proteomefittingpkg

ProteomeFittingPkg()

This class constrains the sum progressions of sets of reactions:

from modelseedpy.fbapkg import ProteomeFittingPkg
proteofit = ProteomeFittingPkg(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 reactions that are defined in the protemoe are constrained and used to refine the objective:

proteofit.build_package(parameters)

• parameters dict: The parameters that will supplant default values

{
           "flux_values":{},
           "kcat_values":{},
           "prot_coef" : 0.1,
           "totalflux" : 1,
           "kcat_coef" : 0.333,
           "obj_kfit":1,
           "obj_kvfit":1,
           "obj_vfit":1,
           "set_objective":1,
           "rescale_vfit_by_flux":true,
           "default_rescaling":0.1,
           "default_expression":10
}

where keys of proteome and condition, which lack default values, must be defined.

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.