Source code for cobra.flux_analysis.reaction

"""Provide functions for analyzing / creating objective functions."""

from operator import attrgetter
from typing import TYPE_CHECKING, Dict, Union
from warnings import warn

from ..core import Reaction


if TYPE_CHECKING:
    from cobra import Model


[docs]def assess( model: "Model", reaction: Union[Reaction, str], flux_coefficient_cutoff: float = 0.001, solver: str = None, ) -> Union[bool, Dict]: """Assess production capacity. Assess the capacity of the `model` to produce the precursors for the `reaction` and absorb the production of the `reaction` while the `reaction` is operating at, or above, the specified `flux_coefficient_cutoff`. .. deprecated:: 0.10.0a1 `solver` argument will be removed in cobrapy 1.0.0, it is replaced by globally setting the solver via cobra.Configuration . Parameters ---------- model : cobra.Model The cobra model to assess production capacity for. reaction : str or cobra.Reaction The reaction to assess. flux_coefficient_cutoff : float, optional The minimum flux that reaction must carry to be considered active (default 0.001). solver : str, optional The solver name. If None, the default solver will be used (default None). Returns ------- bool or dict True if the model can produce the precursors and absorb the products for the reaction operating at, or above, `flux_coefficient_cutoff`. Otherwise, a dictionary of {'precursor': Status, 'product': Status}, where 'Status' is the results from `assess_precursors` and `assess_products`, respectively. """ reaction = model.reactions.get_by_any(reaction)[0] with model as m: m.objective = reaction if m.slim_optimize(error_value=0.0) >= flux_coefficient_cutoff: return True else: results = dict() results["precursors"] = assess_component( model, reaction, "reactants", flux_coefficient_cutoff ) results["products"] = assess_component( model, reaction, "products", flux_coefficient_cutoff ) return results
[docs]def assess_component( model: "Model", reaction: Union[Reaction, str], side: str, flux_coefficient_cutoff: float = 0.001, solver: str = None, ) -> Union[bool, Dict]: """Assess production capacity of components. Assess the ability of the `model` to provide sufficient precursors, or absorb products, for a `reaction` operating at, or beyond, the specified `flux_coefficient_cutoff`. .. deprecated:: 0.10.0a1 `solver` argument will be removed in cobrapy 1.0.0, it is replaced by globally setting the solver via cobra.Configuration . Parameters ---------- model : cobra.Model The cobra model to assess production capacity for. reaction : str or cobra.Reaction The reaction to assess. side : {"products", "reactants"} The side of the reaction to assess. flux_coefficient_cutoff : float, optional The minimum flux that reaction must carry to be considered active (default 0.001). solver : str, optional The solver name. If None, the default solver will be used (default None). Returns ------- bool or dict True if the precursors can be simultaneously produced at the specified cutoff. False, if the model has the capacity to produce each individual precursor at the specified threshold but not all precursors at the required level simultaneously. Otherwise, a dictionary of the required and the produced fluxes for each reactant that is not produced in sufficient quantities. """ reaction = model.reactions.get_by_any(reaction)[0] result_key = dict(reactants="produced", products="capacity")[side] get_components = attrgetter(side) with model as m: m.objective = reaction if m.slim_optimize(error_value=0.0) >= flux_coefficient_cutoff: return True simulation_results = {} # build the demand reactions and add all at once demand_reactions = {} for component in get_components(reaction): coeff = reaction.metabolites[component] demand = m.add_boundary(component, type="demand") demand.metabolites[component] = coeff demand_reactions[demand] = (component, coeff) # First assess whether all precursors can be produced simultaneously joint_demand = Reaction("joint_demand") for demand_reaction in demand_reactions: joint_demand += demand_reaction m.add_reactions([joint_demand]) m.objective = joint_demand if m.slim_optimize(error_value=0.0) >= flux_coefficient_cutoff: return True # Otherwise assess the ability of the model to produce each precursor # individually. Now assess the ability of the model to produce each # reactant for a reaction for demand_reaction, (component, coeff) in demand_reactions.items(): # Calculate the maximum amount of the with m: m.objective = demand_reaction flux = m.slim_optimize(error_value=0.0) # metabolite that can be produced. if flux_coefficient_cutoff > flux: # Scale the results to a single unit simulation_results.update( { component: { "required": flux_coefficient_cutoff / abs(coeff), result_key: flux / abs(coeff), } } ) if len(simulation_results) == 0: simulation_results = False return simulation_results
[docs]def _optimize_or_value(model: "Model", value: float = 0.0) -> float: """Perform quick optimization and return the objective value. The objective value is returned at `value` error value. .. deprecated:: 0.22.0 `_optimize_or_value` will be removed in cobrapy 1.0.0, its functionality can be achieved by using `cobra.Model.slim_optimize`. Parameters ---------- model: cobra.Model The model to optimize. value: float The error value to consider. Returns ------- float The optimized value of the model's objective. """ return model.slim_optimize(error_value=value)
[docs]def assess_precursors( model: "Model", reaction: Reaction, flux_coefficient_cutoff: float = 0.001, solver: str = None, ) -> Union[bool, Dict]: """Assess production capacity of precursors. Assess the ability of the model to provide sufficient precursors for a reaction operating at, or beyond, the `flux_coefficient_cutoff`. .. deprecated:: 0.7.0 `assess_precursors` will be removed in cobrapy 1.0.0, it is replaced by `assess_component`. Parameters ---------- model : cobra.Model The cobra model to assess production capacity for. reaction : str or cobra.Reaction The reaction to assess. flux_coefficient_cutoff : float, optional The minimum flux that reaction must carry to be considered active (default 0.001). solver : str, optional The solver name. If None, the default solver will be used (default None). Returns ------- bool or dict True if the precursors can be simultaneously produced at the specified cutoff. False, if the model has the capacity to produce each individual precursor at the specified threshold but not all precursors at the required level simultaneously. Otherwise, a dictionary of the required and the produced fluxes for each reactant that is not produced in sufficient quantities. """ warn("Use cobra.sampling.reaction.assess_component() instead.", DeprecationWarning) return assess_component( model, reaction, "reactants", flux_coefficient_cutoff, solver
)
[docs]def assess_products( model: "Model", reaction: Reaction, flux_coefficient_cutoff: float = 0.001, solver: str = None, ) -> Union[bool, Dict]: """Assesses absorption capacity of products. Assess the ability of the model to to absorb the products of a reaction at a given flux rate. Useful for identifying which components might be blocking a reaction from achieving a specific flux rate. .. deprecated:: 0.7.0 `assess_products` will be removed in cobrapy 1.0.0, it is replaced by `assess_component`. Parameters ---------- model : cobra.Model The cobra model to assess production capacity for. reaction : str or cobra.Reaction The reaction to assess. flux_coefficient_cutoff : float, optional The minimum flux that reaction must carry to be considered active (default 0.001). solver : str, optional The solver name. If None, the default solver will be used (default None). Returns ------- bool or dict True if the model has the capacity to absorb all the reaction products being simultaneously given the specified cutoff. False, if the model has the capacity to absorb each individual product but not all products at the required level simultaneously. Otherwise, a dictionary of the required and the capacity fluxes for each product that is not absorbed in sufficient quantities. """ warn("Use cobra.sampling.reaction.assess_component() instead.", DeprecationWarning) return assess_component( model, reaction, "products", flux_coefficient_cutoff, solver
)