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.GaussianReader
      - org.jmol.adapter.readers.quantum.GaussianFchkReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class GaussianFchkReader
extends GaussianReader
```
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data

Author:

hansonr Bob Hanson hansonr@stolaf.edu

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 static java.lang.String[] AO_TYPES

private int atomCount

private java.util.Map<java.lang.String,java.lang.Object> fileData
- Fields inherited from class org.jmol.adapter.readers.quantum.GaussianReader
  calculationNumber, namedSets
- 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 inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
- 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

Constructor Summary

Constructors
Constructor Description

GaussianFchkReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`checkForFreq()`
`private float[]`	`fillFloat(float[] f0, int i, int n)`
`private void`	`getOrbitals(float[] e, float[] c, int occ, int nElec)`
`protected void`	`initializeReader()`
`private void`	`readAllData()`
`protected void`	`readAtoms()`
`protected void`	`readBasis()`
`protected void`	`readBonds()`
`protected void`	`readDipoleMoment()`
`protected void`	`readMolecularObitals()`
`protected void`	`readPartialCharges()`	Reads partial charges and assigns them only to the last atom set.

Methods inherited from class org.jmol.adapter.readers.quantum.GaussianReader
checkLine, readFrequencies, readMolecularOrbitals

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

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.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, rd, 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 Detail

fileData

private java.util.Map<java.lang.String,java.lang.Object> fileData

atomCount
```
private int atomCount
```

AO_TYPES

private static java.lang.String[] AO_TYPES

Constructor Detail
- GaussianFchkReader
```
public GaussianFchkReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
                         throws java.lang.Exception
```
Overrides:

initializeReader in class GaussianReader

Throws:

java.lang.Exception

checkForFreq

private void checkForFreq()
                   throws java.lang.Exception

Throws:: java.lang.Exception

fillFloat

private float[] fillFloat(float[] f0,
                          int i,
                          int n)

readAllData

private void readAllData()
                  throws java.lang.Exception

Throws:: java.lang.Exception

readAtoms
```
protected void readAtoms()
                  throws java.lang.Exception
```
Overrides:

readAtoms in class GaussianReader

Throws:

java.lang.Exception

readBonds
```
protected void readBonds()
```

readDipoleMoment
```
protected void readDipoleMoment()
                         throws java.lang.Exception
```
Overrides:

readDipoleMoment in class GaussianReader

Throws:

java.lang.Exception

readPartialCharges
```
protected void readPartialCharges()
                           throws java.lang.Exception
```
Description copied from class: GaussianReader

Reads partial charges and assigns them only to the last atom set.

Overrides:

readPartialCharges in class GaussianReader

Throws:

java.lang.Exception - When an I/O error or discardlines error occurs

readBasis
```
protected void readBasis()
                  throws java.lang.Exception
```
Overrides:

readBasis in class GaussianReader

Throws:

java.lang.Exception

readMolecularObitals

protected void readMolecularObitals()
                             throws java.lang.Exception

Throws:: java.lang.Exception

getOrbitals

private void getOrbitals(float[] e,
                         float[] c,
                         int occ,
                         int nElec)

Modifier and Type	Field	Description
`private static java.lang.String[]`	`AO_TYPES`
`private int`	`atomCount`
`private java.util.Map<java.lang.String,java.lang.Object>`	`fileData`

Class GaussianFchkReader

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.GaussianReader

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.GaussianReader

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 Detail

fileData

atomCount

AO_TYPES

Constructor Detail

GaussianFchkReader

Method Detail

initializeReader

checkForFreq

fillFloat

readAllData

readAtoms

readBonds

readDipoleMoment

readPartialCharges

readBasis

readMolecularObitals

getOrbitals