javajs.api.GenericLineReader
GamessUKReader
, GamessUSReader
public abstract class GamessReader extends MOReader
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field | Description |
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protected javajs.util.Lst<java.lang.String> |
atomNames |
|
private java.util.Map<java.lang.String,java.lang.String> |
calcOptions |
|
private boolean |
isTypeSet |
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
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
Constructor | Description |
---|---|
GamessReader() |
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() |
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
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals, setMOData
protected javajs.util.Lst<java.lang.String> atomNames
private java.util.Map<java.lang.String,java.lang.String> calcOptions
private boolean isTypeSet
protected abstract void readAtomsInBohrCoordinates() throws java.lang.Exception
java.lang.Exception
protected void readEnergy()
protected void readGaussianBasis(java.lang.String initiator, java.lang.String terminator) throws java.lang.Exception
java.lang.Exception
protected abstract java.lang.String fixShellTag(java.lang.String tag)
protected void readFrequencies() throws java.lang.Exception
java.lang.Exception
protected static java.lang.String fixBasisLine(java.lang.String line)
protected void setCalculationType()
protected void readControlInfo() throws java.lang.Exception
java.lang.Exception
protected void readBasisInfo() throws java.lang.Exception
java.lang.Exception
private void readCalculationInfo(java.lang.String type) throws java.lang.Exception
java.lang.Exception