Package org.rcsb.cif.schema.mm

Class EntityPoly

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.EntityPoly
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class EntityPoly
extends DelegatingCategory
Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.

  • 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

    • getNstdChirality

      public StrColumn getNstdChirality()
      A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in _entity_poly.type.
      Returns:
      StrColumn

    • getNstdLinkage

      public StrColumn getNstdLinkage()
      A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by _entity_poly.type.
      Returns:
      StrColumn

    • getNstdMonomer

      public StrColumn getNstdMonomer()
      A flag to indicate whether the polymer contains at least one monomer that is not considered standard.
      Returns:
      StrColumn

    • getNumberOfMonomers

      public IntColumn getNumberOfMonomers()
      The number of monomers in the polymer.
      Returns:
      IntColumn

    • getType

      public StrColumn getType()
      The type of the polymer.
      Returns:
      StrColumn

    • getTypeDetails

      public StrColumn getTypeDetails()
      A description of special aspects of the polymer type.
      Returns:
      StrColumn

    • getPdbxStrandId

      public StrColumn getPdbxStrandId()
      The PDB strand/chain id(s) corresponding to this polymer entity.
      Returns:
      StrColumn

    • getPdbxSeqOneLetterCode

      public StrColumn getPdbxSeqOneLetterCode()
      Chemical sequence expressed as string of one-letter amino acid codes. Modifications and non-standard amino acids are coded as X.
      Returns:
      StrColumn

    • getPdbxSeqOneLetterCodeCan

      public StrColumn getPdbxSeqOneLetterCodeCan()
      Cannonical chemical sequence expressed as string of one-letter amino acid codes. Modifications are coded as the parent amino acid where possible. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil
      Returns:
      StrColumn

    • getPdbxTargetIdentifier

      public StrColumn getPdbxTargetIdentifier()
      For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
      Returns:
      StrColumn

    • getPdbxSeqOneLetterCodeSample

      public StrColumn getPdbxSeqOneLetterCodeSample()
      For cases in which the sample and model sequence differ this item contains the sample chemical sequence expressed as string of one-letter amino acid codes. Modified may be include as 'X' or with their 3-letter codes in parentheses.
      Returns:
      StrColumn

    • getPdbxExplicitLinkingFlag

      public StrColumn getPdbxExplicitLinkingFlag()
      A flag to indicate that linking data is explicitly provided for this polymer in the PDBX_ENTITY_POLY_COMP_LINK_LIST category
      Returns:
      StrColumn

    • getPdbxSequenceEvidenceCode

      public StrColumn getPdbxSequenceEvidenceCode()
      Evidence for the assignment of the polymer sequence.
      Returns:
      StrColumn

    • getPdbxBuildSelfReference

      public StrColumn getPdbxBuildSelfReference()
      A code to indicate that this sequence should be assigned a PDB sequence reference.
      Returns:
      StrColumn

    • getPdbxNTerminalSeqOneLetterCode

      public StrColumn getPdbxNTerminalSeqOneLetterCode()
      N-terminal cloning artifacts and/or HIS tag.
      Returns:
      StrColumn

    • getPdbxCTerminalSeqOneLetterCode

      public StrColumn getPdbxCTerminalSeqOneLetterCode()
      C-terminal cloning artifacts and/or HIS tag.
      Returns:
      StrColumn

    • getPdbxSeqThreeLetterCode

      public StrColumn getPdbxSeqThreeLetterCode()
      Chemical sequence expressed as string of three-letter amino acid codes.
      Returns:
      StrColumn

    • getPdbxSeqDbName

      public StrColumn getPdbxSeqDbName()
      The name of the sequence data base containing a database entry for this sequence.
      Returns:
      StrColumn

    • getPdbxSeqDbId

      public StrColumn getPdbxSeqDbId()
      The identifier for this sequence in the sequence data base.
      Returns:
      StrColumn

    • getPdbxSeqAlignBegin

      public IntColumn getPdbxSeqAlignBegin()
      The sequence position in the database sequence at which the alignment with your sequence begins.
      Returns:
      IntColumn

    • getPdbxSeqAlignEnd

      public IntColumn getPdbxSeqAlignEnd()
      The sequence position in the database sequence at which the alignment with your sequence ends.
      Returns:
      IntColumn