Class SimpleMMcifConsumer

  • All Implemented Interfaces:
    MMcifConsumer

    public class SimpleMMcifConsumer
    extends java.lang.Object
    implements MMcifConsumer
    A MMcifConsumer implementation that build a in-memory representation of the content of a mmcif file as a BioJava Structure object.
    Since:
    1.7
    Author:
    Andreas Prlic
    • Field Detail

      • logger

        public static java.util.logging.Logger logger
    • Constructor Detail

      • SimpleMMcifConsumer

        public SimpleMMcifConsumer()
    • Method Detail

      • isParseCAOnly

        public boolean isParseCAOnly()
      • setParseCAOnly

        public void setParseCAOnly​(boolean parseCAOnly)
      • isAlignSeqRes

        public boolean isAlignSeqRes()
        Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
        Returns:
        flag if SEQRES - ATOM amino acids alignment is enabled
      • setAlignSeqRes

        public void setAlignSeqRes​(boolean alignSeqRes)
        define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
        Parameters:
        alignSeqRes -
      • getStructure

        public Structure getStructure()
        This method will return the parsed protein structure, once the parsing has been finished
        Returns:
        a BioJava protein structure object
      • 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
      • 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
      • newGenericData

        public void newGenericData​(java.lang.String category,
                                   java.util.List<java.lang.String> loopFields,
                                   java.util.List<java.lang.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.