Package org.jmol.adapter.readers.cif
Class BCIFReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.cif.CifReader
org.jmol.adapter.readers.cif.MMCifReader
org.jmol.adapter.readers.cif.BCIFReader
- All Implemented Interfaces:
GenericLineReader
A very simple Binary CIF file reader extention of MMCifReader extends
CifReader.
- Author:
- Bob Hanson (hansonr@stolaf.edu)
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Field Summary
FieldsFields inherited from class org.jmol.adapter.readers.cif.MMCifReader
CAT_ASSEM, CAT_CHEMCOMP, CAT_COMPBOND, CAT_NCS, CAT_OPER, CAT_SEQUENCEDIF, CAT_SHEET, CAT_STRUCSITE, CAT_STRUCTCONF, CAT_STRUCTCONN, done, htHetero, htSites, isBiomolecule, vBiomolecules
Fields inherited from class org.jmol.adapter.readers.cif.CifReader
ac, CAT_ATOM_SITE, CAT_ATOM_SITES, CAT_ATOM_TYPE, CAT_CELL, CELL_TYPE_MAGNETIC_PARENT, CELL_TYPE_MAGNETIC_STANDARD, EMPTY, firstChar, htGroup1, iHaveDesiredModel, isCourseGrained, isLigand, isLoop, isMagCIF, isMMCIF, lastDataSetName, maxSerial, modelMap, nAtoms, nAtoms0, NONE, pdbID, skipping, symops, thisDataSetName, useAuthorChainID
Fields inherited from class org.jmol.adapter.smarter.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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
optional reader-specific method run first.protected GenericCifDataParser
protected float
getFloatColumnData
(int i) Called by processAtomSites to retrieve individual matrix elements and set them by name.protected boolean
protected float
protected float
protected int
protected int
parseIntFieldTok
(byte tok) Get a specific column's item for this category on this row.protected void
parseLoopParameters
(String[] fields) This is the callback the that the MMCifReader and CifReader process.....() methods call initially.protected void
The primare method initiating this readerprotected void
binary must set up initiallyMethods inherited from class org.jmol.adapter.readers.cif.MMCifReader
addAssembly, addHetero, addMatrix, checkFilterAssembly, checkPDBModelField, checkSubclassSymmetry, finalizeSubclass, incrementModel, initSubclass, processAssemblyGenBlock, processChemCompLoopBlock, processCompBondLoopBlock, processSequence, processStructConfLoopBlock, processStructConnLoopBlock, processStructOperListBlock, processStructSheetRangeLoopBlock, processStructSiteBlock, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, sortAssemblyModels
Methods inherited from class org.jmol.adapter.readers.cif.CifReader
addCifAtom, addHeader, applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassSymmetry, fullTrim, getBondOrder, getFieldString, initializeReader, isLoopKey, isNull, newModel, nextAtomSet, processAtomTypeLoopBlock, processCellParameter, processCitationListBlock, processLoopBlock, processUnitCellTransformMatrix, skipLoop, skipLoopKeyword
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setupASCR
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Field Details
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temp
protected static int[] temp
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Constructor Details
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BCIFReader
public BCIFReader()
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Method Details
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getCifDataParser
- Overrides:
getCifDataParser
in classCifReader
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setup
binary must set up initially- Overrides:
setup
in classAtomSetCollectionReader
- Parameters:
fullPath
-htParams
-reader
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processBinaryDocument
The primare method initiating this reader- Overrides:
processBinaryDocument
in classAtomSetCollectionReader
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classCifReader
- Throws:
Exception
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parseLoopParameters
This is the callback the that the MMCifReader and CifReader process.....() methods call initially. Pass this on to our psuedo-parser.- Overrides:
parseLoopParameters
in classCifReader
- Throws:
Exception
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isFieldValid
protected boolean isFieldValid()- Overrides:
isFieldValid
in classCifReader
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parseIntField
protected int parseIntField()- Overrides:
parseIntField
in classCifReader
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parseFloatField
protected float parseFloatField()- Overrides:
parseFloatField
in classCifReader
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parseCartesianField
protected float parseCartesianField()- Overrides:
parseCartesianField
in classCifReader
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parseIntFieldTok
protected int parseIntFieldTok(byte tok) Get a specific column's item for this category on this row. In contrast to MMCifReader, we already have the integer; we don't have to parse it.- Overrides:
parseIntFieldTok
in classMMCifReader
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getFloatColumnData
protected float getFloatColumnData(int i) Called by processAtomSites to retrieve individual matrix elements and set them by name.- Overrides:
getFloatColumnData
in classCifReader
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