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)
