org.jmol.adapter.readers.more
Class QchemReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
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 |
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 |
atomCount
int atomCount
QchemReader
public QchemReader()
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