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org.jmol.adapter.readers.quantum
Class MoldenReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.SlaterReader
              extended by org.jmol.adapter.readers.quantum.MopacSlaterReader
                  extended by 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  BitSet bsAtomOK
           
private  BitSet bsBadIndex
           
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)
           
 void finalizeReader()
           
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()
           
private  void skipTo(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 String orbitalType

modelAtomCount

private int modelAtomCount

bsAtomOK

private BitSet bsAtomOK

bsBadIndex

private BitSet bsBadIndex
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

finalizeReader

public void finalizeReader()
Overrides:
finalizeReader in class AtomSetCollectionReader

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

skipTo

private void skipTo(String key)
             throws Exception
Throws:
Exception

readAtomSet

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