fluxfittingpkg

FluxFittingPkg()

This class constrains metabolites of the biomass reaction and adjusts the objective values:

from modelseedpy.fbapkg import FluxFittingPkg
flexbio = FluxFittingPkg(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:

flexbio.build_package(parameters)

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

{
           "target_flux":{},
           "totalflux":0,
           "set_objective":1,
           "default_rescaling":0.1,
           "rescale_vfit_by_flux":true
}

can be supplanted in the parameters argument by listing the key to be changed with the new value. The target_flux sub-dictionary specifies the fluxes (values) for each reaction ID (keys) that will be constrained through this package.

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.

• pkgmgr modelseedpy.fbapkg.mspackagemanager.MSPackageManager: The collection of associated classes that are used in the FullThermo package.