def copy_no_rules(model):
'''
Copies a model without rules.
Parameters
----------
model : pysb.Model
Model to copy.
'''
m = Model(_export=False)
for comp in model.all_components():
if comp.__class__ is not Rule:
m.add_component(comp)
for ini in model.initial_conditions:
m.initial(*ini)
return m
def make_model(self, initial_conditions=True, policies=None):
model = Model()
# Keep track of which policies we're using
self.policies = policies
self.agent_set = BaseAgentSet()
# Collect information about the monomers/self.agent_set from the
# statements
for stmt in self.statements:
stmt.monomers(self.agent_set, policies=policies)
# Add the monomers to the model based on our BaseAgentSet
for agent_name, agent in self.agent_set.iteritems():
m = Monomer(agent_name, agent.sites, agent.site_states)
model.add_component(m)
# Iterate over the statements to generate rules
for stmt in self.statements:
stmt.assemble(model, self.agent_set, policies=policies)
# Add initial conditions
if initial_conditions:
add_default_initial_conditions(model)
return model
def make_model(self, initial_conditions=True, policies=None):
model = Model()
# Keep track of which policies we're using
self.policies = policies
self.agent_set = BaseAgentSet()
# Collect information about the monomers/self.agent_set from the
# statements
for stmt in self.statements:
stmt.monomers(self.agent_set, policies=policies)
# Add the monomers to the model based on our BaseAgentSet
for agent_name, agent in self.agent_set.iteritems():
m = Monomer(agent_name, agent.sites, agent.site_states)
model.add_component(m)
# Iterate over the statements to generate rules
for stmt in self.statements:
stmt.assemble(model, self.agent_set, policies=policies)
# Add initial conditions
if initial_conditions:
add_default_initial_conditions(model)
return model
class PysbAssembler(object):
def __init__(self, policies=None):
self.statements = []
self.agent_set = None
self.model = None
if policies is None:
self.policies = {'other': 'default'}
elif isinstance(policies, basestring):
self.policies = {'other': policies}
else:
self.policies = {'other': 'default'}
self.policies.update(policies)
def statement_exists(self, stmt):
for s in self.statements:
if stmt == s:
return True
return False
def add_statements(self, stmts):
for stmt in stmts:
if not self.statement_exists(stmt):
self.statements.append(stmt)
def dispatch(self, stmt, stage, *args):
class_name = stmt.__class__.__name__
try:
policy = self.policies[class_name]
except KeyError:
policy = self.policies['other']
func_name = '%s_%s_%s' % (class_name.lower(), stage, policy)
func = globals().get(func_name)
if func is None:
raise UnknownPolicyError('%s function %s not defined' %
(stage, func_name))
return func(stmt, *args)
def monomers(self):
"""Calls the appropriate monomers method based on policies."""
for stmt in self.statements:
self.dispatch(stmt, 'monomers', self.agent_set)
def assemble(self):
for stmt in self.statements:
self.dispatch(stmt, 'assemble', self.model, self.agent_set)
def make_model(self, initial_conditions=True):
self.model = Model()
self.agent_set = BaseAgentSet()
# Collect information about the monomers/self.agent_set from the
# statements
self.monomers()
# Add the monomers to the model based on our BaseAgentSet
for agent_name, agent in self.agent_set.iteritems():
m = Monomer(agent_name, agent.sites, agent.site_states)
self.model.add_component(m)
for db_name, db_ref in agent.db_refs.iteritems():
a = get_annotation(m, db_name, db_ref)
if a is not None:
self.model.add_annotation(a)
# Iterate over the statements to generate rules
self.assemble()
# Add initial conditions
if initial_conditions:
add_default_initial_conditions(self.model)
return self.model
def print_model(self, fname='pysb_model.py'):
if self.model is not None:
with open(fname, 'wt') as fh:
fh.write(pysb.export.export(self.model, 'pysb_flat'))
def print_rst(self, fname='pysb_model.rst', module_name='pysb_module'):
if self.model is not None:
with open(fname, 'wt') as fh:
fh.write('.. _%s:\n\n' % module_name)
fh.write('Module\n======\n\n')
fh.write('INDRA-assembled model\n---------------------\n\n')
fh.write('::\n\n')
model_str = pysb.export.export(self.model, 'pysb_flat')
model_str = '\t' + model_str.replace('\n', '\n\t')
fh.write(model_str)
class PysbAssembler(object):
def __init__(self, policies=None):
self.statements = []
self.agent_set = None
self.model = None
if policies is None:
self.policies = {'other': 'default'}
elif isinstance(policies, basestring):
self.policies = {'other': policies}
else:
self.policies = {'other': 'default'}
self.policies.update(policies)
def statement_exists(self, stmt):
for s in self.statements:
if stmt == s:
return True
return False
def add_statements(self, stmts):
for stmt in stmts:
if not self.statement_exists(stmt):
self.statements.append(stmt)
def dispatch(self, stmt, stage, *args):
class_name = stmt.__class__.__name__
try:
policy = self.policies[class_name]
except KeyError:
policy = self.policies['other']
func_name = '%s_%s_%s' % (class_name.lower(), stage, policy)
func = globals().get(func_name)
if func is None:
raise UnknownPolicyError('%s function %s not defined' %
(stage, func_name))
return func(stmt, *args)
def monomers(self):
"""Calls the appropriate monomers method based on policies."""
for stmt in self.statements:
self.dispatch(stmt, 'monomers', self.agent_set)
def assemble(self):
for stmt in self.statements:
self.dispatch(stmt, 'assemble', self.model, self.agent_set)
def make_model(self, initial_conditions=True):
self.model = Model()
self.agent_set = BaseAgentSet()
# Collect information about the monomers/self.agent_set from the
# statements
self.monomers()
# Add the monomers to the model based on our BaseAgentSet
for agent_name, agent in self.agent_set.iteritems():
m = Monomer(agent_name, agent.sites, agent.site_states)
self.model.add_component(m)
for db_name, db_ref in agent.db_refs.iteritems():
a = get_annotation(m, db_name, db_ref)
if a is not None:
self.model.add_annotation(a)
# Iterate over the statements to generate rules
self.assemble()
# Add initial conditions
if initial_conditions:
add_default_initial_conditions(self.model)
return self.model
def print_model(self, fname='pysb_model.py'):
if self.model is not None:
with open(fname, 'wt') as fh:
fh.write(pysb.export.export(self.model, 'pysb_flat'))
def print_rst(self, fname='pysb_model.rst', module_name='pysb_module'):
if self.model is not None:
with open(fname, 'wt') as fh:
fh.write('.. _%s:\n\n' % module_name)
fh.write('Module\n======\n\n')
fh.write('INDRA-assembled model\n---------------------\n\n')
fh.write('::\n\n')
model_str = pysb.export.export(self.model, 'pysb_flat')
model_str = '\t' + model_str.replace('\n', '\n\t')
fh.write(model_str)