Package org.jmol.adapter.readers.xtal
Class AbinitReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.AbinitReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class AbinitReader extends AtomSetCollectionReader
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Field Summary
Fields Modifier and Type Field Description (package private) float[]cellLatticeprivate booleaninputOnlyprivate intnAtomprivate intnTypeprivate float[]typeArrayprivate float[]znucl-
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 AbinitReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private voidapplySymmetry()protected booleancheckLine()protected voidinitializeReader()private voidreadAtoms()private voidreadAtomSpecies()private voidreadIntiallattice()private voidreadNoatom()private voidreadNotypes()private voidreadSpaceGroup()private voidreadTypesequence()-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
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, 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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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReaderin classAtomSetCollectionReader
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checkLine
protected boolean checkLine() throws java.lang.Exception- Overrides:
checkLinein classAtomSetCollectionReader- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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readNoatom
private void readNoatom() throws java.lang.Exception- Throws:
java.lang.Exception
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readNotypes
private void readNotypes() throws java.lang.Exception- Throws:
java.lang.Exception
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readTypesequence
private void readTypesequence() throws java.lang.Exception- Throws:
java.lang.Exception
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readAtomSpecies
private void readAtomSpecies() throws java.lang.Exception- Throws:
java.lang.Exception
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readSpaceGroup
private void readSpaceGroup() throws java.lang.Exception- Throws:
java.lang.Exception
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readIntiallattice
private void readIntiallattice() throws java.lang.Exception- Throws:
java.lang.Exception
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applySymmetry
private void applySymmetry() 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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