cocomico.community

CoCoMiCo community objects.

Classes

Community

Communities are collections of models, with additional operations to

Module Contents

class cocomico.community.Community(*args, **kwargs)[source]

Bases: dict[cocomico.base.Taxon, Any]

Communities are collections of models, with additional operations to calculate metabolic scope and identify exchanged and limiting metabolites.

Parameters:

sbml_dir (Path) – directory where model files are found

classmethod from_specification(spec: pathlib.Path, sbml_dir: pathlib.Path) → dict[str, Self][source]

Factory method to create a set of communities from a JSON specification.

Parameters:

  • spec (Path) – filename of a JSON specification

  • sbml_dir (pathlib.Path) – directory containing models

Return type:

set[Community]

property products: cocomico.base.MetaboliteSet

Products of all reactions in the models in the community.

Return type:

MetaboliteSet

property reactants: cocomico.base.MetaboliteSet

Reactants of all reactions in the models in the community.

Return type:

MetaboliteSet

property biomolecule: cocomico.base.MetaboliteSet

All biomolecules (molecular species) declared in the models in the community.

Return type:

MetaboliteSet

property reactions: set[cocomico.base.Reaction]

All reactions declared in the models in the community, duplicated in reverse form when the reaction is reversible.

Return type:

list[Reaction]

property taxa: set[cocomico.base.Taxon]

Taxa of all models in the community.

Return type:

set[Taxon]

remove_seed_reactions() → None[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.

Return type:

None

property knowledge_base

Generate LP facts for this community

scope(seeds: cocomico.base.Seeds, choice: cocomico.base.Taxon | None = None) → cocomico.base.MetaboliteSet[source]

Compute community scope :rtype: MetaboliteSet

Parameters:
Return type:

cocomico.base.MetaboliteSet

exchange(seeds: cocomico.base.Seeds) → dict[cocomico.base.Biomolecule, set[cocomico.base.Exchange]][source]

Compute community exchanges :rtype: MetaboliteSet

Parameters:

seeds (cocomico.base.Seeds)

Return type:

dict[cocomico.base.Biomolecule, set[cocomico.base.Exchange]]

polyopsonist(seeds: cocomico.base.Seeds) → dict[cocomico.base.Biomolecule, int][source]

Compute community polyopsonies :rtype: set[Biomolecule]

Parameters:

seeds (cocomico.base.Seeds)

Return type:

dict[cocomico.base.Biomolecule, int]

monopsonist(seeds: cocomico.base.Seeds) → dict[cocomico.base.Biomolecule, int][source]

Compute community monopsonies :rtype: set[Biomolecule]

Parameters:

seeds (cocomico.base.Seeds)

Return type:

dict[cocomico.base.Biomolecule, int]

activated(seeds: cocomico.base.Seeds, choice: cocomico.base.Taxon | None = None) → set[cocomico.base.Reaction][source]

Compute community activated :rtype: set[Reaction]

Parameters:
Return type:

set[cocomico.base.Reaction]

produced_seeds(seeds: cocomico.base.Seeds, choice: cocomico.base.Taxon | None = None) → set[cocomico.base.Biomolecule][source]

Identify community produced seeds :rtype: set[Biomolecule]

Parameters:
Return type:

set[cocomico.base.Biomolecule]

consumed_seeds(seeds: cocomico.base.Seeds, choice: cocomico.base.Taxon | None = None) → set[cocomico.base.Biomolecule][source]

identify community consumed seeds :rtype: set[Biomolecule]

Parameters:
Return type:

set[cocomico.base.Biomolecule]

answers(seeds: cocomico.base.Seeds) → cocomico.answer.Answer[source]

Solve LP for this community

Parameters:

seeds (cocomico.base.Seeds)

Return type:

cocomico.answer.Answer

seeds() → list[cocomico.base.Seeds][source]

Sets of seeds for which answers are known.

Return type:

list[cocomico.base.Seeds]

clear_answers() → None[source]

Clear the cache of answers.

Return type:

None

__str__() → str[source]

String representation.

Return type:

str