public class SpartanSmolReader extends SpartanInputReader
BasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private String |
endCheck |
private boolean |
espCharges |
private boolean |
haveCharges |
private boolean |
iHaveModelStatement |
private boolean |
iHaveNewDir |
private boolean |
inputOnly |
private boolean |
isCompoundDocument |
private boolean |
isInputFirst |
(package private) SpartanArchive |
spartanArchive |
private String |
title |
(package private) Map<String,String> |
titles |
bondData, constraints, modelAtomCountalphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shellsaddedData, 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 and Description |
|---|
SpartanSmolReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
protected void |
initializeReader() |
private void |
makeNewAtomSet() |
private String |
readArchive() |
private String |
readArchiveHeader() |
private void |
readMyTransform() |
private void |
readOutput() |
private void |
readProperties() |
private void |
setCharges() |
void |
setEnergy(float value) |
readInputRecordscanonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, 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, 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, setupASCRprivate boolean iHaveModelStatement
private boolean isCompoundDocument
private boolean inputOnly
private boolean espCharges
private boolean isInputFirst
private boolean iHaveNewDir
private String endCheck
private String title
SpartanArchive spartanArchive
private boolean haveCharges
protected void initializeReader()
throws Exception
initializeReader in class AtomSetCollectionReaderExceptionprotected boolean checkLine()
throws Exception
checkLine in class AtomSetCollectionReaderExceptionprivate void makeNewAtomSet()
protected void finalizeSubclassReader()
throws Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderExceptionprivate void setCharges()
public void setEnergy(float value)