FBA module

Submodules

FBA.build_model

class FBA.build_model.BuildModel(target_organism_ID, inmets, inrxns, db, verbose, media=None)

Bases: object

Constructs a CobraPy FBA metabolic model for aspecific organism and runs FBA on new model

build_model()

Adds compounds and rxns to cobrapy FBA model

run_flux()

Runs FBA on model

set_objective_function(biomass_rxn)

FBA.build_model.verbose_print(verbose, line)

FBA.optimize_target

class FBA.optimize_target.OptimizeTarget(target_compound_ID, target_organism_ID, model, temp_rxns, temp_exmets, compounds_dict, inmets, inrxns, db, verbose, KO=True, remove=True)

Bases: object

Adds compounds and reactions needed to produce target compound into previously constructed CobraPy FBA model and runs FBA

add_external_metabolites()

Adds compounds that need to be present to produce target compound

add_external_reactions()

Adds reactions that need to be present to produce target compound

add_sink_reaction(sink_cpd)

perform_knockouts()

Removes each reaction one at a time and runs FBA to see if there is a difference in production of target compound

remove_modifications()

Removes external reactions and compounds from an FBA model

run_fba()

Runs FBA on CobraPy FBA model with added reactions and compounds optimizing production of target compound and (maybe) biomass

set_objective_function(biomass_rxn)

FBA.optimize_target.verbose_print(verbose, line)

FBA.compare_results

class FBA.compare_results.Compare(target_compound_ID, wtresults, exresults, ex_paths, DB, fold_threshold=1.5)

Bases: object

Compares flux values between simulation without added reactions and compounds and simulation with the reactions and compounds

analyze_fluxes(rxn)

Determines if flux differences between simulations is greater than 2.5 fold

external_pathanalyze_fluxes()

Extracts the external (added reactions) path carrying the most flux

get_flux_differences()

Gets reactions for the flux difference is greater than 2.5 fold

FBA.compareKO_results

class FBA.compareKO_results.CompareKO(target_compound_ID, compounds_dict, wtresults, exresults, ex_paths, DB, fold_threshold=1.5)

Bases: object

Compares flux values between simulation with added reactions simulations for each reaction knockout

analyze_fluxes(r, rko)

Determines if flux differences between simulations is greater than 2.5 fold

external_pathanalyze_fluxes()

Extracts external path carrying the most flux

get_flux_differences()

Gets reactions for the flux difference is greater than 2.5 fold

FBA.retrieve_producable_mets

FBA.retrieve_producable_mets.RetrieveActiveRxnsCompounds(target_organism_ID, inmets, inrxns, DB, output_queue, verbose, media=None)

Identifies active compounds in an organism

FBA.retrieve_producable_mets.add_sink_reaction(sink_cpd, compound_dict, model)

Adds reaction for optimizing production of a specified target compound, used to determine if compound can be produced or not on a provided media

FBA.retrieve_producable_mets.parse_solution(solution, cpd, removerxns, removecpds)

Determines if compound can be produced

FBA.generating_model.generate_model_components