diel_models package

DielModelsCreator

diel_models.diel_models_creator.diel_models_creator(model: Model, storage_pool_metabolites: List[str], photon_reaction_id: List[str], nitrate_exchange_reaction: List[str] = [], biomass_reaction_id: str | None = None, tissues: List[str] | None = None, day_ratio_value: int = 3, night_ratio_value: int = 2) → Model

Function that allows you to run the pipeline in one go, returning the resulting model, where the arguments are all relative to the original model.

Parameters:

• model (cobra.Model) – Metabolic model

• storage_pool_metabolites (List[str]) – list with all the metabolites for storage pool

• photon_reaction_id (List[str]) – id or ids for photon reaction(s) - in case of multi tissues models for example.

• nitrate_exchange_reaction (List[str]) – id for nitrate exchange reaction(s) - in case of multi tissues models for example.

• biomass_reaction_id (str, optional) – id for biomass_reaction, defaults to None in case no biomass reaction defined.

• tissues (List[str], optional) – List of tissues in the multi-tissue model, defaults to None for generic models.

• day_ratio_value (int, optional) – The ratio of nitrate uptake during the day, default is 3.

• night_ratio_value (int, optional) – The ratio of nitrate uptake during the night, default is 2.

Return type:

cobra.Model

Submodules

DayNightCreator

class diel_models.day_night_creator.DayNightCreator(model: Model)

Bases: Step

day_attribution() → None

Loop into the reactions and metabolites of a metabolic model and append “_Day” to reaction and metabolites identifications and names.

duplicate() → None

Function that duplicates the original reactions and replaces the suffix “_Day” with the suffix “_Night” and further duplicates the corresponding metabolites.

run() → Model

Executes the methods of the class DayNightCreator.

validate() → None

Validates the model received initially in terms of reactions, metabolites and objective function.

StoragePoolGenerator

class diel_models.storage_pool_generator.StoragePoolGenerator(model: Model, metabolites: List[str], tissues: List[str] | None = None)

Bases: Step

create_exchange_reaction(metabolite_id: str, metabolite_sp_id: str, direction: str) → Reaction

It creates a Reaction object representing an exchange reaction for the specified metabolite in the specified direction.

Parameters:

• metabolite_id (str) – ID from original metabolite

• metabolite_sp_id (str) – ID from metabolite in sp

• direction (str) – Day or Night

Return type:

cobra.Reaction

create_storage_pool_first_reactions() → None

According to the given metabolite IDs, this function creates the corresponding exchange reaction of the metabolite to the storage pool.

create_storage_pool_metabolites() → None

According to the given metabolite IDs, this function creates new metabolites for a new compartment: storage pool.

If the model is a multi-tissue model (tissues are provided), the metabolites in the storage pool will have the corresponding tissue name in their sp names.

Raises:

• ValueError – If a metabolite ID is not present in the given model.

• ValueError – If no matching tissue found for some metabolite ID.

create_storage_pool_second_reactions() → None

According to the given metabolite IDs, this function creates the complementary reactions, i.e. if it previously created the Day <-> Storage Pool reaction, it now creates the Storage Pool <-> Night reaction and vice versa.

run() → Model

Executes the methods of the class StoragePoolGenerator.

validate() → None

Validates the model, since it has to have metabolites, reactions and a Day and Night compartments.

PhotonReactionInhibitor

class diel_models.photon_reaction_inhibitor.PhotonReactionInhibitor(model: Model, id_photon_reaction_night: List[str])

Bases: Step

restrain() → None

Function that resets the photon reaction(s) limits to zero at night.

Raises:

ValueError – If the photon uptake reaction ID is not present in the given model.

run() → Model

Executes the method of the class PhotonReactionInhibitor.

validate() → None

Validates the model that, in addition to the above factors, it must contain metabolites and storage pool compartments.

NitrateUptakeRatioCalibrator

class diel_models.nitrate_uptake_ratio.NitrateUptakeRatioCalibrator(model: Model, id_nitrate_uptake_reaction_day: List[str], id_nitrate_uptake_reaction_night: List[str], day_ratio_value: int = 3, night_ratio_value: int = 2)

Bases: Step

ratio_set() → None

This function establishes a 3:2 ratio (by default) of nitrate uptake between day and night, respectively. The ratio can be changed.

Raises:

ValueError – If the nitrate uptake reaction ID is not present in the given model.

run() → Model

Executes the method of the class NitrateUptakeRatioCalibrator.

validate() → None

Validates the model of the step.

BiomassAdjuster

class diel_models.biomass_adjuster.BiomassAdjuster(model: Model, id_biomass_reaction_day: str, id_biomass_reaction_night: str)

Bases: Step

run() → Model

Executes the methods of the class BiomassAdjuster.

total_biomass_reaction() → None

Function that joins the two biomass reactions (day and night) into one. Defines this new reaction as the objective function of the model.

Raises:

ValueError – If the biomass reaction ID is not present in the given model.

validate() → None

Validates the model of the step.

Build Pipeline

Pipeline

class diel_models.pipeline.Pipeline(model: Model, steps: list)

Bases: object

run() → None

It runs the validate method followed by the run method. The resulting model is then set as self.model to be used in the next step.

class diel_models.pipeline.Step

Bases: ABC

abstract run() → None

Performs the step.

abstract validate() → None

Validates the model of the step.