drainfluxpkg

DrainFluxPkg()

This class adds drain reactions for each specified drain compound:

from modelseedpy.fbapkg import DrainFluxPkg
drainflux = DrainFluxPkg(model)

• model cobra.core.model.Model: the CobraKBase model that will be expanded with drain reactions. 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:

drainflux.build_package(parameters)

• parameters dict: The parameters that govern how the drain reactions will be created and implemented into the model. The default dictionary

{
           "add_all_intracellular_drains":false,
           "default_uptake":0,
           "default_excretion":100,
           "drain_compounds":{},
           "set_minimal_drain_objective":false,
           "update_drain_fluxes":false
}

can be supplanted in the parameters argument by listing the key to be changed with the new value.

Accessible content

The DrainFluxPkg 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 the simulation parameters, respectively.