public class VaspPoscarReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
protected int |
ac |
protected javajs.util.Lst<String> |
atomLabels |
private boolean |
atomsLabeledInline |
protected String[] |
defaultLabels |
protected String[] |
elementLabel |
(package private) int |
elementPt |
private boolean |
haveAtomLabels |
protected boolean |
quiet |
(package private) int |
radiusPt |
private float |
scaleFac |
protected String |
title |
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
Constructor and Description |
---|
VaspPoscarReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
protected String |
getElement(String token)
allow for any number of characters, for which the first
one or two are an element symbol.
|
protected void |
initializeReader() |
protected String |
rdline() |
protected void |
readCoordinates() |
protected void |
readMolecularFormula()
try various ways to read the optional atom labels.
|
protected void |
readStructure(String titleMsg) |
protected void |
readUnitCellVectors() |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, 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, setupASCR
protected javajs.util.Lst<String> atomLabels
private boolean haveAtomLabels
private boolean atomsLabeledInline
private float scaleFac
protected int ac
protected String title
protected boolean quiet
protected String[] defaultLabels
protected String[] elementLabel
int radiusPt
int elementPt
protected void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
Exception
protected void readMolecularFormula() throws Exception
Exception
protected String getElement(String token)
token
-