SmallMolecule#

class biopax-explorer.biopax.smallmolecule.SmallMolecule(*args, **kwargs)[source]#

Bases: PhysicalEntity

Class SmallMolecule

Definition: A pool of molecules that are neither complexes nor are genetically

encoded. Rationale: Identity of small molecules are based on structure, rather than sequence as in the case of DNA, RNA or Protein. A small molecule reference is a grouping of several small molecule entities that have the same chemical structure. Usage : Smalle Molecules can have a cellular location and binding features. They can’t have modification features as covalent modifications of small molecules are not considered as state changes but treated as different molecules. Some non-genomic macromolecules, such as large complex carbohydrates are currently covered by small molecules despite they lack a static structure. Better coverage for such molecules require representation of generic stoichiometry and polymerization, currently planned for BioPAX level 4. Examples: glucose, penicillin, phosphatidylinositol

code generator : rdfobj (author F.Moreews 2023-2024).

Methods

get_availability()

Attribute _availability getter

get_cellularLocation()

Attribute _cellularLocation getter

get_comment()

Attribute _comment getter

get_dataSource()

Attribute _dataSource getter

get_displayName()

Attribute _displayName getter

get_entityReference()

Attribute _entityReference getter

get_evidence()

Attribute _evidence getter

get_feature()

Attribute _feature getter

get_memberPhysicalEntity()

Attribute _memberPhysicalEntity getter

get_name()

Attribute _name getter

get_notFeature()

Attribute _notFeature getter

get_standardName()

Attribute _standardName getter

get_xref()

Attribute _xref getter

attribute_type_by_name

get_uri_string

object_attributes

set_availability

set_cellularLocation

set_comment

set_dataSource

set_displayName

set_entityReference

set_evidence

set_feature

set_memberPhysicalEntity

set_name

set_notFeature

set_standardName

set_uri_string

set_xref

to_json

type_attributes

Methods Summary

attribute_type_by_name()

get_entityReference()

Attribute _entityReference getter

get_uri_string()

object_attributes()

set_entityReference(value)

set_uri_string(uristr)

to_json()

type_attributes()

Methods Documentation

attribute_type_by_name()[source]#
get_entityReference()[source]#
Attribute _entityReference getter

Reference entity for this physical entity.

get_uri_string()[source]#
object_attributes()[source]#
set_entityReference(value)[source]#
set_uri_string(uristr)[source]#
to_json()[source]#
type_attributes()[source]#