org.jmol.adapter.readers.quantum
Class MoldenReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.SlaterReader
org.jmol.adapter.readers.quantum.MopacSlaterReader
org.jmol.adapter.readers.quantum.MoldenReader
public class MoldenReader
- extends MopacSlaterReader
A molecular structure and orbital reader for MolDen files.
See http://www.cmbi.ru.nl/molden/molden_format.html
updated by Bob Hanson for Jmol 12.0/12.1
- Author:
- Matthew Zwier
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader |
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, 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 |
loadGeometries
private boolean loadGeometries
loadVibrations
private boolean loadVibrations
vibOnly
private boolean vibOnly
optOnly
private boolean optOnly
modelAtomCount
private int modelAtomCount
MoldenReader
public MoldenReader()
initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in class AtomSetCollectionReader
checkLine
protected boolean checkLine()
throws java.lang.Exception
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
readAtoms
private void readAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
readGaussianBasis
private boolean readGaussianBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readMolecularOrbitals
private boolean readMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
readFreqsAndModes
private boolean readFreqsAndModes()
throws java.lang.Exception
- Throws:
java.lang.Exception
readGeometryOptimization
private boolean readGeometryOptimization()
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtomSet
private void readAtomSet(java.lang.String atomSetName,
boolean isBohr,
boolean asClone)
throws java.lang.Exception
- Throws:
java.lang.Exception