def test_missing_monomer_condition():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
entity = Agent('HRAS')
quantity = tra.MolecularQuantityReference('total', entity)
condition = tra.MolecularCondition('multiple', quantity, 10)
tra.apply_condition(model, condition)
def test_assemble_model_chemical_agents():
stmts = [
Activation(Agent('BRAF'), Agent('KRAS')),
Inhibition(Agent('DRUG', db_refs={'CHEBI': '123'}), Agent('BRAF'))
]
model = tra_module.assemble_model(stmts)
assert model.parameters['DRUG_0'].value == 10000.0
def test_assemble_model_targeted_agents():
stmts = [
Activation(Agent('BRAF'), Agent('KRAS')),
Inhibition(Agent('DRUG'), Agent('BRAF'))
]
model = tra_module.assemble_model(stmts)
assert model.parameters['BRAF_0'].value == 50.0
assert model.parameters['BRAF_0_mod'].value == 50.0
def test_assemble_model_no_upstream_active():
stmts = [
Phosphorylation(
Agent('MEK', activity=ActivityCondition('activity', True)),
Agent('ERK'))
]
model = tra_module.assemble_model(stmts)
assert model.parameters['MEK_0'].value == 50.0
assert model.parameters['MEK_0_mod'].value == 50.0
def test_seq_hyp_test():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
entity = Agent('KRAS', activity=ActivityCondition('activity', True))
quantity = tra.MolecularQuantityReference('total', entity)
quant = tra.MolecularQuantity('qualitative', 'high')
pattern = tra.TemporalPattern('sometime_value', [entity],
None,
value=quant)
t = tra.TRA()
from bioagents.tra.model_checker import HypothesisTester
ht = HypothesisTester(alpha=0.1, beta=0.1, delta=0.05, prob=0.8)
res = t.check_property(model,
pattern,
conditions=None,
max_time=20000,
num_times=100,
hypothesis_tester=ht)
sat_rate, num_sim, kpat, pat_obj, fig_path = res
assert sat_rate == 1.0
assert num_sim == 18
def test_missing_monomer_site():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
mc = ModCondition('phosphorylation', None, None, True)
agent = Agent('KRAS', mods=[mc])
tra.get_create_observable(model, agent)
def test_missing_monomer():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
agent = Agent('RAS')
tra.get_create_observable(model, agent)