org.jmol.adapter.readers.more
Class JaguarReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.JaguarReader
public class JaguarReader
- extends AtomSetCollectionReader
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.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
moCount
int moCount
gaussianCount
int gaussianCount
lumoEnergy
float lumoEnergy
moData
java.util.Hashtable moData
orbitals
java.util.Vector orbitals
JaguarReader
public JaguarReader()
readAtomSetCollection
public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
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
readMolecularOrbitals
private void readMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
readFrequencies
private void readFrequencies()
throws java.lang.Exception
- Throws:
java.lang.Exception