Package org.rcsb.cif.schema.mm

Class EntitySrcGen

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.EntitySrcGen
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class EntitySrcGen
extends DelegatingCategory
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).

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • getEntityId

      public StrColumn getEntityId()
      This data item is a pointer to _entity.id in the ENTITY category.
      Returns:
      StrColumn

    • getGeneSrcCommonName

      public StrColumn getGeneSrcCommonName()
      The common name of the natural organism from which the gene was obtained.
      Returns:
      StrColumn

    • getGeneSrcDetails

      public StrColumn getGeneSrcDetails()
      A description of special aspects of the natural organism from which the gene was obtained.
      Returns:
      StrColumn

    • getGeneSrcGenus

      public StrColumn getGeneSrcGenus()
      The genus of the natural organism from which the gene was obtained.
      Returns:
      StrColumn

    • getGeneSrcSpecies

      public StrColumn getGeneSrcSpecies()
      The species of the natural organism from which the gene was obtained.
      Returns:
      StrColumn

    • getGeneSrcStrain

      public StrColumn getGeneSrcStrain()
      The strain of the natural organism from which the gene was obtained, if relevant.
      Returns:
      StrColumn

    • getGeneSrcTissue

      public StrColumn getGeneSrcTissue()
      The tissue of the natural organism from which the gene was obtained.
      Returns:
      StrColumn

    • getGeneSrcTissueFraction

      public StrColumn getGeneSrcTissueFraction()
      The subcellular fraction of the tissue of the natural organism from which the gene was obtained.
      Returns:
      StrColumn

    • getHostOrgGenus

      public StrColumn getHostOrgGenus()
      The genus of the organism that served as host for the production of the entity.
      Returns:
      StrColumn

    • getHostOrgSpecies

      public StrColumn getHostOrgSpecies()
      The species of the organism that served as host for the production of the entity.
      Returns:
      StrColumn

    • getPdbxGeneSrcFragment

      public StrColumn getPdbxGeneSrcFragment()
      A domain or fragment of the molecule.
      Returns:
      StrColumn

    • getPdbxGeneSrcGene

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

    • getPdbxGeneSrcScientificName

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

    • getPdbxGeneSrcVariant

      public StrColumn getPdbxGeneSrcVariant()
      Identifies the variant.
      Returns:
      StrColumn

    • getPdbxGeneSrcCellLine

      public StrColumn getPdbxGeneSrcCellLine()
      The specific line of cells.
      Returns:
      StrColumn

    • getPdbxGeneSrcAtcc

      public StrColumn getPdbxGeneSrcAtcc()
      American Type Culture Collection tissue culture number.
      Returns:
      StrColumn

    • getPdbxGeneSrcOrgan

      public StrColumn getPdbxGeneSrcOrgan()
      Organized group of tissues that carries on a specialized function.
      Returns:
      StrColumn

    • getPdbxGeneSrcOrganelle

      public StrColumn getPdbxGeneSrcOrganelle()
      Organized structure within cell.
      Returns:
      StrColumn

    • getPdbxGeneSrcPlasmid

      public StrColumn getPdbxGeneSrcPlasmid()
      The source plasmid.
      Returns:
      StrColumn

    • getPdbxGeneSrcPlasmidName

      public StrColumn getPdbxGeneSrcPlasmidName()
      The source plasmid.
      Returns:
      StrColumn

    • getPdbxGeneSrcCell

      public StrColumn getPdbxGeneSrcCell()
      Cell type.
      Returns:
      StrColumn

    • getPdbxGeneSrcCellularLocation

      public StrColumn getPdbxGeneSrcCellularLocation()
      Identifies the location inside (or outside) the cell.
      Returns:
      StrColumn

    • getPdbxHostOrgGene

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

    • getPdbxHostOrgOrgan

      public StrColumn getPdbxHostOrgOrgan()
      Specific organ which expressed the molecule.
      Returns:
      StrColumn

    • getPdbxHostOrgOrganelle

      public StrColumn getPdbxHostOrgOrganelle()
      Specific organelle which expressed the molecule.
      Returns:
      StrColumn

    • getPdbxHostOrgCellularLocation

      public StrColumn getPdbxHostOrgCellularLocation()
      Identifies the location inside (or outside) the cell which expressed the molecule.
      Returns:
      StrColumn

    • getPdbxHostOrgStrain

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

    • getPdbxHostOrgTissueFraction

      public StrColumn getPdbxHostOrgTissueFraction()
      The fraction of the tissue which expressed the molecule.
      Returns:
      StrColumn

    • getPdbxDescription

      public StrColumn getPdbxDescription()
      Information on the source which is not given elsewhere.
      Returns:
      StrColumn

    • getHostOrgCommonName

      public StrColumn getHostOrgCommonName()
      The common 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 be derived from _entity_src_gen_express.host_org_common_name or via _entity_src_gen_express.host_org_tax_id
      Returns:
      StrColumn

    • getHostOrgDetails

      public StrColumn getHostOrgDetails()
      A description of special aspects 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 derived from _entity_src_gen_express.host_org_details
      Returns:
      StrColumn

    • getHostOrgStrain

      public StrColumn getHostOrgStrain()
      The strain of the organism in which the entity was expressed. Where full details of the protein production are available it would be expected that this item be derived from _entity_src_gen_express.host_org_strain or via _entity_src_gen_express.host_org_tax_id
      Returns:
      StrColumn

    • getPlasmidDetails

      public StrColumn getPlasmidDetails()
      A description of special aspects 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.details of the construct pointed to from _entity_src_gen_express.plasmid_id.
      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

    • getPdbxHostOrgVariant

      public StrColumn getPdbxHostOrgVariant()
      Variant of the organism used as the expression system. Where full details of the protein production are available it would be expected that this item be derived from entity_src_gen_express.host_org_variant or via _entity_src_gen_express.host_org_tax_id
      Returns:
      StrColumn

    • getPdbxHostOrgCellLine

      public StrColumn getPdbxHostOrgCellLine()
      A specific line of cells used as the expression system. 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_cell_line
      Returns:
      StrColumn

    • getPdbxHostOrgAtcc

      public StrColumn getPdbxHostOrgAtcc()
      Americal Tissue Culture Collection of the expression system. 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_culture_collection
      Returns:
      StrColumn

    • getPdbxHostOrgCultureCollection

      public StrColumn getPdbxHostOrgCultureCollection()
      Culture collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived somehwere, but exactly where is not clear.
      Returns:
      StrColumn

    • getPdbxHostOrgCell

      public StrColumn getPdbxHostOrgCell()
      Cell type from which the gene is derived. Where entity.target_id is provided this should be derived from details of the target.
      Returns:
      StrColumn

    • getPdbxHostOrgScientificName

      public StrColumn getPdbxHostOrgScientificName()
      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

    • getPdbxHostOrgTissue

      public StrColumn getPdbxHostOrgTissue()
      The specific tissue which expressed the molecule. 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_tissue
      Returns:
      StrColumn

    • getPdbxHostOrgVector

      public StrColumn getPdbxHostOrgVector()
      Identifies the vector used. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_clone.vector_name.
      Returns:
      StrColumn

    • getPdbxHostOrgVectorType

      public StrColumn getPdbxHostOrgVectorType()
      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

    • getExpressionSystemId

      public StrColumn getExpressionSystemId()
      A unique identifier for the expression system. This should be extracted from a local list of expression systems.
      Returns:
      StrColumn

    • getGeneSrcDevStage

      public StrColumn getGeneSrcDevStage()
      A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active.
      Returns:
      StrColumn

    • getStartConstructId

      public StrColumn getStartConstructId()
      A pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct.
      Returns:
      StrColumn

    • getPdbxGeneSrcNcbiTaxonomyId

      public StrColumn getPdbxGeneSrcNcbiTaxonomyId()
      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:
      StrColumn

    • getPdbxHostOrgNcbiTaxonomyId

      public StrColumn getPdbxHostOrgNcbiTaxonomyId()
      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:
      StrColumn

    • getPdbxSrcId

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

    • getPdbxAltSourceFlag

      public StrColumn getPdbxAltSourceFlag()
      This data item identifies cases in which an alternative source modeled.
      Returns:
      StrColumn

    • getPdbxSeqType

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

    • getPdbxBegSeqNum

      public IntColumn getPdbxBegSeqNum()
      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

    • getPdbxEndSeqNum

      public IntColumn getPdbxEndSeqNum()
      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

    • getPdbxGeneSrcCultureCollection

      public StrColumn getPdbxGeneSrcCultureCollection()
      Culture collection identifier.
      Returns:
      StrColumn