Package org.jmol.adapter.readers.cif
Class MMTFReader
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.MMTFReader
- All Implemented Interfaces:
GenericLineReader
JmolData RCSB MMTF (macromolecular transmission format) file reader
see https://github.com/rcsb/mmtf/blob/master/spec.md
Note added 2024.01.19
Jose Duarte 2:03 PM (email)
to MMTF-Users From July 2024 the PDB file archive will not be offered in the
compressed MMTF format anymore. Users are strongly encouraged to switch to
the BinaryCIF format, which has been available since 2020. Details on how to
access BinaryCIF (BCIF) data files for the entire PDB archive are available
here.
RCSB PDB support is ready to assist with any issues or questions at
info@rcsb.org.
full specification Version: v0.2+dev (as of 2016.08.08) is
implemented,including:
reading atoms, bonds, and DSSP 1.0 secondary structure
load =1f88.mmtf filter "DSSP1"
[Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0
calculations, while the standard for Jmol itself is DSSP 2.0. These two
calculations differ in their treating of helix kinks as one (1.0) or two
(2.0) helices.]
reading space groups and unit cells, and using those as per other readers
load =1crn.mmtf {1 1 1}
reading bioassemblies (biomolecules) and applying all symmetry
transformations
load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P"
reading both biomolecules and lattices, and loading course-grained using the
filter "BYCHAIN" or "BYSYMOP"
load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0; color
property symop
Many thanks to the MMTF team at RCSB for assistance in this implementation.
- Author:
- Bob Hanson hansonr@stolaf.edu
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Field Summary
Fields 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, 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
void
We must add groups to the proper bsStructure elementvoid
protected void
protected void
standard set upMethods inherited from class org.jmol.adapter.readers.cif.MMCifReader
addAssembly, addHetero, addMatrix, checkFilterAssembly, checkPDBModelField, checkSubclassSymmetry, finalizeSubclass, incrementModel, initSubclass, parseIntFieldTok, processAssemblyGenBlock, processChemCompLoopBlock, processCompBondLoopBlock, processSequence, processStructConfLoopBlock, processStructConnLoopBlock, processStructOperListBlock, processStructSheetRangeLoopBlock, processStructSiteBlock, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, sortAssemblyModels
Methods inherited from class org.jmol.adapter.readers.cif.CifReader
addCifAtom, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, fullTrim, getBondOrder, getCifDataParser, getFieldString, getFloatColumnData, initializeReader, isFieldValid, isLoopKey, isNull, newModel, nextAtomSet, parseCartesianField, parseFloatField, parseIntField, parseLoopParameters, 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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Constructor Details
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MMTFReader
public MMTFReader()
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Method Details
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addHeader
protected void addHeader() -
setup
standard set up- Overrides:
setup
in classAtomSetCollectionReader
- Parameters:
fullPath
-htParams
-reader
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processBinaryDocument
- Overrides:
processBinaryDocument
in classAtomSetCollectionReader
- Throws:
Exception
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applySymmetryAndSetTrajectory
- Overrides:
applySymmetryAndSetTrajectory
in classCifReader
- Throws:
Exception
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addStructureSymmetry
public void addStructureSymmetry()We must add groups to the proper bsStructure element
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