public class VaspPoscarReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
protected int |
ac |
protected javajs.util.Lst<java.lang.String> |
atomLabels |
private boolean |
atomsLabeledInline |
protected java.lang.String[] |
defaultLabels |
protected java.lang.String[] |
elementLabel |
(package private) int |
elementPt |
private boolean |
haveAtomLabels |
protected boolean |
quiet |
(package private) int |
radiusPt |
private float |
scaleFac |
protected java.lang.String |
title |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isFinalized, isSequential, isTrajectory, latticeCells, latticeScaling, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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VaspPoscarReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
protected java.lang.String |
getElement(java.lang.String token)
allow for any number of characters, for which the first
one or two are an element symbol.
|
protected void |
initializeReader() |
protected java.lang.String |
rdline() |
protected void |
readCoordinates() |
protected void |
readMolecularFormula()
try various ways to read the optional atom labels.
|
protected void |
readStructure(java.lang.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, 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<java.lang.String> atomLabels
private boolean haveAtomLabels
private boolean atomsLabeledInline
private float scaleFac
protected int ac
protected java.lang.String title
protected boolean quiet
protected java.lang.String[] defaultLabels
protected java.lang.String[] elementLabel
int radiusPt
int elementPt
protected void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected void readStructure(java.lang.String titleMsg) throws java.lang.Exception
java.lang.Exception
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
protected void readUnitCellVectors() throws java.lang.Exception
java.lang.Exception
protected void readMolecularFormula() throws java.lang.Exception
java.lang.Exception
protected void readCoordinates() throws java.lang.Exception
java.lang.Exception
protected java.lang.String getElement(java.lang.String token)
token
- protected java.lang.String rdline() throws java.lang.Exception
java.lang.Exception