def test_phospho_mod_grounding():
a = Agent('MEK1',
mods=[
ModCondition('phosphorylation', 'S', '218'),
ModCondition('phosphorylation', 'S', '222')
],
db_refs={'HGNC': '6840'})
b = Agent('ERK2', db_refs={'HGNC': '6871'})
a_phos = Agent('Foo',
mods=[ModCondition('phosphorylation', None, None)],
db_refs={'HGNC': '6840'})
st1 = Phosphorylation(a, b, 'T', '185')
pysb_asmb = pa.PysbAssembler([st1])
model = pysb_asmb.make_model(policies='one_step')
mps = list(pa.grounded_monomer_patterns(model, a_phos))
assert len(mps) == 2
assert mps[0].monomer.name == 'MEK1'
assert mps[1].monomer.name == 'MEK1'
sc = [mp.site_conditions for mp in mps]
assert {'S218': ('p', WILD)} in sc
assert {'S222': ('p', WILD)} in sc
# Check if we get the doubly phosphorylated MonomerPattern
mps = list(pa.grounded_monomer_patterns(model, a))
assert len(mps) == 1
assert mps[0].monomer.name == 'MEK1'
assert mps[0].site_conditions == {'S218': ('p', WILD), 'S222': ('p', WILD)}
def check_policy(policy):
pysb_asmb = pa.PysbAssembler([st1])
model = pysb_asmb.make_model(policies=policy)
mps = list(pa.grounded_monomer_patterns(model, b_phos))
assert len(mps) == 1
assert mps[0].monomer.name == 'ERK2'
assert mps[0].site_conditions == {'T185': ('p', WILD)}
def test_multiple_grounding_mods():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
cbl = Agent('CBL', db_refs={'HGNC': '1541'})
ub_phos_erk = Agent(
'ERK2',
mods=[ModCondition('phosphorylation', None, None),
ModCondition('ubiquitination', None, None)],
db_refs={'HGNC': '6871'})
st1 = Phosphorylation(mek, erk, 'T', '185')
st2 = Phosphorylation(mek, erk, 'Y', '187')
st3 = Ubiquitination(cbl, erk, 'K', '40')
st4 = Ubiquitination(cbl, erk, 'K', '50')
pysb_asmb = pa.PysbAssembler([st1, st2, st3, st4])
model = pysb_asmb.make_model(policies='one_step')
mps = list(pa.grounded_monomer_patterns(model, ub_phos_erk))
assert len(mps) == 4
assert mps[0].monomer.name == 'ERK2'
assert mps[1].monomer.name == 'ERK2'
assert mps[2].monomer.name == 'ERK2'
assert mps[3].monomer.name == 'ERK2'
def test_get_grounded_agents_from_model():
mek = Agent('MEK1', db_refs={'HGNC': '6840'})
erk = Agent('ERK2', db_refs={'HGNC': '6871'})
erk_phos = Agent('ERK2', db_refs={'HGNC': '6871'},
mods=[ModCondition('phosphorylation')])
erk_phos_y187 = Agent('ERK2', db_refs={'HGNC': '6871'},
mods=[ModCondition('phosphorylation', 'Y', '187')])
phos_stmt = Phosphorylation(mek, erk)
phos_y187_stmt = Phosphorylation(mek, erk, 'Y', '187')
pysba = pa.PysbAssembler([phos_stmt, phos_y187_stmt])
pysb_model = pysba.make_model()
agents_by_mp, mps_by_rule = pa.get_grounded_agents(pysb_model)
assert isinstance(agents_by_mp, dict)
assert isinstance(mps_by_rule, dict)
model_agents = agents_by_mp.values()
model_keys = set([ag.matches_key() for ag in model_agents])
# TODO add other types of agent conditions here
# TODO do we expect a different agent for af?
test_keys = set([mek.matches_key(), erk_phos.matches_key(),
erk_phos_y187.matches_key()])
assert len(model_keys.intersection(test_keys)) == 3