def test_add_loopless(ll_test_model): """Test add_loopless().""" add_loopless(ll_test_model) feasible_status = ll_test_model.optimize().status ll_test_model.reactions.v3.lower_bound = 1 ll_test_model.slim_optimize() infeasible_status = ll_test_model.solver.status assert feasible_status == OPTIMAL assert infeasible_status == INFEASIBLE
def capitulo_8(): file = open("resultados_capitulo_8.txt", "w") salmonella = cobra.test.create_test_model('salmonella') nominal = salmonella.optimize() loopless = loopless_solution(salmonella) import pandas df = pandas.DataFrame( dict(loopless=loopless.fluxes, nominal=nominal.fluxes)) df.plot.scatter(x='loopless', y='nominal') model = Model() model.add_metabolites([Metabolite(i) for i in "ABC"]) model.add_reactions( [Reaction(i) for i in ["EX_A", "DM_C", "v1", "v2", "v3"]]) model.reactions.EX_A.add_metabolites({"A": 1}) model.reactions.DM_C.add_metabolites({"C": -1}) model.reactions.v1.add_metabolites({"A": -1, "B": 1}) model.reactions.v2.add_metabolites({"B": -1, "C": 1}) model.reactions.v3.add_metabolites({"C": -1, "A": 1}) model.objective = 'DM_C' with model: add_loopless(model) solution = model.optimize() file.write("loopless solution: status = " + solution.status) file.write("\n") file.write("loopless solution flux: v3 = %.1f" % solution.fluxes["v3"]) file.write("\n") solution = pfba(model) file.write("parsimonious solution: status = " + solution.status) file.write("\n") file.write("loopless solution flux: v3 = %.1f" % solution.fluxes["v3"]) file.write("\n") model.reactions.v3.lower_bound = 1 with model: add_loopless(model) try: solution = model.optimize() except: file.write('model is infeasible') file.write("\n") solution = pfba(model) file.write("parsimonious solution: status = " + solution.status) file.write("\n") file.write("loopless solution flux: v3 = %.1f" % solution.fluxes["v3"]) file.write("\n") file.close()
def _(): with test_model: add_loopless(test_model) test_model.optimize()