org.jmol.adapter.readers.quantum

Class JaguarReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.MOReader

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

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
JaguarReader()

Method Summary

Methods

Modifier and Type	Method and Description
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