TemplateReaction#

class biopax-explorer.biopax.templatereaction.TemplateReaction(*args, **kwargs)[source]#

Bases: Interaction

Class TemplateReaction

Definiton: An interaction where a macromolecule is polymerized from a

template macromolecule. Rationale: This is an abstraction over multiple (not explicitly stated) biochemical reactions. The ubiquitous molecules (NTP and amino acids) consumed are also usually omitted. Template reaction is non- stoichiometric, does not obey law of mass conservation and temporally non- atomic. It, however, provides a mechanism to capture processes that are central to all living organisms. Usage: Regulation of TemplateReaction, e.g. via a transcription factor can be captured using TemplateReactionRegulation. TemplateReaction can also be indirect for example, it is not necessary to represent intermediary mRNA for describing expression of a protein. It was decided to not subclass TemplateReaction to subtypes such as transcription of translation for the sake of simplicity. If needed these subclasses can be added in the future. Examples: Transcription, translation, replication, reverse transcription. E.g. DNA to RNA is transcription, RNA to protein is translation and DNA to protein is protein expression from DNA.

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

Methods

get_availability()	Attribute _availability getter
get_comment()	Attribute _comment getter
get_dataSource()	Attribute _dataSource getter
get_displayName()	Attribute _displayName getter
get_evidence()	Attribute _evidence getter
get_interactionType()	Attribute _interactionType getter
get_name()	Attribute _name getter
get_participant()	Attribute _participant getter
get_product()	Attribute _product getter
get_standardName()	Attribute _standardName getter
get_template()	Attribute _template getter
get_templateDirection()	Attribute _templateDirection getter
get_xref()	Attribute _xref getter

attribute_type_by_name
get_uri_string
object_attributes
set_availability
set_comment
set_dataSource
set_displayName
set_evidence
set_interactionType
set_name
set_participant
set_product
set_standardName
set_template
set_templateDirection
set_uri_string
set_xref
to_json
type_attributes

Methods Summary

attribute_type_by_name()
get_product()	Attribute _product getter
get_template()	Attribute _template getter
get_templateDirection()	Attribute _templateDirection getter
get_uri_string()
object_attributes()
set_product(value)
set_template(value)
set_templateDirection(value)
set_uri_string(uristr)
to_json()
type_attributes()

Methods Documentation

attribute_type_by_name()[source]#

get_product()[source]#

Attribute _product getter

The product of a template reaction.

get_template()[source]#

Attribute _template getter

The template molecule that is used in this template reaction.

get_templateDirection()[source]#

Attribute _templateDirection getter

The direction of the template reaction on the template.

get_uri_string()[source]#

object_attributes()[source]#

set_product(value)[source]#

set_template(value)[source]#

set_templateDirection(value)[source]#

set_uri_string(uristr)[source]#

to_json()[source]#

type_attributes()[source]#