def test_reaction_mass_balance(read_only_model): """ Expect all reactions to be mass balanced. This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a formula defined. In steady state, for each metabolite the sum of influx equals the sum of outflux. Hence the net masses of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a charge are not considered to be balanced, even though the remaining metabolites participating in the reaction might be. """ ann = test_reaction_mass_balance.annotation internal_rxns = con_helpers.get_internals(read_only_model) ann["data"] = get_ids( consistency.find_mass_unbalanced_reactions(internal_rxns) ) ann["metric"] = len(ann["data"]) / len(internal_rxns) ann["message"] = wrapper.fill( """A total of {} ({:.2%}) reactions are mass unbalanced with at least one of the metabolites not having a formula or the overall mass not equal to 0: {}""".format( len(ann["data"]), ann["metric"], truncate(ann["data"]))) assert len(ann["data"]) == 0, ann["message"]
def test_reaction_mass_balance(model): """ Expect all reactions to be mass balanced. This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a formula defined. In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net masses of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a formula are not considered to be balanced, even though the remaining metabolites participating in the reaction might be. Implementation: For each reaction that isn't a boundary or biomass reaction check if each metabolite has a non-zero elements attribute and if so calculate if the overall element balance of reactants and products is equal to zero. """ ann = test_reaction_mass_balance.annotation internal_rxns = con_helpers.get_internals(model) ann["data"] = get_ids( consistency.find_mass_unbalanced_reactions(internal_rxns)) ann["metric"] = len(ann["data"]) / len(internal_rxns) ann["message"] = wrapper.fill( """A total of {} ({:.2%}) reactions are mass unbalanced with at least one of the metabolites not having a formula or the overall mass not equal to 0: {}""".format(len(ann["data"]), ann["metric"], truncate(ann["data"]))) assert len(ann["data"]) == 0, ann["message"]
def test_reaction_mass_balance(model): """ Expect all reactions to be mass balanced. This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a formula defined. In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net masses of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a formula are not considered to be balanced, even though the remaining metabolites participating in the reaction might be. Implementation: For each reaction that isn't a boundary or biomass reaction check if each metabolite has a non-zero elements attribute and if so calculate if the overall element balance of reactants and products is equal to zero. """ ann = test_reaction_mass_balance.annotation internal_rxns = con_helpers.get_internals(model) ann["data"] = get_ids( consistency.find_mass_unbalanced_reactions(internal_rxns) ) ann["metric"] = len(ann["data"]) / len(internal_rxns) ann["message"] = wrapper.fill( """A total of {} ({:.2%}) reactions are mass unbalanced with at least one of the metabolites not having a formula or the overall mass not equal to 0: {}""".format( len(ann["data"]), ann["metric"], truncate(ann["data"]))) assert len(ann["data"]) == 0, ann["message"]
def test_find_mass_unbalanced_reactions(model, num): """Expect all reactions to be mass balanced.""" internal_rxns = con_helpers.get_internals(model) reactions = consistency.find_mass_unbalanced_reactions(internal_rxns) assert len(reactions) == num
def test_find_mass_unbalanced_reactions(model, num): """Expect all reactions to be mass balanced.""" internal_rxns = con_helpers.get_internals(model) reactions = consistency.find_mass_unbalanced_reactions(internal_rxns) assert len(reactions) == num