Exemplo n.º 1
0
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)
Exemplo n.º 2
0
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
Exemplo n.º 3
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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
Exemplo n.º 4
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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
Exemplo n.º 5
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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
Exemplo n.º 6
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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)
Exemplo n.º 7
0
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)