org.jmol.adapter.readers.more
Class MoldenReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MopacDataReader
org.jmol.adapter.readers.more.MoldenReader
public class MoldenReader
- extends MopacDataReader
A molecular structure and orbital reader for MolDen files.
See http://www.cmbi.ru.nl/molden/molden_format.html
- Author:
- Matthew Zwier
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 |
frequencies
protected float[] frequencies
freqAtomSet
protected AtomSetCollection freqAtomSet
MoldenReader
public MoldenReader()
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class MopacDataReader
readAtoms
void readAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
readGaussianBasis
void readGaussianBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readMolecularOrbitals
void readMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
readFreqsAndModes
void readFreqsAndModes()
throws java.lang.Exception
- Throws:
java.lang.Exception
splitKeyValue
java.lang.String[] splitKeyValue()
splitKeyValue
java.lang.String[] splitKeyValue(java.lang.String sep)
splitKeyValue
java.lang.String[] splitKeyValue(java.lang.String sep,
java.lang.String text)
throws java.util.NoSuchElementException
- Throws:
java.util.NoSuchElementException