metaboFBApkg

MetaboFBAPkg()

This class constrains metabolites in the parameterized peaks to zero and adds simple thermodynamic constraints:

from modelseedpy.fbapkg import MetaboFBAPkg
metFBA = MetaboFBAPkg(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 COBRA metabolite object is constrained:

metFBA.build_package(parameters)

• parameters dict: The parameters that will govern how the model is constrained, with a default entry

{
           "set_objective":true,
}

and a required key of peaks whose value is a list of paek data that will be used to identify the metabolites that are constrained.

Accessible content

The MetaboFBAPkg 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 MetaboFBAPkg package.