no.uio.labmed.pdb
Class PDBinterpreter

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

public class PDBinterpreter
extends PDBparser


Nested Class Summary
 class PDBinterpreter.PrimaryStructureData
           
 class PDBinterpreter.SecondaryStructure
           
 
Nested classes inherited from class no.uio.labmed.pdb.AbstractPDBparser
AbstractPDBparser.AtomicData
 
Field Summary
 AbstractAminoAcidMap mapModRes
           
 AbstractAminoAcidMap mapStandardRes
           
 java.util.HashMap primaryStructure
           
 java.util.HashMap secondaryStructures
           
 
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
PDBinterpreter()
           
 
Method Summary
 AbstractAminoAcid getResidue(java.lang.String acronym)
           
 java.util.ArrayList getSecondaryStructureList(java.lang.String chainID)
           
 AbstractAminoAcidMap getStandardResMap()
           
 AbstractAminoAcidMap newAminoAcidMap()
           
 void newAtomChain(java.lang.String chain)
           
 void newAtomResidue(java.lang.String acronym)
           
 AbstractAminoAcid newModifiedResidue(java.lang.String acronym)
           
 void newResidue(java.lang.String acronym)
           
 AbstractPDBparser.SecondaryStructureData newSecondaryStructure(java.lang.Object type)
           
 void newSeqresChain(java.lang.String chain)
           
 
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, newAtom, 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, newRevdat, newScale, newSeqadv, 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

primaryStructure

public java.util.HashMap primaryStructure

mapStandardRes

public AbstractAminoAcidMap mapStandardRes

mapModRes

public AbstractAminoAcidMap mapModRes

secondaryStructures

public java.util.HashMap secondaryStructures
Constructor Detail

PDBinterpreter

public PDBinterpreter()
Method Detail

newAminoAcidMap

public AbstractAminoAcidMap newAminoAcidMap()

getStandardResMap

public AbstractAminoAcidMap getStandardResMap()

newModifiedResidue

public AbstractAminoAcid newModifiedResidue(java.lang.String acronym)

getResidue

public AbstractAminoAcid getResidue(java.lang.String acronym)

newSeqresChain

public final void newSeqresChain(java.lang.String chain)
Overrides:
newSeqresChain in class AbstractPDBparser

newResidue

public final void newResidue(java.lang.String acronym)
Overrides:
newResidue in class AbstractPDBparser

newAtomChain

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

newAtomResidue

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

newSecondaryStructure

public AbstractPDBparser.SecondaryStructureData newSecondaryStructure(java.lang.Object type)
Overrides:
newSecondaryStructure in class AbstractPDBparser

getSecondaryStructureList

public java.util.ArrayList getSecondaryStructureList(java.lang.String chainID)