def getOptions(trials, material, duplex_complex, dangle, success_stop_condition, failed_stop_condition):
o = Options(simulation_mode="First Step", substrate_type=material, rate_method="Metropolis",
num_simulations=trials, simulation_time=ATIME_OUT, temperature=T)
o.start_state = [duplex_complex, dangle]
o.stop_conditions = [success_stop_condition, failed_stop_condition]
# FD: The result of this script depend significantly on JS or DNA23 parameterization.
o.unimolecular_scaling = 5.0e6;
o.bimolecular_scaling = 1.4e6;
return o
def helper_create_Multistrand_options(self, sequence, time, count):
""" helper """
s1 = Strand("test_strand1", str(sequence), None)
c1 = Complex(1, "start", [s1], "." * len(sequence))
o = Options()
o.simulation_mode = Constants.SIMULATION_MODE['Python Module']
o.use_stop_states = False
o.num_simulations = count
o.simulation_time = time
o.start_state = [c1]
o.dangles = Constants.DANGLES['All']
o.rate_method = Constants.RATEMETHOD['Kawasaki']
o.bimolecular_scaling = 1.0
o.unimolecular_scaling = 1.0
o.temperature = 37.0
o.boltzmann_sample = False
return o