def standardOptions(simMode=Literals.first_step,
tempIn=25.0,
trials=10,
timeOut=0.1):
output = Options(simulation_mode=simMode,
num_simulations=trials,
simulation_time=timeOut,
temperature=tempIn)
output.DNA23Metropolis()
output.rate_method = Literals.metropolis
return output
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.JSMetropolis25()
o.DNA23Metropolis()
return o
def createOptions(start_complex, stop_complex, simMode):
full_sc = StopCondition("CLOSED",
[(stop_complex, Literals.dissoc_macrostate, 2)])
o1 = Options(
simulation_mode=simMode, # "First Passage Time",
parameter_type="Nupack",
substrate_type="DNA",
temperature=273.15 + 25.0,
num_simulations=10,
simulation_time=0.00001,
# rate_scaling='Calibrated',
verbosity=0,
join_concentration=1.0,
rate_method="Metropolis",
start_state=[start_complex],
stop_conditions=[full_sc])
o1.DNA23Metropolis()
return o1
def setup_options(trials, seq, concentration):
"""
setup_options( seq )
creates an Options object using the sequence passed as a single
domain with initially unpaired structure.
"""
d = Domain(name="initial", sequence=seq, length=len(seq))
s = Strand(domains=[d])
c = Complex(strands=[s], structure=".")
o = Options(simulation_mode="Normal",
parameter_type="Nupack",
substrate_type="DNA",
num_sims=trials,
sim_time=0.008,
start_state=[c])
o.DNA23Metropolis()
o.temperature = 310.15
o.join_concentration = concentration
return o