org.jmol.adapter.readers.quantum.JaguarReader

All Implemented Interfaces:: javajs.api.GenericLineReader

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

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
Field Summary

Fields

Modifier and Type

Field

Description

private boolean

haveLine

private float

lumoEnergy

private int

moCount

private static final float

ROOT3

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor Summary

Constructors

Constructor

Description

JaguarReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

String

rd()

private void

readAtoms()

private void

readBasisNormalized()

private void

readCharges()

private void

readFrequencies()

private void

readJaguarMolecularOrbitals()

private void

readUnnormalizedBasis()

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, addSlaterBasis, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- moCount
  
  private int moCount
- lumoEnergy
  
  private float lumoEnergy
- ROOT3
  
  private static final float ROOT3
  See Also:
  
  Constant Field Values
- haveLine
  
  private boolean haveLine
Constructor Details
- JaguarReader
  
  public JaguarReader()
Method Details
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readAtoms
  
  private void readAtoms() throws Exception
  
  Throws:
  
  Exception
- readCharges
  
  private void readCharges() throws Exception
  
  Throws:
  
  Exception
- readUnnormalizedBasis
  
  private void readUnnormalizedBasis() throws Exception
  
  Throws:
  
  Exception
- readBasisNormalized
  
  private void readBasisNormalized() throws Exception
  
  Throws:
  
  Exception
- readJaguarMolecularOrbitals
  
  private void readJaguarMolecularOrbitals() throws Exception
  
  Throws:
  
  Exception
- readFrequencies
  
  private void readFrequencies() throws Exception
  
  Throws:
  
  Exception
- rd
  
  public String rd() throws Exception
  
  Overrides:
  
  rd in class AtomSetCollectionReader
  
  Throws:
  
  Exception

Class JaguarReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

moCount

lumoEnergy

ROOT3

haveLine

Constructor Details

JaguarReader

Method Details

checkLine

readAtoms

readCharges

readUnnormalizedBasis

readBasisNormalized

readJaguarMolecularOrbitals

readFrequencies

rd