def testRun(self):
model = load_sbml_model(SMALL_TEST_MODEL, kind=GPR_CONSTRAINED)
fix_bigg_model(model)
make_irreversible(model)
self.assertTrue(all([not reaction.reversible for reaction in model.reactions.values()]))
solution = FBA(model)
self.assertEqual(solution.status, Status.OPTIMAL)
self.assertAlmostEqual(solution.fobj, GROWTH_RATE, places=2)
def transform(model, inplace=True):
if not inplace:
model = model.copy()
mapping_rev = make_irreversible(model)
mapping_iso = split_isozymes(model)
u_reactions = genes_to_species(model)
model.convert_fluxes = lambda x, net=True: merge_fluxes(x, mapping_rev, mapping_iso, net)
model.convert_constraints = lambda x: convert_constraints(x, mapping_rev, mapping_iso)
return model
def testRun(self):
model = load_sbml_model(SMALL_TEST_MODEL, kind=GPR_CONSTRAINED)
fix_bigg_model(model)
simplify(model)
make_irreversible(model)
simplify(model) #remove directionally blocked reactions
model2 = load_sbml_model(SMALL_TEST_MODEL, kind=GPR_CONSTRAINED)
fix_bigg_model(model2)
make_irreversible(model2)
simplify(model2)
self.assertEqual(model.id, model2.id)
self.assertListEqual(model.metabolites.keys(), model2.metabolites.keys())
self.assertListEqual(model.reactions.keys(), model2.reactions.keys())
self.assertDictEqual(model.stoichiometry, model2.stoichiometry)
self.assertDictEqual(model.bounds, model2.bounds)
self.assertListEqual(model.genes.keys(), model2.genes.keys())
self.assertDictEqual(model.rules, model2.rules)
def transform(model, inplace=True):
if not inplace:
model = model.copy()
mapping_rev = make_irreversible(model)
mapping_iso = split_isozymes(model)
u_reactions = genes_to_species(model)
model.convert_fluxes = lambda x, net=True: merge_fluxes(
x, mapping_rev, mapping_iso, net)
model.convert_constraints = lambda x: convert_constraints(
x, mapping_rev, mapping_iso)
return model
