Package org.rcsb.cif.schema.mm

Class StructRef

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.StructRef
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class StructRef
extends DelegatingCategory
Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getBiolId

      public StrColumn getBiolId()
      This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category.
      Returns:
      StrColumn

    • getDbCode

      public StrColumn getDbCode()
      The code for this entity or biological unit or for a closely related entity or biological unit in the named database.
      Returns:
      StrColumn

    • getDbName

      public StrColumn getDbName()
      The name of the database containing reference information about this entity or biological unit.
      Returns:
      StrColumn

    • getDetails

      public StrColumn getDetails()
      A description of special aspects of the relationship between the entity or biological unit described in the data block and that in the referenced database entry.
      Returns:
      StrColumn

    • getEntityId

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

    • getId

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

    • getSeqAlign

      public StrColumn getSeqAlign()
      A flag to indicate the scope of the alignment between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. 'entire' indicates that alignment spans the entire length of both sequences (although point differences may occur and can be annotated using the data items in the STRUCT_REF_SEQ_DIF category). 'partial' indicates a partial alignment. The region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. This data item may also take the value '.', indicating that the reference is not to a sequence.
      Returns:
      StrColumn

    • getSeqDif

      public StrColumn getSeqDif()
      A flag to indicate the presence ('yes') or absence ('no') of point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item may also take the value '.', indicating that the reference is not to a sequence.
      Returns:
      StrColumn

    • getPdbxDbAccession

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

    • getPdbxDbIsoform

      public StrColumn getPdbxDbIsoform()
      Database code assigned by the reference database for a sequence isoform. An isoform sequence is an alternative protein sequence that can be generated from the same gene by a single or by a combination of biological events such as: alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting.
      Returns:
      StrColumn

    • getPdbxSeqOneLetterCode

      public StrColumn getPdbxSeqOneLetterCode()
      Database chemical sequence expressed as string of one-letter amino acid codes.
      Returns:
      StrColumn

    • getPdbxAlignBegin

      public StrColumn getPdbxAlignBegin()
      Beginning index in the chemical sequence from the reference database.
      Returns:
      StrColumn

    • getPdbxAlignEnd

      public StrColumn getPdbxAlignEnd()
      Ending index in the chemical sequence from the reference database.
      Returns:
      StrColumn