Package org.rcsb.cif.schema.mm

Class PdbxConstruct

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxConstruct
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxConstruct
extends DelegatingCategory
Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that _pdbx_construct.id would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition).

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getEntryId

      public StrColumn getEntryId()
      The value of _pdbx_construct.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code.
      Returns:
      StrColumn

    • getId

      public StrColumn getId()
      The value of _pdbx_construct.id must uniquely identify a record in the PDBX_CONSTRUCT list and should be arranged so that it is composed of a site-speicific prefix combined with a value that is unique within a given site.Note that this item need not be a number; it can be any unique identifier.
      Returns:
      StrColumn

    • getName

      public StrColumn getName()
      _pdbx_construct.name provides a placeholder for the local name of the construct, for example the plasmid name if this category is used to list plasmids.
      Returns:
      StrColumn

    • getOrganisation

      public StrColumn getOrganisation()
      _pdbx_construct.organisation describes the organisation in which the _pdbx_construct.id is unique. This will normally be the lab in which the constrcut originated. It is envisaged that this item will permit a globally unique identifier to be constructed in cases where this is not possible from the _pdbx_construct.id alone.
      Returns:
      StrColumn

    • getEntityId

      public StrColumn getEntityId()
      In cases where the construct IS found in the co-ordinates then this item provides a pointer to _entity.id in the ENTITY category for the corresponding molecule.
      Returns:
      StrColumn

    • getRobotId

      public StrColumn getRobotId()
      In cases where the sequence has been determined by a robot this data item provides a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category for the robot responsible
      Returns:
      StrColumn

    • getDate

      public StrColumn getDate()
      The date that the sequence was determined.
      Returns:
      StrColumn

    • getDetails

      public StrColumn getDetails()
      Additional details about the construct that cannot be represented in the category _pdbx_construct_feature.
      Returns:
      StrColumn

    • getClazz

      public StrColumn getClazz()
      The primary function of the construct. This should be considered as a guideline only.
      Returns:
      StrColumn

    • getType

      public StrColumn getType()
      The type of nucleic acid sequence in the construct. Note that to find all the DNA molecules it is necessary to search for DNA + cDNA and for RNA, RNA + mRNA + tRNA.
      Returns:
      StrColumn

    • getSeq

      public StrColumn getSeq()
      sequence expressed as string of one-letter base codes or one letter amino acid codes. Unusual residues may be represented either using the appropriate one letter code wild cards or by the three letter code in parentheses.
      Returns:
      StrColumn