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

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 float ROOT3
- Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
  addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
- Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
- Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
  allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount

Fields
Modifier and Type	Field	Description
`private boolean`	`haveLine`
`private float`	`lumoEnergy`
`private int`	`moCount`
`private static float`	`ROOT3`

Constructor Summary

Constructors
Constructor Description

JaguarReader()

Constructors
Constructor	Description
`JaguarReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`java.lang.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.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, 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 org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

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

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

rd

public java.lang.String rd()
                    throws java.lang.Exception

Overrides:: rd in class AtomSetCollectionReader
Throws:: java.lang.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.smarter.AtomSetCollectionReader

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Detail

moCount

lumoEnergy

ROOT3

haveLine

Constructor Detail

JaguarReader

Method Detail

checkLine

readAtoms

readCharges

readUnnormalizedBasis

readBasisNormalized

readJaguarMolecularOrbitals

readFrequencies

rd