Class Cif2Reader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.cif.CifReader
org.jmol.adapter.readers.cif.Cif2Reader
- All Implemented Interfaces:
GenericLineReader
Preliminary Cif2 reader. Just a shell.
See http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html
- Author:
- Bob Hanson (hansonr@stolaf.edu)
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Field Summary
Fields inherited from class CifReader
ac, CAT_ATOM_SITE, CAT_ATOM_SITES, CAT_ATOM_TYPE, CAT_CELL, EMPTY, firstChar, htGroup1, iHaveDesiredModel, isCourseGrained, isLigand, isLoop, isMagCIF, isMMCIF, isSpinCIF, lastDataSetName, maxSerial, modelMap, nAtoms, nAtoms0, NONE, pdbID, skipping, symops, thisDataSetName, useAuthorChainIDFields inherited from class AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class CifReader
addCifAtom, addHeader, applySymmetryAndSetTrajectory, checkAllFieldsPresent, checkPDBModelField, checkSubclassSymmetry, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclass, finalizeSubclassReader, finalizeSubclassSymmetry, fullTrim, getBondOrder, getFieldString, getFloatColumnData, initializeReader, initSubclass, isFieldValid, isLoopKey, isNull, newModel, nextAtomSet, parseCartesianField, parseFloatField, parseIntField, parseLoopParameters, processAtomTypeLoopBlock, processCellParameter, processCitationListBlock, processLoopBlock, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, processUnitCellTransformMatrix, setSymmetryOperator, skipLoop, skipLoopKeywordMethods inherited from class AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR, warnSkippingOperation
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Constructor Details
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Cif2Reader
public Cif2Reader()
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Method Details
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getCifDataParser
- Overrides:
getCifDataParserin classCifReader
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