def test_remove_reaction(self): """ Tests if it is possible to remove a reaction from an SBML model. """ model = SBML() model.load_file("input/model1_bioinformatics.xml") model.remove_reaction("reaction_0") removed_formula = "compartment * k1 * S" all_formula = model.get_all_reaction_formulas() assert (removed_formula not in all_formula)
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)