cocomico.facts

CoCoMiCo LP facts.

Functions

`seed_facts`(→ list[clyngor.as_pyasp.Atom])	Convert a set of nutritional seed metabolites in LP facts,
`network_facts`(→ list[clyngor.as_pyasp.Atom])	Convert an SBML model into list LP facts, lexicographically
`to_metabolite`(→ cocomico.base.MetaboliteSet)	Decode a set of clyngor.as_pyasp.Atom of the form
`to_reaction`(→ set[cocomico.base.Reaction])	Decode a set of clyngor.as_pyasp.Atom of the form
`to_exchange`(→ set[cocomico.base.Exchange])	Decode a tuple of clyngor.as_pyasp.Atom of the form
`to_biomolecule`(→ set[cocomico.base.Biomolecule])	Decode a set of clyngor.as_pyasp.Atom of the form

Module Contents

cocomico.facts.seed_facts(seeds: cocomico.base.Seeds) → list[clyngor.as_pyasp.Atom][source]

Convert a set of nutritional seed metabolites in LP facts, lexicographically ordered for clarity.

seed(Taxon)

Parameters:: seeds (cocomico.base.Seeds) – a set of seed metabolites
Returns:: a set of LP facts
Return type:: list[clyngor.as_pyasp.Atom]

cocomico.facts.network_facts(models: dict[cocomico.base.Taxon, cocomico.model.Model], biomolecules_only=False) → list[clyngor.as_pyasp.Atom][source]

Convert an SBML model into list LP facts, lexicographically ordered by predicate, taxon, and reaction, for clarity.

taxon(Taxon). biomolecule(Metabolite Name, Taxon). reaction(Reaction Id, Taxon). product(Metabolite Name, Reaction Id, Taxon). reactant(Metabolite Name, Reaction Id, Taxon).

Parameters:: models (dict[cocomico.base.Taxon, cocomico.model.Model]) – a dict mapping taxa to models
Returns:: a set of LP facts
Return type:: list[clyngor.as_pyasp.Atom]

cocomico.facts.to_metabolite(atoms: Iterable[clyngor.as_pyasp.Atom]) → cocomico.base.MetaboliteSet[source]

Decode a set of clyngor.as_pyasp.Atom of the form metabolite(Biomolecule,Taxon)

Parameters:: atoms (Iterable[clyngor.as_pyasp.Atom]) – metabolite atoms
Returns:: MetaboliteSet
Return type:: cocomico.base.MetaboliteSet

cocomico.facts.to_reaction(atoms: Iterable[clyngor.as_pyasp.Atom]) → set[cocomico.base.Reaction][source]

Decode a set of clyngor.as_pyasp.Atom of the form reaction(Name,Taxon)

Parameters:: atoms (Iterable[clyngor.as_pyasp.Atom]) – metabolite atoms
Returns:: set[Reaction]
Return type:: set[cocomico.base.Reaction]

cocomico.facts.to_exchange(tuples: Iterable[Tuple[clyngor.as_pyasp.Atom, clyngor.as_pyasp.Atom, clyngor.as_pyasp.Atom]]) → set[cocomico.base.Exchange][source]

Decode a tuple of clyngor.as_pyasp.Atom of the form # reaction(Name,Taxon) (Taxon, Taxon)

Parameters:

atoms – Taxon tuple
tuples (Iterable[Tuple[clyngor.as_pyasp.Atom, clyngor.as_pyasp.Atom, clyngor.as_pyasp.Atom]])

Returns:

set[Tuple[Taxon, Taxon]]

Return type:

set[cocomico.base.Exchange]

cocomico.facts.to_biomolecule(atoms: Iterable[clyngor.as_pyasp.Atom]) → set[cocomico.base.Biomolecule][source]

Decode a set of clyngor.as_pyasp.Atom of the form (Biomolecule)

Parameters:: atoms (Iterable[clyngor.as_pyasp.Atom]) – biomolecule name atoms
Returns:: set[Biomolecule]
Return type:: set[cocomico.base.Biomolecule]