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 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()
def _():
with test_model:
add_loopless(test_model)
test_model.optimize()