Package org.rcsb.cif.model.generated

Class EntityPoly

  • All Implemented Interfaces:
    Category
    @Generated("org.rcsb.cif.generator.SchemaGenerator")
public class EntityPoly
extends BaseCategory
    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 Detail

      • EntityPoly

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

      • EntityPoly

        public EntityPoly​(String name)

    • Method Detail

      • 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