KarrLab/wc_model_gen

Avoid deeply nested control flow statements.

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                        if species == self._rxn_species_modifier[reaction.id][0]:
                            modifier_reactants.append(species)
                else:

Function gen_response_functions has 6 arguments (exceeds 4 allowed). Consider refactoring.

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def gen_response_functions(model, beta, reaction_id, reaction_class, compartment, reaction_factors):

Similar blocks of code found in 13 locations. Consider refactoring.

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            init_reaction.participants.append(metabolites['pi'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=5))

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Avoid deeply nested control flow statements.

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                        if unknown_vmax_count > 0:
                            shared_vmax = (value - known_vmax)/unknown_vmax_count
                        for comp, kcat in comp_kcat.items():                            

Avoid deeply nested control flow statements.

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                        if model_compartment.init_density.function_expressions:
                            volume = model_compartment.init_density.function_expressions[0].function
                            unit_adjusted_term = '{} * {} * {}'.format(param.id, Avogadro.id, volume.id)
                        else:
                            volume = model_compartment.init_volume.mean    

Similar blocks of code found in 13 locations. Consider refactoring.

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            init_reaction.participants.append(metabolites['h2o'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=-5))

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Avoid deeply nested control flow statements.

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                        if part.species.id in met_requirement:
                            met_requirement[part.species.id] += -part.coefficient * mean_concentration * \
                                (1 + doubling_time / half_life)
                # Transcription elongation
                transcription_el_reaction = model.reactions.get_one(id='transcription_elongation_{}'.format(rna_kb.id))

Similar blocks of code found in 13 locations. Consider refactoring.

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            init_reaction.participants.append(metabolites['gdp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=2))

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Avoid deeply nested control flow statements.

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                        if part.species.id in met_requirement:
                            met_requirement[part.species.id] += -part.coefficient * mean_concentration * \
                                (1 + doubling_time / half_life)
            

Avoid deeply nested control flow statements.

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                        for kcat in law.expression.parameters:                                                     
                            kcat.value = kcat.value*value/effective_vmax
                            kcat.comments = 'Measured value adjusted to relax bound'
                elif all(numpy.isnan(kcat.value) for kcat in law.expression.parameters):

Avoid deeply nested control flow statements.

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                        if not numpy.isnan(kcat.value):
                            known_vmax += kcat.value*comp.distribution_init_concentration.mean
                        else:
                            comp_kcat[comp] = kcat    
                    if known_vmax < value and (value - known_vmax)/value > 0.01:

Avoid deeply nested control flow statements.

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                        if not proteasome_st:
                            proteasome_st = model.species_types.get_one(name=proteasome)
                        

Similar blocks of code found in 13 locations. Consider refactoring.

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            init_reaction.participants.append(metabolites['adp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=1))

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Avoid deeply nested control flow statements.

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                        for species in obs.expression.species:    
                            trans_species_counts[species.id] = species.distribution_init_concentration.mean

Avoid deeply nested control flow statements.

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                        if proteasome_species == self._rxn_species_modifier[reaction.id][0]:
                            modifier_reactants.append(proteasome_species)
                    

Similar blocks of code found in 13 locations. Consider refactoring.

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            init_reaction.participants.append(metabolites['amp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=1))

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Similar blocks of code found in 3 locations. Consider refactoring.

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                if modifier == self._rxn_species_modifier[reaction.id][0]:
                    modifier_reactants.append(modifier)

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Similar blocks of code found in 2 locations. Consider refactoring.

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                gvar.protein_aa_usage[mrna_kb.protein.id] = {i:0 for i in list(amino_acid_id_conversion.keys())}

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Similar blocks of code found in 2 locations. Consider refactoring.

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                        el_reaction.participants.append(metabolites['adp'][
                            translation_compartment.id].species_coefficients.get_or_create(

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Avoid deeply nested control flow statements.

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                        if species_init_conc:
                            species_init_conc.mean += flux * participant.coefficient
                            
                        else:
                            conc_model = model.distribution_init_concentrations.create(