no.uio.labmed.pdb
Class AbstractPDBparser

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

public abstract class AbstractPDBparser
extends DataFileReader

Abstract PDBparser which implements empty metods, filtering functionality, and exception handling.


Nested Class Summary
 class AbstractPDBparser.AtomicData
           
 class AbstractPDBparser.SecondaryStructureData
           
 
Field Summary
 AbstractPDBparser.AtomicData forgetAtomicData
           
 AbstractPDBparser.SecondaryStructureData forgetSecondaryStructureData
           
static java.util.HashSet keywordsRecognized
           
static java.lang.String TYPE_HELIX
           
static java.lang.String TYPE_SHEET
           
static java.lang.String TYPE_TURN
           
 
Constructor Summary
AbstractPDBparser()
           
 
Method Summary
 AbstractPDBparser.AtomicData alternateAtom(AbstractPDBparser.AtomicData atom)
           
 void beginConnectivityAnnotationSection()
           
 void beginConnectivitySection()
           
 void beginCoordinateSection()
           
 void beginCoordinateTransformationSection()
           
 void beginHeterogenSection()
           
 void beginMiscellaneousFeaturesSection()
           
 void beginParse()
           
 void beginPrimaryStructureSection()
           
 void beginSecondaryStructureSection()
           
 void beginTitleSection()
           
 void endAtomChain()
           
 void endAtomResidue()
           
 void endConnectivityAnnotationSection()
           
 void endConnectivitySection()
           
 void endCoordinateSection()
           
 void endCoordinateTransformationSection()
           
 void endHeterogenSection()
           
 void endMiscellaneousFeaturesSection()
           
 void endModel()
           
 void endParse()
           
 void endPrimaryStructureSection()
           
 void endSecondaryStructureSection()
           
 void endTitleSection()
           
 boolean keywordRecognized(java.lang.String key)
           
 boolean lineHasKnownKey(java.lang.String line)
           
 void newAnisou()
           
 AbstractPDBparser.AtomicData newAtom(java.lang.String name)
           
 void newAtomChain(java.lang.String chainId)
           
 void newAtomResidue(java.lang.String residue)
           
 void newAuthor(java.lang.String t)
           
 void newCaveat(java.lang.String t)
           
 void newCispep()
           
 void newCompnd(java.lang.String t)
           
 void newConect()
           
 void newCryst1()
           
 void newDbref()
           
 void newExpdta(java.lang.String t)
           
 void newFormul()
           
 void newHeader(java.lang.String head, java.lang.String date, java.lang.String id)
           
 AbstractPDBparser.SecondaryStructureData newHelix()
           
 void newHet()
           
 AbstractPDBparser.AtomicData newHetatm(java.lang.String name)
           
 void newHetnam()
           
 void newHetsyn()
           
 void newHydbnd()
           
 void newJrnl(java.lang.String t)
           
 void newKeywds(java.lang.String t)
           
 void newLink()
           
 void newMaster()
           
 void newModel(int modelId)
           
 void newModres()
           
 void newMtrix()
           
 void newObslte(java.lang.String date, java.lang.String thisID, java.lang.String newID)
           
 void newOrigx()
           
 void newRemark(java.lang.String t)
           
 void newResidue(java.lang.String t)
           
 void newRevdat(java.lang.String t)
           
 void newScale()
           
 AbstractPDBparser.SecondaryStructureData newSecondaryStructure(java.lang.Object type)
           
 void newSeqadv()
           
 void newSeqresChain(java.lang.String t)
           
 AbstractPDBparser.SecondaryStructureData newSheet()
           
 void newSigatm()
           
 void newSiguij()
           
 void newSite()
           
 void newSltbrg()
           
 void newSource(java.lang.String t)
           
 void newSprsde(java.lang.String t)
           
 void newSSbond()
           
 void newTitle(java.lang.String t)
           
 AbstractPDBparser.SecondaryStructureData newTurn()
           
 void newTvect()
           
abstract  void parse()
           
 void 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, readLine, rest, skip, sub, sub
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

forgetAtomicData

public final AbstractPDBparser.AtomicData forgetAtomicData

forgetSecondaryStructureData

public final AbstractPDBparser.SecondaryStructureData forgetSecondaryStructureData

TYPE_HELIX

public static final java.lang.String TYPE_HELIX
See Also:
Constant Field Values

TYPE_SHEET

public static final java.lang.String TYPE_SHEET
See Also:
Constant Field Values

TYPE_TURN

public static final java.lang.String TYPE_TURN
See Also:
Constant Field Values

keywordsRecognized

public static java.util.HashSet keywordsRecognized
Constructor Detail

AbstractPDBparser

public AbstractPDBparser()
Method Detail

parse

public abstract void parse()

keywordRecognized

public boolean keywordRecognized(java.lang.String key)

lineHasKnownKey

public boolean lineHasKnownKey(java.lang.String line)

beginParse

public void beginParse()

beginTitleSection

public void beginTitleSection()

newHeader

public void newHeader(java.lang.String head,
                      java.lang.String date,
                      java.lang.String id)

newObslte

public void newObslte(java.lang.String date,
                      java.lang.String thisID,
                      java.lang.String newID)

newTitle

public void newTitle(java.lang.String t)

newCaveat

public void newCaveat(java.lang.String t)

newCompnd

public void newCompnd(java.lang.String t)

newSource

public void newSource(java.lang.String t)

newKeywds

public void newKeywds(java.lang.String t)

newExpdta

public void newExpdta(java.lang.String t)

newAuthor

public void newAuthor(java.lang.String t)

newRevdat

public void newRevdat(java.lang.String t)

newSprsde

public void newSprsde(java.lang.String t)

newJrnl

public void newJrnl(java.lang.String t)

newRemark

public void newRemark(java.lang.String t)

endTitleSection

public void endTitleSection()

beginPrimaryStructureSection

public void beginPrimaryStructureSection()

newDbref

public void newDbref()

newSeqadv

public void newSeqadv()

newSeqresChain

public void newSeqresChain(java.lang.String t)

newResidue

public void newResidue(java.lang.String t)

newModres

public void newModres()

endPrimaryStructureSection

public void endPrimaryStructureSection()

beginHeterogenSection

public void beginHeterogenSection()

newHet

public void newHet()

newHetnam

public void newHetnam()

newHetsyn

public void newHetsyn()

newFormul

public void newFormul()

endHeterogenSection

public void endHeterogenSection()

beginSecondaryStructureSection

public void beginSecondaryStructureSection()

newHelix

public AbstractPDBparser.SecondaryStructureData newHelix()

newSheet

public AbstractPDBparser.SecondaryStructureData newSheet()

newTurn

public AbstractPDBparser.SecondaryStructureData newTurn()

newSecondaryStructure

public AbstractPDBparser.SecondaryStructureData newSecondaryStructure(java.lang.Object type)

endSecondaryStructureSection

public void endSecondaryStructureSection()

beginConnectivityAnnotationSection

public void beginConnectivityAnnotationSection()

newSSbond

public void newSSbond()

newLink

public void newLink()

newHydbnd

public void newHydbnd()

newSltbrg

public void newSltbrg()

newCispep

public void newCispep()

endConnectivityAnnotationSection

public void endConnectivityAnnotationSection()

beginMiscellaneousFeaturesSection

public void beginMiscellaneousFeaturesSection()

newSite

public void newSite()

endMiscellaneousFeaturesSection

public void endMiscellaneousFeaturesSection()

beginCoordinateTransformationSection

public void beginCoordinateTransformationSection()

newCryst1

public void newCryst1()

newOrigx

public void newOrigx()

newScale

public void newScale()

newMtrix

public void newMtrix()

newTvect

public void newTvect()

endCoordinateTransformationSection

public void endCoordinateTransformationSection()

beginCoordinateSection

public void beginCoordinateSection()

newModel

public void newModel(int modelId)

newAtomChain

public void newAtomChain(java.lang.String chainId)

newAtomResidue

public void newAtomResidue(java.lang.String residue)

newAtom

public AbstractPDBparser.AtomicData newAtom(java.lang.String name)

newHetatm

public AbstractPDBparser.AtomicData newHetatm(java.lang.String name)

alternateAtom

public AbstractPDBparser.AtomicData alternateAtom(AbstractPDBparser.AtomicData atom)

newSigatm

public void newSigatm()

newAnisou

public void newAnisou()

newSiguij

public void newSiguij()

endAtomResidue

public void endAtomResidue()

terChain

public void terChain()

endAtomChain

public void endAtomChain()

endModel

public void endModel()

endCoordinateSection

public void endCoordinateSection()

beginConnectivitySection

public void beginConnectivitySection()

newConect

public void newConect()

endConnectivitySection

public void endConnectivitySection()

newMaster

public void newMaster()

endParse

public void endParse()