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.SlaterReader
      - org.jmol.adapter.readers.quantum.MopacSlaterReader
        
        org.jmol.adapter.readers.quantum.GamessReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

GamessUKReader, GamessUSReader
```
public abstract class GamessReader
extends MopacSlaterReader
```

Nested Class Summary
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
  SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  BasisFunctionReader.MOEnergySorter

Field Summary

Fields
Modifier and Type	Field	Description
`protected javajs.util.Lst<java.lang.String>`	`atomNames`
`private java.util.Map<java.lang.String,java.lang.String>`	`calcOptions`
`private boolean`	`isTypeSet`

Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis

Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters

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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

GamessReader()

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected static java.lang.String`	`fixBasisLine(java.lang.String line)`
`protected abstract java.lang.String`	`fixShellTag(java.lang.String tag)`
`protected void`	`initializeReader()`
`protected abstract void`	`readAtomsInBohrCoordinates()`
`protected void`	`readBasisInfo()`
`private void`	`readCalculationInfo(java.lang.String type)`
`protected void`	`readControlInfo()`
`protected void`	`readEnergy()`
`protected void`	`readFrequencies()`
`protected void`	`readGaussianBasis(java.lang.String initiator, java.lang.String terminator)`
`protected void`	`setAtom(Atom atom, int atomicNumber, java.lang.String name, java.lang.String id)`
`protected void`	`setCalculationType()`

Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData

Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

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

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, checkLine, 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, 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

atomNames

protected javajs.util.Lst<java.lang.String> atomNames

calcOptions

private java.util.Map<java.lang.String,java.lang.String> calcOptions

isTypeSet
```
private boolean isTypeSet
```

Constructor Detail
- GamessReader
```
public GamessReader()
```

Method Detail

readAtomsInBohrCoordinates

protected abstract void readAtomsInBohrCoordinates()
                                            throws java.lang.Exception

Throws:: java.lang.Exception

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:: initializeReader in class MOReader
Throws:: java.lang.Exception

setAtom

protected void setAtom(Atom atom,
                       int atomicNumber,
                       java.lang.String name,
                       java.lang.String id)

readEnergy
```
protected void readEnergy()
```

readGaussianBasis

protected void readGaussianBasis(java.lang.String initiator,
                                 java.lang.String terminator)
                          throws java.lang.Exception

Throws:: java.lang.Exception

fixShellTag

protected abstract java.lang.String fixShellTag(java.lang.String tag)

readFrequencies

protected void readFrequencies()
                        throws java.lang.Exception

Throws:: java.lang.Exception

fixBasisLine

protected static java.lang.String fixBasisLine(java.lang.String line)

setCalculationType
```
protected void setCalculationType()
```

readControlInfo

protected void readControlInfo()
                        throws java.lang.Exception

Throws:: java.lang.Exception

readBasisInfo

protected void readBasisInfo()
                      throws java.lang.Exception

Throws:: java.lang.Exception

readCalculationInfo

private void readCalculationInfo(java.lang.String type)
                          throws java.lang.Exception

Throws:: java.lang.Exception

Class GamessReader

Nested Class Summary

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

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

Field Summary

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

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

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.MopacSlaterReader

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

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

atomNames

calcOptions

isTypeSet

Constructor Detail

GamessReader

Method Detail

readAtomsInBohrCoordinates

initializeReader

setAtom

readEnergy

readGaussianBasis

fixShellTag

readFrequencies

fixBasisLine

setCalculationType

readControlInfo

readBasisInfo

readCalculationInfo