def merge_parameters(model, new_name, parameters):
unique_values = {parameter.value for parameter in parameters}
if len(unique_values) > 1:
raise ValueError("Given parameters have different values: %s" %
(', '.join('%s=%g' % (p.name, p.value)
for p in parameters)))
value = parameters[0].value
rules = ComponentSet()
for parameter in parameters:
rules |= rules_using_parameter(model, parameter)
if not rules:
raise ValueError("Model has no rules using given parameters: %s" %
', '.join(p.name for p in parameters))
try:
new_parameter = model.parameters[new_name]
if new_parameter.value != value:
raise ValueError("Parameter %s is already present in the model "
"with the value %g, which differs from the "
"common value of the given parameters, %g" %
(new_parameter.name, new_parameter.value, value))
except KeyError:
new_parameter = Parameter(new_name, value)
model.add_component(new_parameter)
for rule in rules:
for attr in 'rate_forward', 'rate_reverse':
if getattr(rule, attr) in parameters:
setattr(rule, attr, new_parameter)
def merge_parameters(model, new_name, parameters):
unique_values = {parameter.value for parameter in parameters}
if len(unique_values) > 1:
raise ValueError("Given parameters have different values: %s" %
(', '.join('%s=%g' % (p.name, p.value)
for p in parameters)))
value = parameters[0].value
rules = ComponentSet()
for parameter in parameters:
rules |= rules_using_parameter(model, parameter)
if not rules:
raise ValueError("Model has no rules using given parameters: %s" %
', '.join(p.name for p in parameters))
try:
new_parameter = model.parameters[new_name]
if new_parameter.value != value:
raise ValueError("Parameter %s is already present in the model "
"with the value %g, which differs from the "
"common value of the given parameters, %g" %
(new_parameter.name, new_parameter.value, value))
except KeyError:
new_parameter = Parameter(new_name, value)
model.add_component(new_parameter)
for rule in rules:
for attr in 'rate_forward', 'rate_reverse':
if getattr(rule, attr) in parameters:
setattr(rule, attr, new_parameter)
def test_rules_using_parameter():
"""
Tests for rules_using_parameter() in pysb.util
"""
Monomer('m1')
Monomer('m2')
Monomer('m3')
ka1 = Parameter('ka1', 2e-5)
keff = Parameter('keff', 1e5)
Initial(m2(), Parameter('m2_0', 10000))
Rule('R1', None >> m1(), ka1)
Rule('R2', m1() + m2() >> m1() + m3(), keff)
components = rules_using_parameter(model, 'keff')
assert R2 in components
# Get rules by supplying Parameter object directly
components = rules_using_parameter(model, keff)
assert R2 in components
