org.rcsb.cif.schema.mm.Entity Maven / Gradle / Ivy
package org.rcsb.cif.schema.mm;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* 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.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Entity extends DelegatingCategory {
public Entity(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "details":
return getDetails();
case "formula_weight":
return getFormulaWeight();
case "id":
return getId();
case "src_method":
return getSrcMethod();
case "type":
return getType();
case "pdbx_description":
return getPdbxDescription();
case "pdbx_number_of_molecules":
return getPdbxNumberOfMolecules();
case "pdbx_parent_entity_id":
return getPdbxParentEntityId();
case "pdbx_mutation":
return getPdbxMutation();
case "pdbx_fragment":
return getPdbxFragment();
case "pdbx_ec":
return getPdbxEc();
case "pdbx_modification":
return getPdbxModification();
case "pdbx_formula_weight_exptl":
return getPdbxFormulaWeightExptl();
case "pdbx_formula_weight_exptl_method":
return getPdbxFormulaWeightExptlMethod();
case "pdbx_target_id":
return getPdbxTargetId();
case "pdbx_entities_per_biological_unit":
return getPdbxEntitiesPerBiologicalUnit();
default:
return new DelegatingColumn(column);
}
}
/**
* A description of special aspects of the entity.
* @return StrColumn
*/
public StrColumn getDetails() {
return delegate.getColumn("details", DelegatingStrColumn::new);
}
/**
* Formula mass in daltons of the entity.
* @return FloatColumn
*/
public FloatColumn getFormulaWeight() {
return delegate.getColumn("formula_weight", DelegatingFloatColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getId() {
return delegate.getColumn("id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getSrcMethod() {
return delegate.getColumn("src_method", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getType() {
return delegate.getColumn("type", DelegatingStrColumn::new);
}
/**
* A description of the entity.
*
* Corresponds to the compound name in the PDB format.
* @return StrColumn
*/
public StrColumn getPdbxDescription() {
return delegate.getColumn("pdbx_description", DelegatingStrColumn::new);
}
/**
* A place holder for the number of molecules of the entity in
* the entry.
* @return IntColumn
*/
public IntColumn getPdbxNumberOfMolecules() {
return delegate.getColumn("pdbx_number_of_molecules", DelegatingIntColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getPdbxParentEntityId() {
return delegate.getColumn("pdbx_parent_entity_id", DelegatingStrColumn::new);
}
/**
* Details about any entity mutation(s).
* @return StrColumn
*/
public StrColumn getPdbxMutation() {
return delegate.getColumn("pdbx_mutation", DelegatingStrColumn::new);
}
/**
* Entity fragment description(s).
* @return StrColumn
*/
public StrColumn getPdbxFragment() {
return delegate.getColumn("pdbx_fragment", DelegatingStrColumn::new);
}
/**
* Enzyme Commission (EC) number(s)
* @return StrColumn
*/
public StrColumn getPdbxEc() {
return delegate.getColumn("pdbx_ec", DelegatingStrColumn::new);
}
/**
* Description(s) of any chemical or post-translational modifications
* @return StrColumn
*/
public StrColumn getPdbxModification() {
return delegate.getColumn("pdbx_modification", DelegatingStrColumn::new);
}
/**
* Experimentally determined formula mass in daltons of the entity
* @return FloatColumn
*/
public FloatColumn getPdbxFormulaWeightExptl() {
return delegate.getColumn("pdbx_formula_weight_exptl", DelegatingFloatColumn::new);
}
/**
* Method used to determine _entity.pdbx_formula_weight_exptl.
* @return StrColumn
*/
public StrColumn getPdbxFormulaWeightExptlMethod() {
return delegate.getColumn("pdbx_formula_weight_exptl_method", DelegatingStrColumn::new);
}
/**
* The value of _entity.target_id points to a TARGETDB target idenitifier
* from which this entity was generated.
* @return StrColumn
*/
public StrColumn getPdbxTargetId() {
return delegate.getColumn("pdbx_target_id", DelegatingStrColumn::new);
}
/**
* Number of entity molecules in the biological assembly.
* @return FloatColumn
*/
public FloatColumn getPdbxEntitiesPerBiologicalUnit() {
return delegate.getColumn("pdbx_entities_per_biological_unit", DelegatingFloatColumn::new);
}
}