public class AimsReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private boolean |
globalDoApplySymmetry |
private boolean |
isFractional |
private int |
nLatticeVectors |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
AimsReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
protected void |
finalizeReader() |
protected void |
initializeReader() |
private void |
readAtom(java.lang.String[] tokens,
boolean isFractional) |
private void |
readLatticeVector(java.lang.String[] tokens) |
private void |
readMultipole(java.lang.String[] tokens) |
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, initializeTrajectoryFile, 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, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private boolean globalDoApplySymmetry
private boolean isFractional
private int nLatticeVectors
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine()
checkLine
in class AtomSetCollectionReader
protected void finalizeReader() throws java.lang.Exception
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
private void readLatticeVector(java.lang.String[] tokens)
private void readAtom(java.lang.String[] tokens, boolean isFractional)
private void readMultipole(java.lang.String[] tokens)