def __init__(self, parameter_values=None):
Model.__init__(self, name="chapter2")
self.volume = 1
# Parameters
self.add_parameter(Parameter(name="birth_A", expression="1"))
self.add_parameter(Parameter(name="birth_B", expression="0.1"))
self.add_parameter(Parameter(name="death_B", expression="0.05"))
# Variables
self.add_species(Species(name="A", initial_value=100, mode="discrete"))
self.add_species(Species(name="B", initial_value=0, mode="discrete"))
# Reactions
self.add_reaction(
Reaction(name="birthA",
reactants={},
products={'A': 1},
rate=self.listOfParameters["birth_A"]))
self.add_reaction(
Reaction(name="birthB",
reactants={'B': 1},
products={},
rate=self.listOfParameters["death_B"]))
self.add_reaction(
Reaction(name="birthC",
reactants={'A': 1},
products={'B': 1},
rate=self.listOfParameters["birth_B"]))
# Timespan
self.timespan(np.arange(0, 100, 1.0))
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=0.6))
## 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 build_specie(self, args, is_ode):
'''
Build a GillesPy2 species.
Atrributes
----------
args : dict
A json representation of a species.
'''
name = args['name'].strip()
value = args['value']
if not is_ode:
mode = args['mode']
else:
mode = 'continuous'
switch_tol = args['switchTol']
if args['isSwitchTol']:
switch_min = 0
else:
switch_min = args['switchMin']
return Species(name=name,
initial_value=value,
mode=mode,
switch_tol=switch_tol,
switch_min=switch_min)
def test__create_mass_action__species_obj_reactant(self):
""" Test Reaction._create_mass_action when reactants is keyed by species object. """
test_species = Species(name="A", initial_value=1)
self.valid_ma_reaction.reactants = {test_species: 1}
self.valid_ma_reaction._create_mass_action()
self.assertEqual(self.valid_ma_reaction.propensity_function, "(k1*A)")
self.assertEqual(self.valid_ma_reaction.ode_propensity_function,
"(k1*A)")
def test_constructor__products_keyed_by_species_obj(self):
""" Test the Reaction constructor with products keyed by species objs. """
test_species = Species(name="B", initial_value=0)
reaction = Reaction(name="test_reaction",
reactants={"A": 1},
products={test_species: 1},
rate="k2")
self.assertEqual(reaction.products, {"B": 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 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)