def test_constructor__reactants_keyed_by_species_obj(self):
""" Test the Reaction constructor with reactants keyed by species objs. """
test_species = Species(name="A", initial_value=0)
reaction = Reaction(name="test_reaction",
reactants={test_species: 1},
products={"B": 1},
rate="k2")
self.assertEqual(reaction.reactants, {"A": 1})
def test_add_reactant__customized_reaction_species_object(self):
""" Test Reaction.add_reactant when reaction is customized and species is GillesPy2.Species. """
test_species = Species(name="X", initial_value=1)
self.valid_cp_reaction.add_reactant(test_species, 1)
self.assertIn(test_species.name, self.valid_cp_reaction.reactants)
self.assertEqual(self.valid_cp_reaction.reactants[test_species.name],
1)
self.assertEqual(self.valid_cp_reaction.propensity_function, "(k1*A)")
self.assertEqual(self.valid_cp_reaction.ode_propensity_function,
"(k1*A)")
def test_add_reactant__massaction_reaction_species_object(self):
""" Test Reaction.add_reactant when reaction is mass-action and species is GillesPy2.Species. """
test_species = Species(name="X", initial_value=1)
self.valid_ma_reaction.add_reactant(test_species, 1)
self.assertIn(test_species.name, self.valid_ma_reaction.reactants)
self.assertEqual(self.valid_ma_reaction.reactants[test_species.name],
1)
self.assertEqual(self.valid_ma_reaction.propensity_function,
f"(((k1*A)*{test_species.name})/vol)")
self.assertEqual(self.valid_ma_reaction.ode_propensity_function,
f"((k1*A)*{test_species.name})")
def __init__(self, parameter_values=None):
Model.__init__(self, name="lotka_volterra")
self.volume = 1
# Parameters
self.add_parameter(Parameter(name="k1", expression=1.0))
self.add_parameter(Parameter(name="k2", expression=0.005))
self.add_parameter(Parameter(name="k3", expression=1.0))
# Species
self.add_species(Species(name='prey', initial_value = 100, mode = 'discrete'))
self.add_species(Species(name='predator', initial_value = 100, mode = 'discrete'))
# Reactions
self.add_reaction(Reaction(name="r1", reactants = {'prey' : 1}, products = {'prey' : 2}, rate = self.listOfParameters['k1']))
self.add_reaction(Reaction(name="r2", reactants = {'predator' : 1, 'prey' : 1}, products = {'predator' : 2}, rate = self.listOfParameters['k2']))
self.add_reaction(Reaction(name="r3", reactants = {'predator' : 1}, products = {}, rate = self.listOfParameters['k3']))
# Timespan
self.timespan(np.linspace(0, 50, 51))
def test_model_add__species(self):
from gillespy2 import Species
s3 = Species(name="s3", initial_value=29)
self.model.add(s3)
self.assertIn("s3", self.model.listOfSpecies)
def test_add_product__species_object(self):
""" Test Reaction.add_product when species is GillesPy2.Species. """
test_species = Species(name="X", initial_value=1)
self.valid_ma_reaction.add_product(test_species, 1)
self.assertIn(test_species.name, self.valid_ma_reaction.products)
self.assertEqual(self.valid_ma_reaction.products[test_species.name], 1)