javajs.api.GenericLineReader
public class AFLOWReader extends VaspPoscarReader
Modifier and Type | Field | Description |
---|---|---|
private java.lang.String |
aabb |
|
private java.util.Map<java.lang.String,float[]> |
compositions |
|
private int |
fileModelNumber |
|
private float |
fracB |
|
private boolean |
getComposition |
|
private boolean |
havePRE |
|
private java.util.Map<java.lang.String,java.lang.String> |
keyMap |
|
private java.lang.String |
listKey |
|
private java.lang.String |
listKeyCase |
|
private boolean |
readPRE |
|
private java.lang.String |
titleMsg |
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
ac, atomLabels, defaultLabels, elementLabel, quiet, title
Constructor | Description |
---|---|
AFLOWReader() |
Modifier and Type | Method | Description |
---|---|---|
private void |
alignUnitCells() |
|
protected boolean |
checkLine() |
|
private java.lang.String |
cleanKey(java.lang.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() |
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getElement, rdline, readCoordinates, readMolecularFormula, readStructure, readUnitCellVectors
private java.lang.String aabb
private boolean readPRE
private float fracB
private java.util.Map<java.lang.String,float[]> compositions
private boolean getComposition
private java.lang.String listKey
private java.lang.String listKeyCase
private int fileModelNumber
private boolean havePRE
private java.lang.String titleMsg
private java.util.Map<java.lang.String,java.lang.String> keyMap
protected void initializeReader() throws java.lang.Exception
initializeReader
in class VaspPoscarReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private boolean readPrePost() throws java.lang.Exception
java.lang.Exception
private void finalizeModel() throws java.lang.Exception
java.lang.Exception
private void readElementLabelsOnly() throws java.lang.Exception
java.lang.Exception
private boolean getData() throws java.lang.Exception
java.lang.Exception
private java.lang.String cleanKey(java.lang.String key)
key
- protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class VaspPoscarReader
java.lang.Exception
private void listCompositions()
private void alignUnitCells()