Package org.rcsb.cif.schema.mm

Class StructRefSeq

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.StructRefSeq
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class StructRefSeq
extends DelegatingCategory
Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getAlignId

      public StrColumn getAlignId()
      The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier.
      Returns:
      StrColumn

    • getDbAlignBeg

      public IntColumn getDbAlignBeg()
      The sequence position in the referenced database entry at which the alignment begins.
      Returns:
      IntColumn

    • getDbAlignEnd

      public IntColumn getDbAlignEnd()
      The sequence position in the referenced database entry at which the alignment ends.
      Returns:
      IntColumn

    • getDetails

      public StrColumn getDetails()
      A description of special aspects of the sequence alignment.
      Returns:
      StrColumn

    • getRefId

      public StrColumn getRefId()
      This data item is a pointer to _struct_ref.id in the STRUCT_REF category.
      Returns:
      StrColumn

    • getSeqAlignBeg

      public IntColumn getSeqAlignBeg()
      The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
      Returns:
      IntColumn

    • getSeqAlignEnd

      public IntColumn getSeqAlignEnd()
      The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
      Returns:
      IntColumn

    • getPdbxStrandId

      public StrColumn getPdbxStrandId()
      The PDB strand/chain ID .
      Returns:
      StrColumn

    • getPdbxDbAccession

      public StrColumn getPdbxDbAccession()
      Accession code of the reference database.
      Returns:
      StrColumn

    • getPdbxDbAlignBegInsCode

      public StrColumn getPdbxDbAlignBegInsCode()
      Initial insertion code of the sequence segment of the reference database.
      Returns:
      StrColumn

    • getPdbxDbAlignEndInsCode

      public StrColumn getPdbxDbAlignEndInsCode()
      Ending insertion code of the sequence segment of the reference database.
      Returns:
      StrColumn

    • getPdbxPDBIdCode

      public StrColumn getPdbxPDBIdCode()
      The PDB code of the structure.
      Returns:
      StrColumn

    • getPdbxAuthSeqAlignBeg

      public StrColumn getPdbxAuthSeqAlignBeg()
      Initial position in the PDB sequence segment.
      Returns:
      StrColumn

    • getPdbxAuthSeqAlignEnd

      public StrColumn getPdbxAuthSeqAlignEnd()
      Ending position in the PDB sequence segment
      Returns:
      StrColumn

    • getPdbxSeqAlignBegInsCode

      public StrColumn getPdbxSeqAlignBegInsCode()
      Initial insertion code of the PDB sequence segment.
      Returns:
      StrColumn

    • getPdbxSeqAlignEndInsCode

      public StrColumn getPdbxSeqAlignEndInsCode()
      Ending insertion code of the sequence segment
      Returns:
      StrColumn