KBasemediapkg

KBaseMediaPkg()

This class constrains exchange reactions and media compounds:

from modelseedpy.fbapkg import KBaseMediaPkg
kbmedia = KBaseMediaPkg(model)

• model cobra.core.model.Model: the CobraKBase model that will be edited. 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:

kbmedia.build_package(media_or_parameters, default_uptake=None, default_excretion=None)

• media_or_parameters dict | cobrakbase.core.kbasebiochem.media.Media: The parameters that govern flux bounds of the exchange reactions, or the media that will be simulated with the specified model. The default parameters

{
               "default_uptake": 0,
               "default_excretion": 100,
               "media": null
}

can be supplanted in the parameters argument by replacing the value of each key.

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.

• modelutl modelseedpy.core.msmodelutl.MSModelUtil: A utilities class that converts between COBRA and CobraKBase nomenclature and performs helpful tasks.