org.jmol.adapter.readers.molxyz
Class XyzReader

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

public class XyzReader
extends AtomSetCollectionReader

Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c


Field Summary
 
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
XyzReader()
           
 
Method Summary
private  int readAtomCount()
           
private  void readAtoms(int modelAtomCount)
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
private  void readAtomSetName()
           
private  void skipAtomSet(int modelAtomCount)
           
 
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
 

Constructor Detail

XyzReader

public XyzReader()
Method Detail

readAtomSetCollection

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

skipAtomSet

private void skipAtomSet(int modelAtomCount)
                  throws java.lang.Exception
Throws:
java.lang.Exception

readAtomCount

private int readAtomCount()
                   throws java.lang.Exception
Throws:
java.lang.Exception

readAtomSetName

private void readAtomSetName()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readAtoms

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