sbol3.subcomponent

Module Contents

Classes

SubComponent

The SubComponent class can be used to specify structural

Functions

build_subcomponent(→ sbol3.Identified)

Used by Document to construct a SubComponent when reading an SBOL file.
class SubComponent(instance_of: Union[sbol3.Identified, str], *, role_integration: Optional[str] = None, locations: Union[sbol3.Location, List[sbol3.Location]] = None, source_locations: Union[sbol3.Location, List[sbol3.Location]] = None, roles: List[str] = None, orientation: str = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, identity: str = None, type_uri: str = SBOL_SUBCOMPONENT)

Bases: sbol3.feature.Feature

The SubComponent class can be used to specify structural hierarchy. For example, the Component of a gene might contain four SubComponent objects: a promoter, RBS, CDS, and terminator, each linked to a Component that provides the complete definition. In turn, the Component of the promoter SubComponent might itself contain SubComponent objects defining various operator sites, etc.

Parameters

  • identity – this object’s Uniform Resource Identifier (URI). this URI MUST be globally unique among all other Identified object URIs. See SBOL 3.0.1 specification section 5.1. This can also be a displayId, which will be concatenated to a default namespace automatically.

  • type_uri – the concrete type of this object, specified as a URI. These are typically in the SBOL3 namespace, like http://sbols.org/v3#Sequence or http://sbols.org/v3#Component. This can also be the type URI of an extension class.

  • name – A human-readable name for this object, for display purposes.

  • description – Per the SBOL 3.0.1 specification, “a more thorough text description” of this object.

  • derived_from – The URIs of one or more SBOL or non-SBOL objects from which this object was derived. This property is defined by the PROV-O ontology.

  • generated_by – The URIs of one or more prov:Activity objects that describe how this object was generated. This property is defined by the PROV-O ontology.

  • measures – The URIs of one or more om:Measure objects, each of which refers to a om:Measure object that describes measured parameters for this object. om:Measure objects are defined by the OM ontology

accept(visitor: Any) → Any

Invokes visit_sub_component on visitor with self as the only argument.

Parameters

visitor (Any) – The visitor instance

Raises

AttributeError – If visitor lacks a visit_sub_component method

Returns

Whatever visitor.visit_sub_component returns

Return type

Any

build_subcomponent(identity: str, type_uri: str = SBOL_SUBCOMPONENT) → sbol3.Identified

Used by Document to construct a SubComponent when reading an SBOL file.