public class SpartanSmolReader extends SpartanInputReader
BasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private static java.lang.String |
endCheck |
private boolean |
espCharges |
private boolean |
haveCharges |
private boolean |
iHaveModelStatement |
private boolean |
iHaveNewDir |
private boolean |
inputOnly |
private boolean |
isCompoundDocument |
private boolean |
isInputFirst |
private boolean |
natCharges |
(package private) SpartanArchive |
spartanArchive |
private java.lang.String |
title |
(package private) java.util.Map<java.lang.String,java.lang.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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, 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 java.lang.String |
readArchive() |
private java.lang.String |
readArchiveHeader() |
private void |
readMyTransform() |
private void |
readOutput() |
private void |
readProperties() |
private void |
setCharges() |
void |
setEnergy(float value) |
readInputRecordscanonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, 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 natCharges
private boolean isInputFirst
private boolean iHaveNewDir
private static final java.lang.String endCheck
private java.lang.String title
SpartanArchive spartanArchive
java.util.Map<java.lang.String,java.lang.String> titles
private boolean haveCharges
protected void initializeReader()
throws java.lang.Exception
initializeReader in class AtomSetCollectionReaderjava.lang.Exceptionprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate void makeNewAtomSet()
protected void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readMyTransform()
throws java.lang.Exception
java.lang.Exceptionprivate void readOutput()
throws java.lang.Exception
java.lang.Exceptionprivate java.lang.String readArchive()
throws java.lang.Exception
java.lang.Exceptionprivate void setCharges()
private void readProperties()
throws java.lang.Exception
java.lang.Exceptionprivate java.lang.String readArchiveHeader()
throws java.lang.Exception
java.lang.Exceptionpublic void setEnergy(float value)