org.jmol.adapter.readers.more
Class JaguarReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MOReader
org.jmol.adapter.readers.more.JaguarReader
public class JaguarReader
- extends MOReader
Jaguar reader tested for the two samples files in CVS. Both
these files were created with Jaguar version 4.0, release 20.
Fields inherited from class org.jmol.adapter.readers.more.MOReader |
alphaBeta, continuing, energyUnits, gaussianCount, gaussians, haveNboCharges, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, ignoreMOs, iHaveAtoms, moData, moTypes, orbitals, shellCount, shells |
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 |
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 |
moCount
int moCount
lumoEnergy
float lumoEnergy
JaguarReader
public JaguarReader()
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class MOReader
checkLine
protected boolean checkLine()
throws java.lang.Exception
- Specified by:
checkLine
in class MOReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
readAtoms
private void readAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
readCharges
private void readCharges()
throws java.lang.Exception
- Throws:
java.lang.Exception
readBasis
void readBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readBasisNormalized
void readBasisNormalized()
throws java.lang.Exception
- Throws:
java.lang.Exception
readJaguarMolecularOrbitals
private void readJaguarMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
readFrequencies
private void readFrequencies()
throws java.lang.Exception
- Throws:
java.lang.Exception