org.jmol.adapter.readers.cif.MMCifReader

All Implemented Interfaces:: GenericLineReader

Direct Known Subclasses:: BCIFReader, MMTFReader

public class MMCifReader extends CifReader

mmCIF files are recognized prior to class creation. Required fields include one of: _entry.id _database_PDB_ _pdbx_ _chem_comp.pdbx_type _audit_author.name _atom_site.

Author:: Bob Hanson (hansonr@stolaf.edu)

Field Summary

Fields

Modifier and Type

Field

Description

protected static final String

CAT_ASSEM

protected static final String

CAT_CHEMCOMP

protected static final String

CAT_COMPBOND

protected static final String

CAT_NCS

protected static final String

CAT_OPER

protected static final String

CAT_SEQUENCEDIF

protected static final String

CAT_SHEET

protected static final String

CAT_STRUCSITE

protected static final String

CAT_STRUCTCONF

protected static final String

CAT_STRUCTCONN

protected boolean

done

protected Map<String,String>

htHetero

protected Map<String, Map<String,Object>>

htSites

protected boolean

isBiomolecule

protected Lst<Map<String,Object>>

vBiomolecules

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, useAuthorChainID

Fields 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

Constructor

Description

MMCifReader()
Method Summary

Modifier and Type

Method

Description

protected void

addAssembly(String[] assem)

protected void

addHetero(String groupName, String hetName, String groupType, boolean doCheck, boolean addNote)

protected void

addMatrix(String id, M4 m4, boolean isNCS)

protected void

checkFilterAssembly(String id, Map<String,Object> info)

protected int

checkPDBModelField(int modelField, int currentModelNo)

protected boolean

checkSubclassSymmetry()

/////////////////////////////////////////////////////////////

protected boolean

finalizeSubclass()

protected int

incrementModel(int modelNo)

protected void

initSubclass()

protected int

parseIntFieldTok(byte tok)

protected boolean

processAssemblyGenBlock()

protected boolean

processChemCompLoopBlock()

a general name definition field.

protected boolean

processCompBondLoopBlock()

protected boolean

processSequence()

get canonical 1-letter DNA/RNA sequence code from 3-letter code.

protected boolean

processStructConfLoopBlock()

identifies ranges for HELIX and TURN

protected boolean

processStructConnLoopBlock()

protected boolean

processStructOperListBlock(boolean isNCS)

protected boolean

processStructSheetRangeLoopBlock()

identifies sheet ranges

protected boolean

processStructSiteBlock()

identifies structure sites

boolean

processSubclassAtom(Atom atom, String assemblyId, String strChain)

protected void

processSubclassEntry()

protected boolean

processSubclassLoopBlock()

protected void

sortAssemblyModels()

issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...

Methods inherited from class CifReader
addCifAtom, addHeader, applySymmetryAndSetTrajectory, 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, setSymmetryOperator, skipLoop, skipLoopKeyword

Methods 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

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- isBiomolecule
  
  protected boolean isBiomolecule
- vBiomolecules
  
  protected Lst<Map<String,Object>> vBiomolecules
- htSites
  
  protected Map<String, Map<String,Object>> htSites
- htHetero
  
  protected Map<String,String> htHetero
- CAT_NCS
  protected static final String CAT_NCS
  
  See Also:
  
  Constant Field Values
- CAT_OPER
  protected static final String CAT_OPER
  
  See Also:
  
  Constant Field Values
- CAT_ASSEM
  protected static final String CAT_ASSEM
  
  See Also:
  
  Constant Field Values
- CAT_SEQUENCEDIF
  protected static final String CAT_SEQUENCEDIF
  
  See Also:
  
  Constant Field Values
- CAT_CHEMCOMP
  protected static final String CAT_CHEMCOMP
  
  See Also:
  
  Constant Field Values
- CAT_STRUCTCONF
  protected static final String CAT_STRUCTCONF
  
  See Also:
  
  Constant Field Values
- CAT_SHEET
  protected static final String CAT_SHEET
  
  See Also:
  
  Constant Field Values
- CAT_STRUCSITE
  protected static final String CAT_STRUCSITE
  
  See Also:
  
  Constant Field Values
- CAT_STRUCTCONN
  protected static final String CAT_STRUCTCONN
  
  See Also:
  
  Constant Field Values
- CAT_COMPBOND
  protected static final String CAT_COMPBOND
  
  See Also:
  
  Constant Field Values
- done
  
  protected boolean done
Constructor Details
- MMCifReader
  
  public MMCifReader()
Method Details
- initSubclass
  
  protected void initSubclass()
  
  Overrides:
  
  initSubclass in class CifReader
- processSubclassEntry
  
  protected void processSubclassEntry() throws Exception
  
  Overrides:
  
  processSubclassEntry in class CifReader
  
  Throws:
  
  Exception
- processSubclassLoopBlock
  
  protected boolean processSubclassLoopBlock() throws Exception
  
  Overrides:
  
  processSubclassLoopBlock in class CifReader
  
  Throws:
  
  Exception
- sortAssemblyModels
  
  protected void sortAssemblyModels()
  
  issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ... and so assigned to too many atom sets.
- finalizeSubclass
  
  protected boolean finalizeSubclass() throws Exception
  
  Overrides:
  
  finalizeSubclass in class CifReader
  
  Throws:
  
  Exception
- checkSubclassSymmetry
  
  protected boolean checkSubclassSymmetry()
  
  /////////////////////////////////////////////////////////////
  
  Overrides:
  
  checkSubclassSymmetry in class CifReader
- processSequence
  
  protected boolean processSequence() throws Exception
  
  get canonical 1-letter DNA/RNA sequence code from 3-letter code. For example, "2MG" --> "G"
  
  Returns:
  
  true
  
  Throws:
  
  Exception
- processAssemblyGenBlock
  
  protected boolean processAssemblyGenBlock() throws Exception
  
  Throws:
  
  Exception
- addAssembly
  
  protected void addAssembly(String[] assem) throws Exception
  
  Throws:
  
  Exception
- checkFilterAssembly
  
  protected void checkFilterAssembly(String id, Map<String,Object> info)
- processStructOperListBlock
  
  protected boolean processStructOperListBlock(boolean isNCS) throws Exception
  
  Throws:
  
  Exception
- addMatrix
  
  protected void addMatrix(String id, M4 m4, boolean isNCS)
- processChemCompLoopBlock
  
  protected boolean processChemCompLoopBlock() throws Exception
  
  a general name definition field. Not all hetero
  
  Returns:
  
  true if successful; false to skip
  
  Throws:
  
  Exception
- addHetero
  
  protected void addHetero(String groupName, String hetName, String groupType, boolean doCheck, boolean addNote)
- processStructConfLoopBlock
  
  protected boolean processStructConfLoopBlock() throws Exception
  
  identifies ranges for HELIX and TURN
  
  Returns:
  
  true if successful; false to skip
  
  Throws:
  
  Exception
- parseIntFieldTok
  
  protected int parseIntFieldTok(byte tok)
- processStructSheetRangeLoopBlock
  
  protected boolean processStructSheetRangeLoopBlock() throws Exception
  
  identifies sheet ranges
  
  Returns:
  
  true if successful; false to skip
  
  Throws:
  
  Exception
- processStructSiteBlock
  
  protected boolean processStructSiteBlock() throws Exception
  
  identifies structure sites
  
  Returns:
  
  true if successful; false to skip
  
  Throws:
  
  Exception
- processStructConnLoopBlock
  
  protected boolean processStructConnLoopBlock() throws Exception
  
  Throws:
  
  Exception
- processCompBondLoopBlock
  
  protected boolean processCompBondLoopBlock() throws Exception
  
  Throws:
  
  Exception
- processSubclassAtom
  
  public boolean processSubclassAtom(Atom atom, String assemblyId, String strChain)
  
  Overrides:
  
  processSubclassAtom in class CifReader
  
  Parameters:
  
  atom -
  
  assemblyId -
  
  strChain -
  
  Returns:
  
  true if valid atom
- checkPDBModelField
  
  protected int checkPDBModelField(int modelField, int currentModelNo) throws Exception
  
  Overrides:
  
  checkPDBModelField in class CifReader
  
  Parameters:
  
  modelField -
  
  currentModelNo -
  
  Returns:
  
  new currentModelNo
  
  Throws:
  
  Exception
- incrementModel
  
  protected int incrementModel(int modelNo) throws Exception
  
  Throws:
  
  Exception

Class MMCifReader

Field Summary

Fields inherited from class CifReader

Fields inherited from class AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class CifReader

Methods inherited from class AtomSetCollectionReader

Methods inherited from class Object

Field Details

isBiomolecule

vBiomolecules

htSites

htHetero

CAT_NCS

CAT_OPER

CAT_ASSEM

CAT_SEQUENCEDIF

CAT_CHEMCOMP

CAT_STRUCTCONF

CAT_SHEET

CAT_STRUCSITE

CAT_STRUCTCONN

CAT_COMPBOND

done

Constructor Details

MMCifReader

Method Details

initSubclass

processSubclassEntry

processSubclassLoopBlock

sortAssemblyModels

finalizeSubclass

checkSubclassSymmetry

processSequence

processAssemblyGenBlock

addAssembly

checkFilterAssembly

processStructOperListBlock

addMatrix

processChemCompLoopBlock

addHetero

processStructConfLoopBlock

parseIntFieldTok

processStructSheetRangeLoopBlock

processStructSiteBlock

processStructConnLoopBlock

processCompBondLoopBlock

processSubclassAtom

checkPDBModelField

incrementModel