def testRun(self):
model = load_cbmodel(SMALL_TEST_MODEL, flavor='cobra')
simplify(model)
make_irreversible(model)
simplify(model) #remove directionally blocked reactions
model2 = load_cbmodel(SMALL_TEST_MODEL, flavor='cobra')
make_irreversible(model2)
simplify(model2)
self.assertEqual(model.id, model2.id)
self.assertListEqual(list(model.metabolites.keys()),
list(model2.metabolites.keys()))
self.assertListEqual(list(model.reactions.keys()),
list(model2.reactions.keys()))
self.assertListEqual(list(model.genes.keys()),
list(model2.genes.keys()))
for r1, r2 in zip(list(model.reactions.values()),
list(model2.reactions.values())):
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.reversible, r2.reversible)
self.assertDictEqual(r1.stoichiometry, r2.stoichiometry)
self.assertEqual(r1.lb, r2.lb)
self.assertEqual(r1.ub, r2.ub)
self.assertEqual(str(r1.gpr), str(r2.gpr))
self.assertSetEqual(set(model.genes.keys()), set(model2.genes.keys()))
def testRun(self):
model = load_cbmodel(SMALL_TEST_MODEL, flavor='cobra')
simplify(model)
make_irreversible(model)
simplify(model) #remove directionally blocked reactions
model2 = load_cbmodel(SMALL_TEST_MODEL, flavor='cobra')
make_irreversible(model2)
simplify(model2)
self.assertEqual(model.id, model2.id)
self.assertListEqual(list(model.metabolites.keys()), list(model2.metabolites.keys()))
self.assertListEqual(list(model.reactions.keys()), list(model2.reactions.keys()))
self.assertListEqual(list(model.genes.keys()), list(model2.genes.keys()))
for r1, r2 in zip(list(model.reactions.values()), list(model2.reactions.values())):
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.reversible, r2.reversible)
self.assertDictEqual(r1.stoichiometry, r2.stoichiometry)
self.assertEqual(r1.lb, r2.lb)
self.assertEqual(r1.ub, r2.ub)
self.assertEqual(str(r1.gpr), str(r2.gpr))
self.assertSetEqual(set(model.genes.keys()), set(model2.genes.keys()))
def testRun(self):
model = load_cbmodel(SMALL_TEST_MODEL, flavor='cobra')
simplify(model)
solution = FBA(model)
self.assertEqual(solution.status, Status.OPTIMAL)
self.assertAlmostEqual(solution.fobj, GROWTH_RATE, places=2)
def testRun(self):
model = load_cbmodel(SMALL_TEST_MODEL, flavor='cobra')
simplify(model)
solution = FBA(model)
self.assertEqual(solution.status, Status.OPTIMAL)
self.assertAlmostEqual(solution.fobj, GROWTH_RATE, places=2)