org.jmol.adapter.readers.quantum
Class JaguarReader

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.MOReader
              extended by org.jmol.adapter.readers.quantum.JaguarReader

public class JaguarReader
extends MOReader

Jaguar reader tested for the two samples files in CVS. Both these files were created with Jaguar version 4.0, release 20. MO reader corrected 9/28/11 by Bob Hanson -- reading NORMALIZED set TODO: slight question about application of SQRT(3) in XY XZ YZ set if that turns out to be an issue, we can multiply coefficients


Field Summary
private  boolean haveLine
           
private  float lumoEnergy
           
private  int moCount
           
private static float ROOT3
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
 
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
JaguarReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  void readAtoms()
           
private  void readBasisNormalized()
           
private  void readCharges()
           
private  void readFrequencies()
           
private  void readJaguarMolecularOrbitals()
           
 java.lang.String readLine()
           
private  void readUnnormalizedBasis()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData, setMOType
 
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, 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

moCount

private int moCount

lumoEnergy

private float lumoEnergy

ROOT3

private static final float ROOT3
See Also:
Constant Field Values

haveLine

private boolean haveLine
Constructor Detail

JaguarReader

public JaguarReader()
Method Detail

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

readCharges

private void readCharges()
                  throws java.lang.Exception
Throws:
java.lang.Exception

readUnnormalizedBasis

private void readUnnormalizedBasis()
                            throws java.lang.Exception
Throws:
java.lang.Exception

readBasisNormalized

private void readBasisNormalized()
                          throws java.lang.Exception
Throws:
java.lang.Exception

readJaguarMolecularOrbitals

private void readJaguarMolecularOrbitals()
                                  throws java.lang.Exception
Throws:
java.lang.Exception

readFrequencies

private void readFrequencies()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readLine

public java.lang.String readLine()
                          throws java.lang.Exception
Overrides:
readLine in class AtomSetCollectionReader
Throws:
java.lang.Exception