelList
           
 Compound topMolecule
           
 
Fields inherited from class no.uio.labmed.pdb.PDBparser
exceptionList, exceptionPrintStream, nullAtomicData
 
Fields inherited from class no.uio.labmed.pdb.AbstractPDBparser
forgetAtomicData, forgetSecondaryStructureData, keywordsRecognized, TYPE_HELIX, TYPE_SHEET, TYPE_TURN
 
Constructor Summary
ReadPDB()
           
 
Method Summary
 AbstractPDBparser.AtomicData newAtom(java.lang.String name)
           
 void newAtomChain(java.lang.String chainID)
           
 void newAtomResidue(java.lang.String residueName)
           
 void newModel(int modelID)
           
 
Methods inherited from class no.uio.labmed.pdb.PDBparser
addException, addParseException, addParseException, addParseException, getChainId, getResidueID, parse, printException, readLine, setExceptionPrintStream
 
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, newAuthor, newCaveat, newCispep, newCompnd, newConect, newCryst1, newDbref, newExpdta, newFormul, newHeader, newHelix, newHet, newHetatm, newHetnam, newHetsyn, newHydbnd, newJrnl, newKeywds, newLink, newMaster, 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

modelList

public java.util.ArrayList modelList

topMolecule

public Compound topMolecule
Constructor Detail

ReadPDB

public ReadPDB()
Method Detail

newModel

public void newModel(int modelID)
Overrides:
newModel in class AbstractPDBparser

newAtomChain

public void newAtomChain(java.lang.String chainID)
Overrides:
newAtomChain in class AbstractPDBparser

newAtomResidue

public void newAtomResidue(java.lang.String residueName)
Overrides:
newAtomResidue in class AbstractPDBparser

newAtom

public AbstractPDBparser.AtomicData newAtom(java.lang.String name)
Overrides:
newAtom in class AbstractPDBparser