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

Fields

Modifier and Type	Field and Description
private java.util.BitSet	bsAtomOK
private java.util.BitSet	bsBadIndex
private boolean	loadGeometries
private boolean	loadVibrations
private int	modelAtomCount
private boolean	optOnly
private java.lang.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

Constructors

Constructor and Description
MoldenReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
private boolean	checkOrbitalType(java.lang.String line)
void	finalizeReader()
private void	fixOrbitalType()
private java.lang.String[]	getMoTokens(java.lang.String line)
protected void	initializeReader()
private void	readAtoms()
private void	readAtomSet(java.lang.String atomSetName, boolean isBohr, boolean asClone)
private boolean	readFreqsAndModes()
private boolean	readGaussianBasis()
private boolean	readGeometryOptimization()
private boolean	readMolecularOrbitals()
private void	skipTo(java.lang.String key)

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, 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 java.lang.String orbitalType

modelAtomCount

private int modelAtomCount

bsAtomOK

private java.util.BitSet bsAtomOK

bsBadIndex

private java.util.BitSet bsBadIndex

Constructor Detail

MoldenReader

public MoldenReader()

Method Detail

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

finalizeReader

public void finalizeReader()

Overrides:

finalizeReader in class AtomSetCollectionReader

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

skipTo

private void skipTo(java.lang.String key)
             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