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

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader

SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter

Field Summary

private boolean	loadGeometries
private boolean	loadVibrations
private int	modelAtomCount
private boolean	optOnly
private String	orbitalType
private boolean	vibOnly

Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader

atomicNumbers, MIN_COEF

Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader

slaterArray, slaters

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

Constructor Summary

MoldenReader()

Method Summary

protected boolean	checkLine()
private boolean	checkOrbitalType(String line)
private void	fixOrbitalType()
private String[]	getMoTokens(String line)
protected void	initializeReader()
private void	readAtoms()
private void	readAtomSet(String atomSetName, boolean isBohr, boolean asClone)
private boolean	readFreqsAndModes()
private boolean	readGaussianBasis()
private boolean	readGeometryOptimization()
private boolean	readMolecularOrbitals()

Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader

createSphericalSlaterByType, scaleSlater

Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader

addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO

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

Field Detail

loadGeometries

private boolean loadGeometries

loadVibrations

private boolean loadVibrations

vibOnly

private boolean vibOnly

optOnly

private boolean optOnly

orbitalType

private String orbitalType

modelAtomCount

private int modelAtomCount

Constructor Detail

MoldenReader

public MoldenReader()

Method Detail

initializeReader

protected void initializeReader()

Overrides:

initializeReader in class AtomSetCollectionReader

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readAtoms

private void readAtoms()
                throws Exception

Throws:

Exception

readGaussianBasis

private boolean readGaussianBasis()
                           throws Exception

Throws:

Exception

readMolecularOrbitals

private boolean readMolecularOrbitals()
                               throws Exception

Throws:

Exception

getMoTokens

private String[] getMoTokens(String line)
                      throws Exception

Throws:

Exception

checkOrbitalType

private boolean checkOrbitalType(String line)

fixOrbitalType

private void fixOrbitalType()

readFreqsAndModes

private boolean readFreqsAndModes()
                           throws Exception

Throws:

Exception

readGeometryOptimization

private boolean readGeometryOptimization()
                                  throws Exception

Throws:

Exception

readAtomSet

private void readAtomSet(String atomSetName,
                         boolean isBohr,
                         boolean asClone)
                  throws Exception

Throws:

Exception