def run_as_libsbmlsim_time_course(self, model, res):
if res is None:
res = result.TimeSeries()
steps = self.get_number_of_points()
start = self.get_output_start_time()
end = self.get_output_end_time()
step = (end - start) / steps
mod = model.get_sbml_doc()
# TODO: acquire KiSAO description of the algorithm
r = libsbmlsim.simulateSBMLFromString(
mod.toSBML(),
end,
step,
1,
0,
libsbmlsim.MTHD_RUNGE_KUTTA,
0)
res.import_from_libsbmlsim(r, start)
return res
# Simulation conditions
model_file = "FEBS_antimony.xml"
start = 0.0
end = 20.0
steps = 100.0
step = (end - start) / steps
# Open SBML file
reader = libsbml.SBMLReader()
doc = reader.readSBMLFromFile(model_file)
# Simulate model with stiff solver
r_stiff = libsbmlsim.simulateSBMLFromString(
doc.toSBML(),
end,
step,
1,
0,
libsbmlsim.MTHD_RUNGE_KUTTA,
0)
stiff_result = result.TimeSeries()
stiff_result.import_from_libsbmlsim(r_stiff, 0.0)
# Simulate model with non-stiff solver
r_non_stiff = libsbmlsim.simulateSBMLFromString(
doc.toSBML(),
end,
step,
1,
0,
libsbmlsim.MTHD_ADAMS_MOULTON_2,
0)
