Package org.rcsb.cif.model.generated

Class PdbxEntitySrcGenDepositorInfo

  • All Implemented Interfaces:
    Category
    @Generated("org.rcsb.cif.generator.SchemaGenerator")
public class PdbxEntitySrcGenDepositorInfo
extends BaseCategory
    Data items in the PDBX_ENTITY_SRC_GEN_DEPOSITOR_INFO 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).

    • Constructor Detail

      • PdbxEntitySrcGenDepositorInfo

        public PdbxEntitySrcGenDepositorInfo​(String name,
                                     Map<String,​Column> columns)

      • PdbxEntitySrcGenDepositorInfo

        public PdbxEntitySrcGenDepositorInfo​(String name,
                                     int rowCount,
                                     Object[] encodedColumns)

      • PdbxEntitySrcGenDepositorInfo

        public PdbxEntitySrcGenDepositorInfo​(String name)

    • Method Detail

      • getSrcId

        public IntColumn getSrcId()
        This data item is an ordinal identifier for entity_src_gen data records.
        Returns:
        IntColumn

      • getEntityId

        public StrColumn getEntityId()
        The entity id for this chimeric entity. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
        Returns:
        StrColumn

      • getSeqType

        public StrColumn getSeqType()
        This data item povides additional information about the sequence type.
        Returns:
        StrColumn

      • getBegSeqNum

        public IntColumn getBegSeqNum()
        The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category.
        Returns:
        IntColumn

      • getEndSeqNum

        public IntColumn getEndSeqNum()
        The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category.
        Returns:
        IntColumn

      • getGeneSrcGene

        public StrColumn getGeneSrcGene()
        Identifies the gene.
        Returns:
        StrColumn

      • getGeneSrcScientificName

        public StrColumn getGeneSrcScientificName()
        Scientific name of the organism.
        Returns:
        StrColumn

      • getHostOrgGene

        public StrColumn getHostOrgGene()
        Specific gene which expressed the molecule.
        Returns:
        StrColumn

      • getHostOrgScientificName

        public StrColumn getHostOrgScientificName()
        The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_scientific_name or via _entity_src_gen_express.host_org_tax_id
        Returns:
        StrColumn

      • getHostOrgStrain

        public StrColumn getHostOrgStrain()
        The strain of the organism in which the entity was expressed.
        Returns:
        StrColumn

      • getGeneSrcNcbiTaxonomyId

        public IntColumn getGeneSrcNcbiTaxonomyId()
        NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
        Returns:
        IntColumn

      • getHostOrgNcbiTaxonomyId

        public IntColumn getHostOrgNcbiTaxonomyId()
        NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
        Returns:
        IntColumn

      • getHostOrgVectorType

        public StrColumn getHostOrgVectorType()
        Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.vector_type.
        Returns:
        StrColumn

      • getPlasmidName

        public StrColumn getPlasmidName()
        The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from _pdbx_construct.name of the construct pointed to from _entity_src_gen_express.plasmid_id.
        Returns:
        StrColumn