cocomico.base

CoCoMiCo base semantic domains.

Classes

`Reaction`	Reactions with the same name but in different taxa are distinct.
`Metabolite`	Metabolites are metabolite biomolecules tagged with organism biomolecules.
`MetaboliteSet`	MetaboliteSets are sets of metabolites with additional operations
`Seeds`	Seeds are sets of metabolite biomolecules that define inputs to a community.
`Exchange`	Reactions with the same name but in different taxa are distinct.
`ExchangeNM`	An Exchanged defines an n to m relation between producers and consumers.

Module Contents

class cocomico.base.Reaction[source]

Bases: NamedTuple

Reactions with the same name but in different taxa are distinct.

class cocomico.base.Metabolite(provenance: Taxon, biomolecule: Biomolecule)[source]

Metabolites are metabolite biomolecules tagged with organism biomolecules.

Parameters:

provenance (Taxon) – provenance organism
biomolecule (Biomolecule) – generic metabolite biomolecule

property provenance: Taxon

Metabolite provenance organism biomolecule.

Return type:: Taxon

property biomolecule: Biomolecule

Metabolite generic biomolecule.

Return type:: Biomolecule

classmethod from_string(identifier: str) → Self[source]

Factory method to create a metabolite from a string.

Parameters:: identifier (str) – string-coded metabolite “NAME.TAXON”
Return type:: Metabolite

class cocomico.base.MetaboliteSet[source]

Bases: Set[Metabolite]

MetaboliteSets are sets of metabolites with additional operations for taxa.

property taxa: set[Taxon]

The taxa of a metabolite set.

Return type:: set[Taxon]

property biomolecules: set[Biomolecule]

The taxa of a metabolite set.

Return type:: set[Biomolecule]

select(taxa: set[Taxon]) → Self[source]

Subset of a metabolite set from the given taxa.

Parameters:: taxa (set[Taxon])
Return type:: Self

__str__() → str[source]

Return str(self).

Return type:: str

class cocomico.base.Seeds[source]

Bases: FrozenSet[Biomolecule]

Seeds are sets of metabolite biomolecules that define inputs to a community.

Parameters:

seeds (Iterable[Biomolecule]) – set of metabolite biomolecules
name (str, optional) – symbolic name for the set of seeds

classmethod from_file(file: pathlib.Path) → Self[source]

Read new seed object from an SBML file

Parameters:: file (Path) – path to SBML file containing seed molecular species
Return type:: Self

__str__() → str[source]

String representation.

Return type:: str

class cocomico.base.Exchange[source]

Bases: NamedTuple

Reactions with the same name but in different taxa are distinct.

class cocomico.base.ExchangeNM(relations: set[tuple[Taxon, Taxon]] | set[Exchange] | None = None, producers: Iterable[Taxon] | None = None, consumers: Iterable[Taxon] | None = None)[source]

An Exchanged defines an n to m relation between producers and consumers. Designed to represent metabolite exchanges.

Exchange objects act like a set of pairs of producer-consumer relations that can be queried for membership. Sets of roducers and consumers can also be retrieved separately.

Parameters:

producers (Iterable[Taxon] | None) – set of producer taxa for this exchange
consumers (Iterable[Taxon] | None) – set of consumer taxa for this exchange
relations (set[tuple[Taxon, Taxon]] | set[Exchange] | None)

__iter__()[source]: A exchange is iterable, and iterates over (producer,consumer) tuples.

__contains__(item: tuple[Taxon, Taxon]) → bool[source]

Test for membership without iterating.

Parameters:: item (tuple[Taxon, Taxon])
Return type:: bool

__eq__(other) → bool[source]

Exchanges are equal if their producer and consumer sets are equal.

Return type:: bool