fbahelper¶

FBAHelper()¶

This class offers a suite of static method functions that assist users in editing and expanding COBRA models:

from modelseedpy.core import FBAHelper

add_autodrain_reactions_to_community_model()¶

Drain reactions are added to a model:

fbahelper.add_autodrain_reactions_to_community_model(model,auto_sink = ["cpd02701", "cpd15302"])

model cobra.core.model.Model: The COBRA model that contains the reactions which are to be reformatted for the template.
auto_sink list: The collection of metabolites for which drain reactions will be created and added to the model.

add_drain_from_metabolite_id()¶

A drain reaction is constructed for a specified metabolite:

drain_reaction = fbahelper.add_drain_from_metabolite_id(model, cpd_id, uptake, excretion, prefix='EX_', prefix_name='Exchange for ')

model cobra.core.model.Model: The COBRA model that contains the reactions which are to be reformatted for the template.
cpd_id str: The ID of the compound for which a drain reaction will be constructed.
uptake & excretion float: The magnitudes of metabolite uptake and excretion that define the lower and upper bounds of the drain reaction.
prefix & prefix_name str: The prefixes for the drain reaction ID and name, respectively.

returns drain_reaction cobra.core.model.Reaction: The drain reaction of the respective metabolite.

test_condition_list()¶

A collection of simulation conditions are examined for the specified model:

test_result = fbahelper.test_condition_list(model, condition_list, pkgmgr)

model cobra.core.model.Model: The COBRA model that contains the reactions which are to be reformatted for the template.
condition_list list: A list of simulation conditions that will be each examined during the simulation.
pkgmgr modelseedpy.fbapkg.mspackagemanager.MSPackageManager: The collection of associated classes that are used in the FullThermo package.

returns test_result bool: specifies whether all of the conditions yielded feasible solutions and objective values that surpassed the provided threshold with each condition.

reaction_expansion_test()¶

The reactions that cause simulations to not pass all conditions is collected and returned:

filtered_list = fbahelper.reaction_expansion_test(model, reaction_list, condition_list, pkgmgr)

model cobra.core.model.Model: The COBRA model that contains the reactions which are to be reformatted for the template.
reaction_list list: The collections of COBRA reactions that will be knocked-out and then are iteratively restored while assessing whether all of the conditions pass the reaction.
condition_list list: and simulation conditions that will be simulated.
pkgmgr modelseedpy.fbapkg.mspackagemanager.MSPackageManager: The collection of associated classes that are used in the FullThermo package.

returns filtered_list list: The collection of reactions from the reaction_list for which at least one of the simulation conditions failed.

set_reaction_bounds_from_direction()¶

The reaction bounds are set based upon the reaction direction:

fbahelper.set_reaction_bounds_from_direction(reaction, direction, add=False)

reaction cobra.core.model.Reaction: A COBRA reaction whose flux bounds will be adjusted based upon the direction of the reaction.
direction str: The < or > designation of the reaction direction.
add bool: specifies whether the upper bound for < directions or the lower bound for > directions will be assigned to zero.

set_objective_from_target_reaction()¶

The FBA reaction objective is defined:

target_reaction = fbahelper.set_objective_from_target_reaction(model,target_reaction,minimize = False)

model cobra.core.model.Model: The COBRA model that contains the reactions which are to be reformatted for the template.
target_reaction str: The ID of the COBRA reaction in the parameterized model that will be set as the model objective.
minimize bool: specifies whether the simulation will minimize the objective.

returns target_reaction cobra.core.model.Reaction: The reaction that is specified to be the simulation objective.

compute_flux_values_from_variables()¶

Defines the reaction fluxes for all model reactions:

flux_values = fbahelper.compute_flux_values_from_variables(model)

model cobra.core.model.Model: The COBRA model that contains the reactions which will be interpreted for the fluxes.

returns flux_values cobra.core.model.Reaction: The reaction that is specified to be the simulation objective.

modelseed_id_from_cobra_metabolite()¶

A ModelSEED compound ID is determined from a COBRA metabolite ID:

msid = fbahelper.modelseed_id_from_cobra_metabolite(metabolite)

model cobra.core.model.Metabolite: The COBRA metabolite whose ModelSEED ID will be returned from a COBRA ID.

returns msid str: The ModelSEED metabolite ID that is parsed from the COBRA ID.

modelseed_id_from_cobra_reaction()¶

A ModelSEED reaction ID is determined from a COBRA reaction ID:

msid = fbahelper.modelseed_id_from_cobra_reaction(reaction)

model cobra.core.model.Reaction: The COBRA reaction whose ModelSEED ID will be returned from a COBRA ID.

returns msid str: The ModelSEED reaction ID that is parsed from the COBRA reaction ID.

metabolite_mw()¶

The molecular weight of a metabolite is calculated from its elemental composition, or its chemical formula when the elements are unavailable:

mw = fbahelper.metabolite_mw(metabolite)

model cobra.core.model.Metabolite: The COBRA metabolite whose molecular weight will be calculated.

returns mw float: The molecular weight of the parameterized metabolite.

elemental_mass()¶

returns elementmasses dict: A dictionary of all elemental masses (values) for all chemical symbols (keys).

get_modelseed_db_api()¶

returns modelseed_api ModelSEED: The ModelSEED Database that can be used for ModelSEEDpy operations.

is_ex() & is_biomass()¶

Functions that determine whether parameterized reactions are exchange or biomass reactions, respectively:

result = fbahelper.is_ex(reaction)
result = fbahelper.is_biomass(reaction)

reaction cobra.core.model.Reaction: The COBRA reaction that will be examined as being either an exchange or biomass reaction, respectively.

returns result bool: specifies whether the parameterized reaction is one of the two reaction types.

find_reaction()¶

Identifies a reaction in a model based upon reaction stoichiometry:

reaction = fbahelper.find_reaction(model, stoichiometry)

model cobra.core.model.Model: The COBRA model in which the reaction will be searched.
stoichiometry dict: The stoichiometry of the reaction that will be searched in the model.

returns reaction cobra.core.model.Model: The located COBRA reaction, if its reaction string is identified in the model, or None otherwise.

msid_hash()¶

Assembles all of the COBRA metabolites that correspond to the same ModelSEED metabolite ID:

reaction = fbahelper.msid_hash(model)

model cobra.core.model.Model: The COBRA model where all of the metabolites will be searched.

returns metabolites dict: Lists of all COBRA metabolites (values) that are represented by a ModelSEED compound ID.

rxn_hash()¶

Pairs all reaction strings, in both directions, with their corresponding COBRA reaction object:

reaction = fbahelper.rxn_hash(model)

model cobra.core.model.Model: The COBRA model where all of the metabolites will be searched.

returns reactions dict: Lists of all COBRA reaction objects with a designation of their directionality (values) according to their reaction strings (keys).

rxn_compartment()¶

Determines the non-extracellular compartment of the parameterized reaction:

compartment = fbahelper.rxn_compartment(reaction)

model cobra.core.model.Reaction: The COBRA reaction whose non-extracellular compartment will be provided.

returns compartment str: The non-extracellular reaction compartment.

add_atp_hydrolysis()¶

Adds an ATP Hydrolysis reaction to the parameterized model in the specified compartment:

reaction_dict = fbahelper.add_atp_hydrolysis(model,compartment)

model cobra.core.model.Model: The COBRA model into which an ATP hydrolysis reaction will be added.
compartment str: The compartment of the ATP hydrolysis reaction, which is sensitive to community models where each species is represented with a unique compartment.

returns reaction_dict dict: The reaction string, direction, and newness of the reaction (values) are specified for the constructed ATP hydrolysis reaction (keys).

parse_id()¶