def test_get_mp_with_grounding_2():
a1 = Agent('A',
mods=[ModCondition('phosphorylation', None, None)],
db_refs={'HGNC': '6840'})
a2 = Agent('A',
mods=[ModCondition('phosphorylation', 'Y', '187')],
db_refs={'HGNC': '6840'})
Monomer('A_monomer', ['phospho', 'T185', 'Y187'], {
'phospho': 'y',
'T185': ['u', 'p'],
'Y187': ['u', 'p']
})
Annotation(A_monomer, 'http://identifiers.org/hgnc/HGNC:6840')
A_monomer.site_annotations = [
Annotation(('phospho', 'y'), 'phosphorylation', 'is_modification'),
Annotation(('T185', 'p'), 'phosphorylation', 'is_modification'),
Annotation(('Y187', 'p'), 'phosphorylation', 'is_modification'),
Annotation('T185', 'T', 'is_residue'),
Annotation('T185', '185', 'is_position'),
Annotation('Y187', 'Y', 'is_residue'),
Annotation('Y187', '187', 'is_position')
]
mps_1 = list(pa.grounded_monomer_patterns(model, a1))
assert len(mps_1) == 3
mps_2 = list(pa.grounded_monomer_patterns(model, a2))
assert len(mps_2) == 1
mp = mps_2[0]
assert mp.monomer == A_monomer
assert mp.site_conditions == {'Y187': ('p', WILD)}
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(policies='one_step')
pysb_asmb.add_statements([st1])
model = pysb_asmb.make_model()
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 test_get_mp_with_grounding():
foo = Agent('Foo', db_refs={'HGNC': 'foo'})
a = Agent('A', db_refs={'HGNC': '6840'})
b = Agent('B', db_refs={'HGNC': '6871'})
Monomer('A_monomer')
Monomer('B_monomer')
Annotation(A_monomer, 'http://identifiers.org/hgnc/HGNC:6840')
Annotation(B_monomer, 'http://identifiers.org/hgnc/HGNC:6871')
mps = list(pa.grounded_monomer_patterns(model, foo))
assert len(mps) == 0
mps = list(pa.grounded_monomer_patterns(model, a))
assert len(mps) == 1
assert mps[0].monomer == A_monomer
mps = list(pa.grounded_monomer_patterns(model, b))
assert len(mps) == 1
assert mps[0].monomer == B_monomer
def _check_modification(self, stmt, max_paths, max_path_length):
"""Check a Modification statement."""
# Identify the observable we're looking for in the model, which
# may not exist!
# The observable is the modified form of the substrate
logger.info('Checking stmt: %s' % stmt)
# Look for an agent with the appropriate grounding in the model
if stmt.enz is not None:
enz_mps = list(pa.grounded_monomer_patterns(self.model, stmt.enz))
if not enz_mps:
logger.debug('No monomers found corresponding to agent %s' %
stmt.enz)
return PathResult(False, 'SUBJECT_MONOMERS_NOT_FOUND',
max_paths, max_path_length)
else:
enz_mps = [None]
# Get target polarity
target_polarity = -1 if isinstance(stmt, RemoveModification) else 1
obs_names = self.stmt_to_obs[stmt]
if not obs_names:
logger.debug("No observables for stmt %s, returning False" % stmt)
return PathResult(False, 'OBSERVABLES_NOT_FOUND', max_paths,
max_path_length)
for enz_mp, obs_name in itertools.product(enz_mps, obs_names):
# FIXME Returns on the path found for the first enz_mp/obs combo
result = self._find_im_paths(enz_mp, obs_name, target_polarity,
max_paths, max_path_length)
# If result for this observable is not False, then we return it;
# otherwise, that means there was no path for this observable, so
# we have to try the next one
if result.path_found:
return result
# If we got here, then there was no path for any observable
return PathResult(False, 'NO_PATHS_FOUND', max_paths, max_path_length)
def test_get_mp_with_grounding():
foo = Agent('Foo', db_refs={'HGNC': 'foo'})
a = Agent('A', db_refs={'HGNC': '6840'})
b = Agent('B', db_refs={'HGNC': '6871'})
Monomer('A_monomer')
Monomer('B_monomer')
Annotation(A_monomer, 'http://identifiers.org/hgnc/HGNC:6840')
Annotation(B_monomer, 'http://identifiers.org/hgnc/HGNC:6871')
mps = list(pa.grounded_monomer_patterns(model, foo))
assert len(mps) == 0
mps = list(pa.grounded_monomer_patterns(model, a))
assert len(mps) == 1
assert mps[0].monomer == A_monomer
mps = list(pa.grounded_monomer_patterns(model, b))
assert len(mps) == 1
assert mps[0].monomer == B_monomer
def check_policy(policy):
pysb_asmb = pa.PysbAssembler(policies=policy)
pysb_asmb.add_statements([st1])
model = pysb_asmb.make_model()
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 check_policy(policy):
pysb_asmb = pa.PysbAssembler(policies=policy)
pysb_asmb.add_statements([st1])
model = pysb_asmb.make_model()
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 _check_modification(self, stmt):
"""Check a Modification statement."""
# Identify the observable we're looking for in the model, which
# may not exist!
# The observable is the modified form of the substrate
logger.info('Checking stmt: %s' % stmt)
# Look for an agent with the appropriate grounding in the model
if stmt.enz is not None:
enz_mps = list(pa.grounded_monomer_patterns(self.model, stmt.enz))
if not enz_mps:
logger.info('No monomers found corresponding to agent %s' %
stmt.enz)
return False
else:
enz_mps = [None]
# Get target polarity
demodify_list = (Dephosphorylation, Dehydroxylation, Desumoylation,
Deacetylation, Deglycosylation, Deribosylation,
Deubiquitination, Defarnesylation)
target_polarity = -1 if type(stmt) in demodify_list else 1
# Add modification to substrate agent
# TODO TODO TODO: Should be updated to get a valid mod condition name
mod_condition_name = stmt.__class__.__name__.lower()
if mod_condition_name.startswith('de'):
mod_condition_name = mod_condition_name[2:]
# TODO TODO TODO
modified_sub = _add_modification_to_agent(stmt.sub, mod_condition_name,
stmt.residue, stmt.position)
obs_name = pa.get_agent_rule_str(modified_sub) + '_obs'
obj_mps = list(pa.grounded_monomer_patterns(self.model, modified_sub))
if not obj_mps:
logger.info('Failed to create observable; returning False')
return False
# Try to find paths between pairs of matching subj and object monomer
# patterns
for enz_mp, obj_mp in itertools.product(enz_mps, obj_mps):
obj_obs = Observable(obs_name, obj_mp, _export=False)
# Return True for the first valid path we find
if self._find_im_paths(enz_mp, obj_obs, target_polarity):
return True
# If we got here, then there was no path for any observable
return False
def _check_modification(self, stmt):
"""Check a Modification statement."""
# Identify the observable we're looking for in the model, which
# may not exist!
# The observable is the modified form of the substrate
logger.info('Checking stmt: %s' % stmt)
# Look for an agent with the appropriate grounding in the model
if stmt.enz is not None:
enz_mps = list(pa.grounded_monomer_patterns(self.model, stmt.enz))
if not enz_mps:
logger.info('No monomers found corresponding to agent %s' %
stmt.enz)
return False
else:
enz_mps = [None]
# Get target polarity
demodify_list = (Dephosphorylation, Dehydroxylation, Desumoylation,
Deacetylation, Deglycosylation, Deribosylation,
Deubiquitination, Defarnesylation)
target_polarity = -1 if type(stmt) in demodify_list else 1
# Add modification to substrate agent
# TODO TODO TODO: Should be updated to get a valid mod condition name
mod_condition_name = stmt.__class__.__name__.lower()
if mod_condition_name.startswith('de'):
mod_condition_name = mod_condition_name[2:]
# TODO TODO TODO
modified_sub = _add_modification_to_agent(stmt.sub, mod_condition_name,
stmt.residue, stmt.position)
obs_name = pa.get_agent_rule_str(modified_sub) + '_obs'
obj_mps = list(pa.grounded_monomer_patterns(self.model, modified_sub))
if not obj_mps:
logger.info('Failed to create observable; returning False')
return False
# Try to find paths between pairs of matching subj and object monomer
# patterns
for enz_mp, obj_mp in itertools.product(enz_mps, obj_mps):
obj_obs = Observable(obs_name, obj_mp, _export=False)
# Return True for the first valid path we find
if self._find_im_paths(enz_mp, obj_obs, target_polarity):
return True
# If we got here, then there was no path for any observable
return False
def test_grounded_active_pattern():
a = Agent('A', db_refs={'HGNC': '1234'})
b = Agent('B', db_refs={'HGNC': '5678'})
b_phos = Agent('B', mods=[ModCondition('phosphorylation', 'S', '100')],
db_refs={'HGNC': '5678'})
b_act = Agent('B', activity=ActivityCondition('activity', True),
db_refs={'HGNC': '5678'})
st1 = Phosphorylation(a, b, 'S', '100')
st2 = ActiveForm(b_phos, 'activity', True)
pysba = PysbAssembler(policies='one_step')
pysba.add_statements([st1, st2])
model = pysba.make_model()
mps = list(pa.grounded_monomer_patterns(model, b_act))
def test_get_mp_with_grounding_2():
a1 = Agent('A', mods=[ModCondition('phosphorylation', None, None)],
db_refs={'HGNC': '6840'})
a2 = Agent('A', mods=[ModCondition('phosphorylation', 'Y', '187')],
db_refs={'HGNC': '6840'})
Monomer('A_monomer', ['phospho', 'T185', 'Y187'],
{'phospho': 'y', 'T185':['u', 'p'], 'Y187':['u','p']})
Annotation(A_monomer, 'http://identifiers.org/hgnc/HGNC:6840')
A_monomer.site_annotations = [
Annotation(('phospho', 'y'), 'phosphorylation', 'is_modification'),
Annotation(('T185', 'p'), 'phosphorylation', 'is_modification'),
Annotation(('Y187', 'p'), 'phosphorylation', 'is_modification'),
Annotation('T185', 'T', 'is_residue'),
Annotation('T185', '185', 'is_position'),
Annotation('Y187', 'Y', 'is_residue'),
Annotation('Y187', '187', 'is_position')
]
mps_1 = list(pa.grounded_monomer_patterns(model, a1))
assert len(mps_1) == 3
mps_2 = list(pa.grounded_monomer_patterns(model, a2))
assert len(mps_2) == 1
mp = mps_2[0]
assert mp.monomer == A_monomer
assert mp.site_conditions == {'Y187': ('p', WILD)}
def add_obs_for_agent(agent):
obj_mps = list(pa.grounded_monomer_patterns(self.model, agent))
if not obj_mps:
logger.debug('No monomer patterns found in model for agent %s, '
'skipping' % agent)
return
obs_list = []
for obj_mp in obj_mps:
obs_name = _monomer_pattern_label(obj_mp) + '_obs'
# Add the observable
obj_obs = Observable(obs_name, obj_mp, _export=False)
obs_list.append(obs_name)
try:
self.model.add_component(obj_obs)
except ComponentDuplicateNameError as e:
pass
return obs_list
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(policies='one_step')
pysb_asmb.add_statements([st1])
model = pysb_asmb.make_model()
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
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(policies='one_step')
pysb_asmb.add_statements([st1, st2, st3, st4])
model = pysb_asmb.make_model()
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'
