org.jmol.adapter.readers.more
Class QchemReader

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

public class QchemReader
extends AtomSetCollectionReader

A reader for Q-Chem 2.1 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc. (http://www.q-chem.com/)

Molecular coordinates and normal coordinates of vibrations are read.

This reader was developed from a single output file, and therefore, is not guaranteed to properly read all Q-chem output. If you have problems, please contact the author of this code, not the developers of Q-chem.

This is a hacked version of Miguel's GaussianReader

Version:
1.0
Author:
Steven E. Wheeler (swheele2@ccqc.uga.edu)

Field Summary
(package private)  int atomCount
           
 
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
QchemReader()
           
 
Method Summary
(package private)  void readAtoms()
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readFrequencies()
           
(package private)  void readPartialCharges()
           
(package private)  void recordAtomVector(int modelNumber, int atomCenterNumber, float x, float y, float z)
           
 
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

atomCount

int atomCount
Constructor Detail

QchemReader

public QchemReader()
Method Detail

readAtomSetCollection

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

readAtoms

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

readFrequencies

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

recordAtomVector

void recordAtomVector(int modelNumber,
                      int atomCenterNumber,
                      float x,
                      float y,
                      float z)
                throws java.lang.Exception
Throws:
java.lang.Exception

readPartialCharges

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