def assemble_model(stmts):
pa = PysbAssembler(policies='one_step')
pa.add_statements(stmts)
model = pa.make_model()
pa.add_default_initial_conditions(100.0)
try:
targeted_agents = get_targeted_agents(stmts)
no_upstream_active_agents = get_no_upstream_active_agents(stmts)
except:
targeted_agents = []
no_upstream_active_agents = []
try:
chemical_agents = get_chemical_agents(stmts)
except:
chemical_agents = []
for m in model.monomers:
try:
if m.name in targeted_agents or m.name in no_upstream_active_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 50.0)
pysb_assembler.set_extended_initial_condition(model, m, 50.0)
elif m.name in chemical_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 10000.0)
else:
pysb_assembler.set_extended_initial_condition(model, m, 0)
except:
pysb_assembler.set_extended_initial_condition(model, m, 0)
# Tweak parameters
for param in model.parameters:
if 'kf' in param.name and 'bind' in param.name:
param.value = param.value * 100
return model
def replace_agent(self, agent_name, agent_replacement_names, model_id):
"""Replace an agent in a model with other agents.
This is used, for instance, to expand a protein family to
multiple specific proteins.
"""
for stmt in self.statements[model_id - 1]:
agent_key = [
i for i, m in enumerate(stmt.agent_list())
if m is not None and m.name == agent_name
]
if agent_key:
self.statements[model_id - 1].remove(stmt)
for p in agent_replacement_names:
s = copy.deepcopy(stmt)
if isinstance(stmt, Complex):
s.members[agent_key[0]].name = p
else:
s.__dict__[agent_key[0]].name = p
self.extend_statements([s], model_id)
pa = PysbAssembler()
pa.add_statements(self.statements[model_id - 1])
model = pa.make_model()
pa.add_default_initial_conditions(self.default_initial_amount)
return model
def assemble_model(model_indra_str):
stmts = decode_indra_stmts(model_indra_str)
pa = PysbAssembler(policies='two_step')
pa.add_statements(stmts)
model = pa.make_model()
pa.add_default_initial_conditions(100.0)
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
return model
def assemble_pysb(self, stmts):
pa = PysbAssembler(policies=self.default_policy)
pa.add_statements(stmts)
pa.make_model()
pa.add_default_initial_conditions(self.default_initial_amount)
return pa.model
