reactionusepkg

ReactionUsePkg()

This class constrains the sum progressions of sets of reactions:

from modelseedpy.fbapkg import ReactionUsePkg
rxnuse = ReactionUsePkg(model)

• model cobra.core.model.Model: The CobraKBase model that will be constrained. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

build_package()

The drain reactions are created through this function:

rxnuse.build_package(rxn_filter = None, reversibility = 0)

• rxn_filter dict: The reaction directions (values) for all reaction IDs (keys) that will be constrained, where None signifies that all reactions will be constrained as equilibria.

• reversibility bool: specifies whether the constrained reactions are reversible.

build_exclusion_constraint()

The drain reactions are created through this function:

rxnuse.build_exclusion_constraint(flux_values = None)

• flux_values dict: A dictionary of the fluxes (values) for the reactions IDs (keys) that will be constrained, which determines whether the reaction proceeds forwards or backwards. The None value defaults to determining the fluxes for all reactions in the model.

Accessible content

The FluxFittingPkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

• model cobra.core.model.Model: The cobrakbase model that possesses the implemented drain reactions.

• variables & parameters dict: Dictionaries of the linear programming variables and simulation parameters, respectively.