no.uio.labmed.pdb
Class PDBreader

java.lang.Object
  |
  +--no.uio.labmed.pdb.PDBformat
        |
        +--no.uio.labmed.pdb.PDBreader
All Implemented Interfaces:
PDBreaderConstants

public class PDBreader
extends PDBformat
implements PDBreaderConstants


Field Summary
 Token jj_nt
           
 Token token
           
 PDBreaderTokenManager token_source
           
 
Fields inherited from interface no.uio.labmed.pdb.PDBreaderConstants
ALFANUM, ANISOU, ANYTHING, ATOM, AUTHOR, CAVEAT, CHAINID, CISPEP, COMPND, CONECT, CRYST1, DBREF, DECIMAL, DEFAULT, DIGIT, END, ENDMDL, EOF, EOL, EXPDTA, FORMUL, HEADER, HELIX, HET, HETATM, HETNAM, HETSYN, HYDBND, ID, IGNORELINE, INT, JRNL, KEYWDS, LETTER, LINE, LINEEND, LINEFIELD, LINK, MASTER, MODEL, MODRES, MTRIX, NOT_EOL, OBSLTE, ORIGX, REMARK, RESIDUE, REVDAT, SCALE, SEQADV, SEQRES, SEQRESFIELD, SEQRESFIELD1, SEQRESFIELD2, SEQRESFIELD3, SEQRESLENGTH, SEQRESLINENO, SHEET, SIGATM, SIGUIJ, SITE, SLTBRG, SOURCE, SPRSDE, SSBOND, TER, TITLE, tokenImage, TURN, TVECT, WORD, XLINEEND
 
Constructor Summary
PDBreader(java.io.InputStream stream)
           
PDBreader(PDBreaderTokenManager tm)
           
PDBreader(java.io.Reader stream)
           
 
Method Summary
 void disable_tracing()
           
 void enable_tracing()
           
 no.uio.labmed.pdb.ParseException generateParseException()
           
 Token getNextToken()
           
 Token getToken(int index)
           
 void model()
           
 void read()
           
 void ReInit(java.io.InputStream stream)
           
 void ReInit(PDBreaderTokenManager tm)
           
 void ReInit(java.io.Reader stream)
           
 
Methods inherited from class no.uio.labmed.pdb.PDBformat
end, endConnectivityAnnotationSection, endHeterogenSection, endMiscellaneousFeaturesSection, endModel, endPrimaryStructureSection, endSecondaryStructureSection, endTitleSection, getChainId, ifNewChainId, newAuthor, newCaveat, newChainId, newCompnd, newExpdta, newHeader, newHelix, newJrnl, newKeywds, newModel, newObslte, newRemark, newResidue, newRevdat, newSheet, newSource, newSprsde, newTitle, newTurn, startConnectivityAnnotationSection, startHeterogenSection, startMiscellaneousFeaturesSection, startPDBparse, startPrimaryStructureSection, startSecondaryStructureSection, startTitleSection
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

token_source

public PDBreaderTokenManager token_source

token

public Token token

jj_nt

public Token jj_nt
Constructor Detail

PDBreader

public PDBreader(java.io.InputStream stream)

PDBreader

public PDBreader(java.io.Reader stream)

PDBreader

public PDBreader(PDBreaderTokenManager tm)
Method Detail

read

public final void read()
                throws no.uio.labmed.pdb.ParseException
no.uio.labmed.pdb.ParseException

model

public final void model()
                 throws no.uio.labmed.pdb.ParseException
no.uio.labmed.pdb.ParseException

ReInit

public void ReInit(java.io.InputStream stream)

ReInit

public void ReInit(java.io.Reader stream)

ReInit

public void ReInit(PDBreaderTokenManager tm)

getNextToken

public final Token getNextToken()

getToken

public final Token getToken(int index)

generateParseException

public final no.uio.labmed.pdb.ParseException generateParseException()

enable_tracing

public final void enable_tracing()

disable_tracing

public final void disable_tracing()