Package org.jmol.adapter.readers.xtal
Class Wien2kReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.Wien2kReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class Wien2kReader extends AtomSetCollectionReader
A reader for Wein2k DFT files. http://www.wien2k.at/reg_user/textbooks/usersguide.pdf Bob Hanson hansonr@stolaf.edu 5/14/2009
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Field Summary
Fields Modifier and Type Field Description private java.lang.Stringcxyzprivate booleandoSymmetryprivate booleanisrhombohedralprivate charlatticeCode-
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
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
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Constructor Summary
Constructors Constructor Description Wien2kReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private voidaddAtom()private java.lang.StringgetJones()voidinitializeReader()private voidreadAtoms()private voidreadEmbeddedScript()private voidreadSymmetry()private voidreadUnitCell()-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
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, finalizeSubclassReader, 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
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Field Detail
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isrhombohedral
private boolean isrhombohedral
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latticeCode
private char latticeCode
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doSymmetry
private boolean doSymmetry
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cxyz
private final java.lang.String cxyz
- See Also:
- Constant Field Values
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Method Detail
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initializeReader
public void initializeReader() throws java.lang.Exception- Overrides:
initializeReaderin classAtomSetCollectionReader- Throws:
java.lang.Exception
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readUnitCell
private void readUnitCell() throws java.lang.Exception- Throws:
java.lang.Exception
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readAtoms
private void readAtoms() throws java.lang.Exception- Throws:
java.lang.Exception
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addAtom
private void addAtom()
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readSymmetry
private void readSymmetry() throws java.lang.Exception- Throws:
java.lang.Exception
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getJones
private java.lang.String getJones() throws java.lang.Exception- Throws:
java.lang.Exception
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readEmbeddedScript
private void readEmbeddedScript() throws java.lang.Exception- Throws:
java.lang.Exception
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