def test_name_standardize():
n = pa._n('.*/- ^&#@$')
assert(isinstance(n, str))
assert(n == '__________')
n = pa._n('14-3-3')
assert(isinstance(n, str))
assert(n == 'p14_3_3')
n = pa._n('\U0001F4A9bar')
assert(isinstance(n, str))
assert(n == 'bar')
def test_name_standardize():
n = pa._n('.*/- ^&#@$')
assert(isinstance(n, str))
assert(n == '__________')
n = pa._n('14-3-3')
assert(isinstance(n, str))
assert(n == 'p14_3_3')
n = pa._n('\U0001F4A9bar')
assert(isinstance(n, str))
assert(n == 'bar')
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 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_chemical_agents(stmts):
chemicals = set()
for stmt in stmts:
for agent in stmt.agent_list():
if agent is not None and ('CHEBI' in agent.db_refs or
'PC' in agent.db_refs):
chemicals.add(pysb_assembler._n(agent.name))
return list(chemicals)
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