Reaction

class modules.gemtractor.network.reaction.Reaction(identifier, name, reversible=True)

Bases: object

a reaction in a network

Parameters:

• identifier (str) – the reaction’s identifier
• name (str) – the reaction’s name
• reversible (bool) – is the reaction reversible?

add_input(species)

adds a species that is consumed by this reaction

Parameters:species (species.Species) – the consumed species

add_output(species)

adds a species that is produced by this reaction

Parameters:species (species.Species) – the produced species

serialize(species_mapper, gene_mapper, gene_complex_mapper)

serialize to a JSON-dumpable object

the object will contain the following information:

• id: the reaction’s identifier
• name: the reaction’s name
• rev: is the reaction reversible?
• cons: consumed species - as list of integers pointing into the serialized species
• prod: produced species - as list of integers pointing into the serialized species
• enzs: enzymes that catalyze this reaction - as list of integers pointing into the serialized enzymes
• enzc: enzyme complexes that catalyze this reaction - as list of integers pointing into the serialized enzyme complexes

Parameters:

• species_mapper (dict) – dict that maps a species id to an integer, which corresponds to the entry in the serialized species list
• gene_mapper (dict) – dict that maps a gene id to an integer, which corresponds to the entry in the serialized genes list
• gene_complex_mapper (dict) – dict that maps a gene complex id to an integer, which corresponds to the entry in the serialized gene complex list

Returns:

JSON-dumpable object

Return type:

dict