GamessReader

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.GamessReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

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

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
`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.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

Constructor Summary

Constructors
Constructor Description

GamessReader()

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 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`	`setCalculationType()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, 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 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

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

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.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

atomNames

calcOptions

isTypeSet

Constructor Detail

GamessReader

Method Detail

readAtomsInBohrCoordinates

readEnergy

readGaussianBasis

fixShellTag

readFrequencies

fixBasisLine

setCalculationType

readControlInfo

readBasisInfo

readCalculationInfo