Package org.rcsb.cif.schema.mm

Class Entity

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.Entity
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Entity
extends DelegatingCategory
Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getDetails

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

    • getFormulaWeight

      public FloatColumn getFormulaWeight()
      Formula mass in daltons of the entity.
      Returns:
      FloatColumn

    • getId

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

    • getSrcMethod

      public StrColumn getSrcMethod()
      The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category.
      Returns:
      StrColumn

    • getType

      public StrColumn getType()
      Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category.
      Returns:
      StrColumn

    • getPdbxDescription

      public StrColumn getPdbxDescription()
      A description of the entity. Corresponds to the compound name in the PDB format.
      Returns:
      StrColumn

    • getPdbxNumberOfMolecules

      public IntColumn getPdbxNumberOfMolecules()
      A place holder for the number of molecules of the entity in the entry.
      Returns:
      IntColumn

    • getPdbxParentEntityId

      public StrColumn getPdbxParentEntityId()
      An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source.
      Returns:
      StrColumn

    • getPdbxMutation

      public StrColumn getPdbxMutation()
      Details about any entity mutation(s).
      Returns:
      StrColumn

    • getPdbxFragment

      public StrColumn getPdbxFragment()
      Entity fragment description(s).
      Returns:
      StrColumn

    • getPdbxEc

      public StrColumn getPdbxEc()
      Enzyme Commission (EC) number(s)
      Returns:
      StrColumn

    • getPdbxModification

      public StrColumn getPdbxModification()
      Description(s) of any chemical or post-translational modifications
      Returns:
      StrColumn

    • getPdbxFormulaWeightExptl

      public FloatColumn getPdbxFormulaWeightExptl()
      Experimentally determined formula mass in daltons of the entity
      Returns:
      FloatColumn

    • getPdbxFormulaWeightExptlMethod

      public StrColumn getPdbxFormulaWeightExptlMethod()
      Method used to determine _entity.pdbx_formula_weight_exptl.
      Returns:
      StrColumn

    • getPdbxTargetId

      public StrColumn getPdbxTargetId()
      The value of _entity.target_id points to a TARGETDB target idenitifier from which this entity was generated.
      Returns:
      StrColumn

    • getPdbxEntitiesPerBiologicalUnit

      public FloatColumn getPdbxEntitiesPerBiologicalUnit()
      Number of entity molecules in the biological assembly.
      Returns:
      FloatColumn