public class AFLOWReader extends VaspPoscarReader
Modifier and Type | Field and Description |
---|---|
private String |
aabb |
private Map<String,float[]> |
compositions |
private int |
fileModelNumber |
private float |
fracB |
private boolean |
getComposition |
private boolean |
havePRE |
private Map<String,String> |
keyMap |
private String |
listKey |
private String |
listKeyCase |
private boolean |
readPRE |
private String |
titleMsg |
ac, atomLabels, defaultLabels, elementLabel, quiet, 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 |
---|
AFLOWReader() |
Modifier and Type | Method and Description |
---|---|
private void |
alignUnitCells() |
protected boolean |
checkLine() |
private String |
cleanKey(String key)
cleans key to just letters and digits
|
private void |
finalizeModel() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private boolean |
getData() |
protected void |
initializeReader() |
private void |
listCompositions() |
private void |
readElementLabelsOnly()
scan the AFLOWReader PRE structure for elements in coord section
|
private boolean |
readPrePost() |
getElement, rdline, readCoordinates, readMolecularFormula, readStructure, readUnitCellVectors
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, 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
private String aabb
private boolean readPRE
private float fracB
private boolean getComposition
private String listKey
private String listKeyCase
private int fileModelNumber
private boolean havePRE
private String titleMsg
protected void initializeReader() throws Exception
initializeReader
in class VaspPoscarReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private void readElementLabelsOnly() throws Exception
Exception
private String cleanKey(String key)
key
- protected void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class VaspPoscarReader
Exception
private void listCompositions()
private void alignUnitCells()