Class SimpleMMcifConsumer

Method Details

• newEntity

  public void newEntity(Entity entity)

  Specified by:

  newEntity in interface MMcifConsumer

• newPdbxStructOperList

  public void newPdbxStructOperList(PdbxStructOperList structOper)

  Specified by:

  newPdbxStructOperList in interface MMcifConsumer

• newStructAsym

  public void newStructAsym(StructAsym sasym)

  Specified by:

  newStructAsym in interface MMcifConsumer

• newStructKeywords

  public void newStructKeywords(StructKeywords kw)

  Specified by:

  newStructKeywords in interface MMcifConsumer

• setStruct

  public void setStruct(Struct struct)

  Specified by:

  setStruct in interface MMcifConsumer

• newAtomSite

  public void newAtomSite(AtomSite atom)

  Description copied from interface: MMcifConsumer

  A new AtomSite record has been read. Contains the Atom data

  Specified by:

  newAtomSite in interface MMcifConsumer

• documentStart

  public void documentStart()

  Start the parsing

  Specified by:

  documentStart in interface MMcifConsumer

• documentEnd

  public void documentEnd()

  Description copied from interface: MMcifConsumer

  called at end of document

  Specified by:

  documentEnd in interface MMcifConsumer

• getStructure

  public Structure getStructure()

  This method will return the parsed protein structure, once the parsing has been finished

  Returns:

  a BioJava protein structure object

• newDatabasePDBrevRecord

  public void newDatabasePDBrevRecord(DatabasePdbrevRecord record)

  Specified by:

  newDatabasePDBrevRecord in interface MMcifConsumer

• newDatabasePDBrev

  public void newDatabasePDBrev(DatabasePDBrev dbrev)

  Specified by:

  newDatabasePDBrev in interface MMcifConsumer

• newDatabasePDBremark

  public void newDatabasePDBremark(DatabasePDBremark remark)

  Specified by:

  newDatabasePDBremark in interface MMcifConsumer

• newRefine

  public void newRefine(Refine r)

  Specified by:

  newRefine in interface MMcifConsumer

• newAuditAuthor

  public void newAuditAuthor(AuditAuthor aa)

  Description copied from interface: MMcifConsumer

  AuditAuthor contains the info from the PDB-AUTHOR records.

  Specified by:

  newAuditAuthor in interface MMcifConsumer

• newExptl

  public void newExptl(Exptl exptl)

  Specified by:

  newExptl in interface MMcifConsumer

• newCell

  public void newCell(Cell cell)

  Specified by:

  newCell in interface MMcifConsumer

• newSymmetry

  public void newSymmetry(Symmetry symmetry)

  Specified by:

  newSymmetry in interface MMcifConsumer

• newStructNcsOper

  public void newStructNcsOper(StructNcsOper sNcsOper)

  Specified by:

  newStructNcsOper in interface MMcifConsumer

• newAtomSites

  public void newAtomSites(AtomSites atomSites)

  Specified by:

  newAtomSites in interface MMcifConsumer

• newStructRef

  public void newStructRef(StructRef sref)

  Specified by:

  newStructRef in interface MMcifConsumer

• newStructRefSeq

  public void newStructRefSeq(StructRefSeq sref)

  create a DBRef record from the StrucRefSeq record:

   PDB record                    DBREF
   Field Name                    mmCIF Data Item
   Section                       n.a.
   PDB_ID_Code                   _struct_ref_seq.pdbx_PDB_id_code
   Strand_ID                     _struct_ref_seq.pdbx_strand_id
   Begin_Residue_Number          _struct_ref_seq.pdbx_auth_seq_align_beg
   Begin_Ins_Code                _struct_ref_seq.pdbx_seq_align_beg_ins_code
   End_Residue_Number            _struct_ref_seq.pdbx_auth_seq_align_end
   End_Ins_Code                  _struct_ref_seq.pdbx_seq_align_end_ins_code
   Database                      _struct_ref.db_name
   Database_Accession_No         _struct_ref_seq.pdbx_db_accession
   Database_ID_Code              _struct_ref.db_code
   Database_Begin_Residue_Number _struct_ref_seq.db_align_beg
   Databaes_Begin_Ins_Code       _struct_ref_seq.pdbx_db_align_beg_ins_code
   Database_End_Residue_Number   _struct_ref_seq.db_align_end
   Databaes_End_Ins_Code         _struct_ref_seq.pdbx_db_align_end_ins_code
   

  Specified by:

  newStructRefSeq in interface MMcifConsumer

• newStructRefSeqDif

  public void newStructRefSeqDif(StructRefSeqDif sref)

  Specified by:

  newStructRefSeqDif in interface MMcifConsumer

• newEntitySrcGen

  public void newEntitySrcGen(EntitySrcGen entitySrcGen)

  Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).

  Specified by:

  newEntitySrcGen in interface MMcifConsumer

• newEntitySrcNat

  public void newEntitySrcNat(EntitySrcNat entitySrcNat)

  Specified by:

  newEntitySrcNat in interface MMcifConsumer

• newEntitySrcSyn

  public void newEntitySrcSyn(EntitySrcSyn entitySrcSyn)

  Specified by:

  newEntitySrcSyn in interface MMcifConsumer

• newEntityPolySeq

  public void newEntityPolySeq(EntityPolySeq epolseq)

  The EntityPolySeq object provide the amino acid sequence objects for the Entities. Later on the entities are mapped to the BioJava Chain and Compound objects.

  Specified by:

  newEntityPolySeq in interface MMcifConsumer

  Parameters:

  epolseq - the EntityPolySeq record for one amino acid

• newPdbxPolySeqScheme

  public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)

  Specified by:

  newPdbxPolySeqScheme in interface MMcifConsumer

• newPdbxNonPolyScheme

  public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)

  Specified by:

  newPdbxNonPolyScheme in interface MMcifConsumer

• newPdbxEntityNonPoly

  public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)

  Specified by:

  newPdbxEntityNonPoly in interface MMcifConsumer

• newChemComp

  public void newChemComp(ChemComp c)

  Specified by:

  newChemComp in interface MMcifConsumer

• newGenericData

  public void newGenericData(String category, List<String> loopFields, List<String> lineData)

  Description copied from interface: MMcifConsumer

  This method is called if no particular handler for the provided cif category has been implemented so far.

  Specified by:

  newGenericData in interface MMcifConsumer

  Parameters:

  category - The category that is being processed.

  loopFields - the fields of this category.

  lineData - the data that is being provided.

• getFileParsingParameters

  public FileParsingParameters getFileParsingParameters()

  Specified by:

  getFileParsingParameters in interface MMcifConsumer

• setFileParsingParameters

  public void setFileParsingParameters(FileParsingParameters params)

  Specified by:

  setFileParsingParameters in interface MMcifConsumer

• newChemCompDescriptor

  public void newChemCompDescriptor(ChemCompDescriptor ccd)

  Specified by:

  newChemCompDescriptor in interface MMcifConsumer

• getStructOpers

  public List<PdbxStructOperList> getStructOpers()

• newPdbxStrucAssembly

  public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)

  Specified by:

  newPdbxStrucAssembly in interface MMcifConsumer

• getStructAssemblies

  public List<PdbxStructAssembly> getStructAssemblies()

• newPdbxStrucAssemblyGen

  public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)

  Specified by:

  newPdbxStrucAssemblyGen in interface MMcifConsumer

• getStructAssemblyGens

  public List<PdbxStructAssemblyGen> getStructAssemblyGens()

• newChemCompAtom

  public void newChemCompAtom(ChemCompAtom atom)

  Specified by:

  newChemCompAtom in interface MMcifConsumer

• newPdbxChemCompIndentifier

  public void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)

  Specified by:

  newPdbxChemCompIndentifier in interface MMcifConsumer

• newChemCompBond

  public void newChemCompBond(ChemCompBond bond)

  Specified by:

  newChemCompBond in interface MMcifConsumer

• newPdbxChemCompDescriptor

  public void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)

  Specified by:

  newPdbxChemCompDescriptor in interface MMcifConsumer

• newStructConn

  public void newStructConn(StructConn structConn)

  Specified by:

  newStructConn in interface MMcifConsumer

• newStructSiteGen

  public void newStructSiteGen(StructSiteGen siteGen)

  Specified by:

  newStructSiteGen in interface MMcifConsumer

• newStructSite

  public void newStructSite(StructSite structSite)

  Specified by:

  newStructSite in interface MMcifConsumer