def make_reaction_network(pysb_model, model_id):
"""Generate a PySB/BNG reaction network as a PNG file."""
try:
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
fname = 'model%d_rxn' % model_id
diagram_dot = render_reactions.run(pysb_model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
logger.error('Could not generate model diagram.')
logger.error(e)
return None
try:
with open(fname + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(
('dot -T png -o %s.png %s.dot' % (fname, fname)).split(' '))
abs_path = os.path.abspath(os.getcwd())
full_path = os.path.join(abs_path, fname + '.png')
except Exception as e:
logger.error('Could not save model diagram.')
logger.error(e)
return None
return full_path
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 make_sbgn(pysb_model, model_id):
pa = PysbAssembler()
pa.model = pysb_model
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
try:
sbgn_str = pa.export_model('sbgn')
except BngInterfaceError:
logger.error('Reaction network could not be generated for SBGN.')
return None
return sbgn_str
def get_model_diagram(model, model_id=None):
try:
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
fname = "model%d" % ("" if model_id is None else model_id)
diagram_dot = render_reactions.run(model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
raise DiagramGenerationError(e)
try:
with open(fname + ".dot", "wt") as fh:
fh.write(diagram_dot)
subprocess.call(("dot -T png -o %s.png %s.dot" % (fname, fname)).split(" "))
abs_path = os.path.abspath(os.getcwd())
if abs_path[-1] != "/":
abs_path = abs_path + "/"
full_path = abs_path + fname + ".png"
except Exception as e:
raise DiagramConversionError(e)
return full_path
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 get_model_diagram(model, model_id=None):
try:
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
fname = 'model%d' % ('' if model_id is None else model_id)
diagram_dot = render_reactions.run(model)
#TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
raise DiagramGenerationError(e)
try:
with open(fname + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(
('dot -T png -o %s.png %s.dot' % (fname, fname)).split(' '))
abs_path = os.path.abspath(os.getcwd())
if abs_path[-1] != '/':
abs_path = abs_path + '/'
full_path = abs_path + fname + '.png'
except Exception as e:
raise DiagramConversionError(e)
return full_path