org.jmol.adapter.readers.more
Class MoldenReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.MopacDataReader
          extended by org.jmol.adapter.readers.more.MoldenReader

public class MoldenReader
extends MopacDataReader

A molecular structure and orbital reader for MolDen files. See http://www.cmbi.ru.nl/molden/molden_format.html

Author:
Matthew Zwier

Field Summary
protected  AtomSetCollection freqAtomSet
           
protected  float[] frequencies
           
 
Fields inherited from class org.jmol.adapter.readers.more.MopacDataReader
dValues, floatinfo, intinfo, MIN_COEF, moData, nOrbitals, orbitals
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
MoldenReader()
           
 
Method Summary
(package private)  void readAtoms()
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
(package private)  void readFreqsAndModes()
           
(package private)  void readGaussianBasis()
           
(package private)  void readMolecularOrbitals()
           
(package private)  java.lang.String[] splitKeyValue()
           
(package private)  java.lang.String[] splitKeyValue(java.lang.String sep)
           
(package private)  java.lang.String[] splitKeyValue(java.lang.String sep, java.lang.String text)
           
 
Methods inherited from class org.jmol.adapter.readers.more.MopacDataReader
addSlater, setMOs, setSlaters
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, 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
 

Field Detail

frequencies

protected float[] frequencies

freqAtomSet

protected AtomSetCollection freqAtomSet
Constructor Detail

MoldenReader

public MoldenReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class MopacDataReader

readAtoms

void readAtoms()
         throws java.lang.Exception
Throws:
java.lang.Exception

readGaussianBasis

void readGaussianBasis()
                 throws java.lang.Exception
Throws:
java.lang.Exception

readMolecularOrbitals

void readMolecularOrbitals()
                     throws java.lang.Exception
Throws:
java.lang.Exception

readFreqsAndModes

void readFreqsAndModes()
                 throws java.lang.Exception
Throws:
java.lang.Exception

splitKeyValue

java.lang.String[] splitKeyValue()

splitKeyValue

java.lang.String[] splitKeyValue(java.lang.String sep)

splitKeyValue

java.lang.String[] splitKeyValue(java.lang.String sep,
                                 java.lang.String text)
                           throws java.util.NoSuchElementException
Throws:
java.util.NoSuchElementException