def test_cost_rules(self):
# prepare the cost model
g1 = mnm_repr.Gene('g1')
p1 = mnm_repr.Protein('p1')
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
cplx1 = mnm_repr.Complex('cplx1')
cytosol = mnm_repr.Cytosol()
cond1 = mnm_repr.PresentEntity(met1, cytosol)
cond2 = mnm_repr.PresentEntity(met2, cytosol)
cond3 = mnm_repr.PresentEntity(p1, cytosol)
cond4 = mnm_repr.PresentEntity(cplx1, cytosol)
growth = mnm_repr.Growth('growth', [cond2])
r1 = mnm_repr.Reaction('r1', [cond1], [cond2])
r2 = mnm_repr.Reaction('r2', [cond3], [cond4])
entities = [g1, p1, met1, met2, cplx1]
compartments = [cytosol]
activities = [growth, r1, r2]
setup_conds = [cond1, cond3]
model = CostModel(entities, compartments, activities, setup_conds)
model.set_all_basic_costs_to_1()
model.calculate_derived_costs(activities)
# test
out = exporter.cost_rules(model)
# self.assertIn('\ncost(1, 0) :- add(setup_present(met1, none, c_01)).', out)
self.assertEqual(len(out), 55)
def test_export_experiment_specification_elements(self):
# prepare the cost model
g1 = mnm_repr.Gene('g1')
p1 = mnm_repr.Protein('p1')
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
cplx1 = mnm_repr.Complex('cplx1')
cytosol = mnm_repr.Cytosol()
cond1 = mnm_repr.PresentEntity(met1, cytosol)
cond2 = mnm_repr.PresentEntity(met2, cytosol)
cond3 = mnm_repr.PresentEntity(p1, cytosol)
cond4 = mnm_repr.PresentEntity(cplx1, cytosol)
growth = mnm_repr.Growth('growth', [cond2])
r1 = mnm_repr.Reaction('r1', [cond1], [cond2])
r2 = mnm_repr.Reaction('r2', [cond3], [cond4])
entities = [g1, p1, met1, met2, cplx1]
compartments = [cytosol]
activities = [growth, r1, r2]
setup_conds = [cond1, cond3]
model = CostModel(entities, compartments, activities, setup_conds)
model.set_all_basic_costs_to_1()
model.calculate_derived_costs(activities)
# test
out = exporter.export_experiment_specification_elements(model)
self.assertEqual(len(out.keys()), 55)
self.assertNotIn(None, out.values())
def test_modeh_replacement(self):
# prepare the cost model
g1 = mnm_repr.Gene('g1')
p1 = mnm_repr.Protein('p1')
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
cplx1 = mnm_repr.Complex('cplx1')
cytosol = mnm_repr.Cytosol()
cond1 = mnm_repr.PresentEntity(met1, cytosol)
cond2 = mnm_repr.PresentEntity(met2, cytosol)
cond3 = mnm_repr.PresentEntity(p1, cytosol)
cond4 = mnm_repr.PresentEntity(cplx1, cytosol)
growth = mnm_repr.Growth('growth', [cond2])
r1 = mnm_repr.Reaction('r1', [cond1], [cond2])
r2 = mnm_repr.Reaction('r2', [cond3], [cond4])
entities = [g1, p1, met1, met2, cplx1]
compartments = [cytosol]
activities = [growth, r1, r2]
setup_conds = [cond1, cond3]
model = CostModel(entities, compartments, activities, setup_conds)
model.set_all_basic_costs_to_1()
model.calculate_derived_costs(activities)
# test
out = exporter.modeh_replacement(model)
self.assertIsInstance(out, str)
def test_export_entities_alone(self):
# get one of entity types; no need to test all (they do the same thing)
ent1 = mnm_repr.Gene('e1')
ent2 = mnm_repr.Metabolite('e2')
ent3 = mnm_repr.Protein('e3')
ent4 = mnm_repr.Complex('e4')
exported = exporter.export_entities([ent1, ent2, ent3, ent4])
self.assertEqual("\ngene(e1,none).", exported[0])
self.assertEqual("\nmetabolite(e2,none).", exported[1])
self.assertEqual("\nprotein(e3,none).", exported[2])
self.assertEqual("\ncomplex(e4,none).", exported[3])
def test_export_entities_properties(self):
# entity with properties to test the second part of the method
ent3 = mnm_repr.Protein(
'e3', 'none', 'none',
[mnm_repr.Catalyses(mnm_repr.Activity('a1', None, [], []))])
ent4 = mnm_repr.Complex(
'e4', 'none', 'none',
[mnm_repr.Transports(mnm_repr.Activity('a2', None, [], []))])
exported = exporter.export_entities([ent3, ent4])
self.assertEqual("\nprotein(e3,none).", exported[0])
self.assertEqual("\ncatalyses(e3,none,a1).", exported[1])
self.assertEqual("\ncomplex(e4,none).", exported[2])
self.assertEqual("\ntransports(e4,none,a2).", exported[3])