msmodelutils

MSModelUtil()

This class offers a suite of utility functions that support editing and manipulating FBA models:

from modelseedpy.fbapkg import MSModelUtil
msutil = MSModelUtil(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.

find_met()

The COBRA metabolite object is located based upon the metabolite name:

metabolite = msutil.find_met(name)

  • name str: The name of the metabolite that is will be returned by the function.

returns metabolite cobra.core.model.Metabolite: The metabolite that was located by the function, or an empty list if the metabolite was not discovered.

exchange_list()

The returns a list of all COBRA reaction objects for the instantiated model whose reaction IDs possess an “EX_”, which signifies an exchange reaction:

exchange_reactions = msutil.exchange_list()

returns exchange_reactions list: The collection of exchange reactions for the instantiated model.

exchange_hash()

The returns a dictionary of COBRA metabolite (key) : reaction (value) pairs for all metabolites in the exchange reactions from msutil.exchange_list():

exchange_reactions = msutil.exchange_hash()

returns exchange_reactions dict: The COBRA metabolite (key) : reaction (value) pairs for all model exchange reactions.

add_missing_exchanges()

The media compounds that are defined in the exchange reactions of the model are defined with drain reactions:

media_compounds = msutil.add_missing_exchanges()

returns media_compounds list: The collection of media compounds that are represented in the exchange reactions of the model and for which drain reactions have been created.

add_exchanges_for_metabolites()

The media compounds that are defined in the exchange reactions of the model are defined with drain reactions:

drain_reactions = msutil.add_exchanges_for_metabolites(cpds, uptake=0, excretion=0, prefix='EX_', prefix_name='Exchange for ')

  • cpds list: The collection of media metabolites that represented in the model and will be added to the model as drain reactions.

  • uptake & excretion int: The magnitudes of the lower and upper bounds of the drain reaction, respectively.

  • prefix & prefix_name str: The prefixes of the compound ID and name, respectively.

returns drain_reactions list: The drain reactions that were created for the parameterized list of compounds.

convert_cobra_compound_to_kbcompound()

The information of the parameterized compound will be organized into an amenable format for addition to the modelcompounds attribute of CobraKBase models:

cpd_data = msutil.convert_cobra_compound_to_kbcompound(cpd, kbmodel = None)

  • cpd cobra.core.model.Metaoblite: The COBRA metabolite whose information will be formatted as a KBase metabolite.

  • kbmodel cobra.core.model.Model: The CobraKBase model whose modelcompounds attribute will be appended with data from the COBRA metabolite, where None specifies that the defined dictionary of compound information will not be added to a model.

returns cpd_data dict: The dictionary of compound information in the format of the modelcompounds attribute of CobraKBase models.

convert_cobra_reaction_to_kbreaction()

The information of the parameterized reaction will be organized into an amenable format for addition to the modelreactions attribute of CobraKBase models:

rxn_data = msutil.convert_cobra_reaction_to_kbreaction(rxn, kbmodel, cpd_hash, direction = "=", add_to_model = 1, reaction_genes = {})

  • rxn cobra.core.model.Reaction: The COBRA reaction whose information will be formatted as a KBase reaction.

  • kbmodel cobra.core.model.Model: The CobraKBase model whose modelreactions attribute will be appended with data from the COBRA reaction, where None specifies that the defined dictionary of compound information will not be added to a model.

  • direction str: Signification of the reversibility of the reaction as either “<”, “>”, or “=” as equilibrium.

  • reaction_genes dict: The collection of contribution (values) for each gene (keys) that contribute to each reaction (keys).

returns rxn_data dict: The dictionary of reaction information in the format of the modelreactions attribute of CobraKBase models.

add_gapfilling_solution_to_kbase_model()

The parameterized CobraKBase model will be expanded with the content of a gapfilling solution:

rxn_data = msutil.add_gapfilling_solution_to_kbase_model(newmodel, gapfilled_reactions, gfid=None, media_ref = None, reaction_genes = None)

  • newmodel cobra.core.model.Model: The CobraKBase model whose information will be formatted as a KBase reaction.

  • gapfilled_reactions dict: The collection of COBRA reactions (values) in each “new” and “reversed” category of reactions (keys).

  • gfid str: The gapfilling ID, which defaults to “gf.#” where # is the smallest unused index.

  • media_ref str: The reference for the gapfilling media.

  • reaction_genes dict: The collection of contribution (values) for each gene (keys) that contribute to each reaction (keys).

returns rxn_table list: A collection of dictionaries, one for each reaction that is added to the CobraKBase model.

Accessible content

The MSModelUtil 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 MSModelUtil package.

  • metabolite_hash & search_metabolite_hash dict: Lists of metabolite matches (values) for each metabolite name and refined search name, respectively.