cocomico.model

CoCoMiCo model objects.

Classes

Models store bipartite metabolite-reaction relations.

Module Contents

class cocomico.model.Model(biomolecule: set[cocomico.base.Metabolite], tuples: set[tuple[cocomico.base.Metabolite, cocomico.base.Reaction] | tuple[cocomico.base.Reaction, cocomico.base.Metabolite]] | None = None, relations: dict[str, set[MRT]] | None = None)[source]

Models store bipartite metabolite-reaction relations.

Parameters:

biomolecule (set[cocomico.base.Metabolite]) – metabolites M in the model
reactions – reactions R in the model
relations (dict[str, set[MRT]] | None) – relations M x R or R x M in the model
tuples (set[tuple[cocomico.base.Metabolite, cocomico.base.Reaction] | tuple[cocomico.base.Reaction, cocomico.base.Metabolite]] | None)

property reactions: set[cocomico.base.Reaction]

The set of reactions defined by this model, extracted from the reaction and product triples.

Return type:: set[cocomico.base.Reaction]

remove_seed_reactions()[source]: Remove reactions with empty products or reactants, which otherwise would implicitly create seeds. Some modeling tools generate these to represent exchanges with the environment.

__str__() → str[source]

String representation of class Model.

Return type:: str