org.jmol.adapter.readers.quantum
public class SpartanSmolReader extends SpartanInputReader
Modifier and Type | Field and Description |
---|---|
private String |
endCheck |
private boolean |
espCharges |
private boolean |
haveCharges |
private boolean |
iHaveModelStatement |
private boolean |
inputOnly |
private boolean |
isCompoundDocument |
(package private) SpartanArchive |
spartanArchive |
private String |
title |
(package private) Map<String,String> |
titles |
atomCount, bondData, constraints, modelAtomCount, modelName
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
SpartanSmolReader() |
Modifier and Type | Method and Description |
---|---|
private float |
bytesToDoubleToFloat(byte[] bytes,
int j) |
protected boolean |
checkLine() |
protected void |
finalizeReader() |
private int |
getModelNumber() |
protected void |
initializeReader() |
private void |
readArchive() |
private boolean |
readArchiveHeader() |
private void |
readOutput() |
private void |
readProperties() |
private void |
readTransform() |
private void |
setCharges() |
readInputRecords
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private boolean iHaveModelStatement
private boolean isCompoundDocument
private boolean inputOnly
private boolean espCharges
private String endCheck
private String title
SpartanArchive spartanArchive
private boolean haveCharges
protected void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
protected void finalizeReader() throws Exception
finalizeReader
in class AtomSetCollectionReader
Exception
private float bytesToDoubleToFloat(byte[] bytes, int j)
private void setCharges()
private int getModelNumber()