def test_add_reaction_with_former_unused_species(self): """ Tests if it we can add a new reaction using a species that was already defined in the model but was never present in any reaction. """ model = SBML() model.load_file("input/model_unused_species.xml") parameters = [{ "name": "kcat", "value": .5 }, { "name": "Km", "value": 5 }] new_reaction = Reaction (\ "unused --Rpp--> S", ["unused"], ["S"], ["Rpp"], \ parameters, "kcat * Rpp * unused / (Km + unused)") nof_species_before = len(model.get_species_list()) model.add_reaction(new_reaction) nof_species_after = len(model.get_species_list()) self.assertEqual(nof_species_after, nof_species_before)
def test_add_reaction(self): """ Tests if it is possible to add a reaction to an SBML model. """ model = SBML() model.load_file("input/model1_bioinformatics.xml") parameters = [{ "name": "kcat", "value": .5 }, { "name": "Km", "value": 5 }] new_reaction = Reaction("R --dS--> Rpp", ["R"], ["Rpp"], ["dS"], parameters, "kcat * dS * R / (Km + R)") model.add_reaction(new_reaction) all_formula = model.get_all_reaction_formulas() assert (new_reaction.formula in all_formula) # new products/reactants model = SBML() model.load_file("input/model1_bioinformatics.xml") new_reaction = Reaction("Dummy ---> Dummy2", ["Dummy"], ["Dummy2"], [], parameters, "kcat * Dummy / (Km + Dummy)") model.add_reaction(new_reaction) all_formula = model.get_all_reaction_formulas() assert (new_reaction.formula in all_formula) # new modifiers model = SBML() model.load_file("input/model1_bioinformatics.xml") new_reaction = Reaction("R --Dummy--> Rpp", ["R"], ["Rpp"], ["Dummy"], parameters, "kcat * Dummy * R / (Km + R)") model.add_reaction(new_reaction) all_formula = model.get_all_reaction_formulas() assert (new_reaction.formula in all_formula)