def apply_condition(model, condition):
agent = condition.quantity.entity
monomer = model.monomers[pa._n(agent.name)]
site_pattern = pa.get_site_pattern(agent)
# TODO: handle modified patterns
if site_pattern:
logger.warning('Cannot handle initial conditions on' +
' modified monomers.')
if condition.condition_type == 'exact':
ic_name = monomer.name + '_0'
if condition.value.quant_type == 'number':
pa.set_base_initial_condition(model, monomer,
condition.value.value)
else:
logger.warning('Cannot handle non-number initial conditions')
elif condition.condition_type == 'multiple':
# TODO: refer to annotations for the IC name
ic_name = monomer.name + '_0'
model.parameters[ic_name].value *= condition.value
elif condition.condition_type == 'decrease':
ic_name = monomer.name + '_0'
model.parameters[ic_name].value *= 0.9
elif condition.condition_type == 'increase':
ic_name = monomer.name + '_0'
model.parameters[ic_name].value *= 1.1
logger.info('New initial condition: %s' % model.parameters[ic_name])
def get_create_observable(model, agent):
site_pattern = pa.get_site_pattern(agent)
obs_name = pa.get_agent_rule_str(agent) + '_obs'
monomer = model.monomers[pa._n(agent.name)]
obs = Observable(obs_name.encode('utf-8'), monomer(site_pattern))
model.add_component(obs)
return obs
def _check_regulate_activity(self, stmt):
"""Check a RegulateActivity statement."""
logger.info('Checking stmt: %s' % stmt)
# FIXME Currently this will match rules with the corresponding monomer
# pattern from the Activation/Inhibition statement, which will nearly
# always have no state conditions on it. In future, this statement foo
# should also match rules in which 1) the agent is in its active form,
# or 2) the agent is tagged as the enzyme in a rule of the appropriate
# activity (e.g., a phosphorylation rule) FIXME
subj_mp = pa.get_monomer_pattern(self.model, stmt.subj)
target_polarity = 1 if stmt.is_activation else -1
# This may fail, since there may be no rule in the model activating the
# object, and the object may not have an "active" site of the
# appropriate type
obj_obs_name = pa.get_agent_rule_str(stmt.obj) + '_obs'
try:
obj_site_pattern = pa.get_site_pattern(stmt.obj)
obj_site_pattern.update({stmt.obj_activity: 'active'})
obj_monomer = self.model.monomers[stmt.obj.name]
obj_mp = obj_monomer(**obj_site_pattern)
except Exception as e:
logger.info("Could not create obj monomer pattern: %s" % e)
return False
obj_obs = Observable(obj_obs_name, obj_mp, _export=False)
return self._find_im_paths(subj_mp, obj_obs, target_polarity)
def _check_regulate_activity(self, stmt):
"""Check a RegulateActivity statement."""
logger.info('Checking stmt: %s' % stmt)
# FIXME Currently this will match rules with the corresponding monomer
# pattern from the Activation/Inhibition statement, which will nearly
# always have no state conditions on it. In future, this statement foo
# should also match rules in which 1) the agent is in its active form,
# or 2) the agent is tagged as the enzyme in a rule of the appropriate
# activity (e.g., a phosphorylation rule) FIXME
subj_mp = pa.get_monomer_pattern(self.model, stmt.subj)
target_polarity = 1 if stmt.is_activation else -1
# This may fail, since there may be no rule in the model activating the
# object, and the object may not have an "active" site of the
# appropriate type
obj_obs_name = pa.get_agent_rule_str(stmt.obj) + '_obs'
try:
obj_site_pattern = pa.get_site_pattern(stmt.obj)
obj_site_pattern.update({stmt.obj_activity: 'active'})
obj_monomer = self.model.monomers[stmt.obj.name]
obj_mp = obj_monomer(**obj_site_pattern)
except Exception as e:
logger.info("Could not create obj monomer pattern: %s" % e)
return False
obj_obs = Observable(obj_obs_name, obj_mp, _export=False)
return self._find_im_paths(subj_mp, obj_obs, target_polarity)
def get_create_observable(model, agent):
site_pattern = pa.get_site_pattern(agent)
obs_name = pa.get_agent_rule_str(agent) + '_obs'
monomer = model.monomers[agent.name]
obs = Observable(obs_name, monomer(site_pattern))
model.add_component(obs)
return obs
def apply_condition(model, condition):
agent = condition.quantity.entity
monomer = model.monomers[agent.name]
site_pattern = pa.get_site_pattern(agent)
# TODO: handle modified patterns
if site_pattern:
logger.warning('Cannot handle initial conditions on' +
' modified monomers.')
if condition.condition_type == 'exact':
ic_name = monomer.name + '_0'
if condition.value.quant_type == 'number':
pa.set_base_initial_condition(model, monomer,
condition.value.value)
else:
logger.warning('Cannot handle non-number initial conditions')
elif condition.condition_type == 'multiple':
# TODO: refer to annotations for the IC name
ic_name = monomer.name + '_0'
model.parameters[ic_name].value *= condition.value
elif condition.condition_type == 'decrease':
ic_name = monomer.name + '_0'
model.parameters[ic_name].value *= 0.9
elif condition.condition_type == 'increase':
ic_name = monomer.name + '_0'
model.parameters[ic_name].value *= 1.1
logger.info('New initial condition: %s' % model.parameters[ic_name])
def get_create_observable(model, agent):
site_pattern = pa.get_site_pattern(agent)
obs_name = pa.get_agent_rule_str(agent) + '_obs'
try:
monomer = model.monomers[pa._n(agent.name)]
except KeyError:
raise MissingMonomerError('%s is not in the model ' % agent.name)
try:
monomer_state = monomer(site_pattern)
except Exception as e:
msg = 'Site pattern %s invalid for monomer %s' % \
(site_pattern, monomer.name)
raise MissingMonomerSiteError(msg)
obs = Observable(obs_name, monomer(site_pattern))
model.add_component(obs)
return obs
