org.jmol.adapter.readers.molxyz
Class MolReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.molxyz.MolReader

public class MolReader
extends AtomSetCollectionReader

A reader for MDLI mol and sdf files.

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

also: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory()


Field Summary
(package private)  java.lang.String header
           
private static java.lang.String isotopeMap0
           
private static java.lang.String isotopeMap1
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
MolReader()
           
 
Method Summary
(package private)  void flushLines()
           
(package private)  void processCtab()
           
(package private)  void processMolSdHeader()
           
(package private)  void processRgHeader()
           
(package private)  void readAtoms(int atomCount)
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readBonds(int atom0, int bondCount)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

header

java.lang.String header

isotopeMap0

private static final java.lang.String isotopeMap0
See Also:
Constant Field Values

isotopeMap1

private static final java.lang.String isotopeMap1
See Also:
Constant Field Values
Constructor Detail

MolReader

public MolReader()
Method Detail

readAtomSetCollection

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

processMolSdHeader

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

processRgHeader

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

processCtab

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

flushLines

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

readAtoms

void readAtoms(int atomCount)
         throws java.lang.Exception
Throws:
java.lang.Exception

readBonds

void readBonds(int atom0,
               int bondCount)
         throws java.lang.Exception
Throws:
java.lang.Exception