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, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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
orbitalType
private java.lang.String orbitalType
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
getMoTokens
private java.lang.String[] getMoTokens(java.lang.String line)
throws java.lang.Exception
- Throws:
java.lang.Exception
checkOrbitalType
private boolean checkOrbitalType(java.lang.String line)
fixOrbitalType
private void fixOrbitalType()
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