org.jmol.adapter.readers.more
Class V3000Reader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.V3000Reader

public class V3000Reader
extends AtomSetCollectionReader

A reader for MDL V3000 files

http://www.mdli.com/downloads/public/ctfile/ctfile.jsp


Field Summary
(package private)  int headerAtomCount
           
(package private)  int headerBondCount
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup
 
Constructor Summary
V3000Reader()
           
 
Method Summary
(package private)  void flushLines()
           
(package private)  java.lang.String processAtomBlock()
           
(package private)  void processBondBlock()
           
(package private)  void processCtab()
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readLineWithContinuation()
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

headerAtomCount

int headerAtomCount

headerBondCount

int headerBondCount
Constructor Detail

V3000Reader

public V3000Reader()
Method Detail

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

processCtab

void processCtab()
           throws java.lang.Exception
Throws:
java.lang.Exception

processAtomBlock

java.lang.String processAtomBlock()
                            throws java.lang.Exception
Throws:
java.lang.Exception

processBondBlock

void processBondBlock()
                throws java.lang.Exception
Throws:
java.lang.Exception

readLineWithContinuation

void readLineWithContinuation()
                        throws java.lang.Exception
Throws:
java.lang.Exception

flushLines

void flushLines()
          throws java.lang.Exception
Throws:
java.lang.Exception