def assemble_model(stmts):
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model(policies='one_step')
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 apply_condition(model, condition):
agent = condition.quantity.entity
try:
monomer = model.monomers[pa._n(agent.name)]
except KeyError:
raise MissingMonomerError('%s is not in the model ' % agent.name,
agent)
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 assemble_model(stmts):
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model(policies='one_step')
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 apply_condition(model, condition):
agent = condition.quantity.entity
try:
monomer = model.monomers[pa._n(agent.name)]
except KeyError:
raise MissingMonomerError('%s is not in the model ' % 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])