org.jmol.adapter.readers.molxyz
Class XyzReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      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) applySymmetry() 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, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup

Constructor Summary

XyzReader()

Method Summary

(package private) int	readAtomCount()
(package private) void	readAtoms(int modelAtomCount)
AtomSetCollection	readAtomSetCollection(java.io.BufferedReader reader)
(package private) void	readAtomSetName()
(package private) void	skipAtomSet(int modelAtomCount)

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

Constructor Detail

XyzReader

public XyzReader()

Method Detail

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)

Specified by:

readAtomSetCollection in class AtomSetCollectionReader

skipAtomSet

void skipAtomSet(int modelAtomCount)
           throws java.lang.Exception

Throws:

java.lang.Exception

readAtomCount

int readAtomCount()
            throws java.lang.Exception

Throws:

java.lang.Exception

readAtomSetName

void readAtomSetName()
               throws java.lang.Exception

Throws:

java.lang.Exception

readAtoms

void readAtoms(int modelAtomCount)
         throws java.lang.Exception

Throws:

java.lang.Exception