def create_setup(num_traj, strand_seq):
options = standardOptions("First Step", GLOBAL_TEMPERATURE, num_traj, ATIME_OUT)
hybridization(options, strand_seq, num_traj)
setSaltGao2006(options)
return options
def getOptions(trials):
o = standardOptions(Options.firstStep, TEMPERATURE, trials, ATIME_OUT)
hybridization(o, strand_seq, trials)
setSaltGao2006(o)
return o
def getOptions(trials):
o = standardOptions(Literals.first_step, TEMPERATURE, trials,
ATIME_OUT)
hybridization(o, strand_seq, trials)
setSaltGao2006(o)
o.DNA23Metropolis()
return o
def getOptions(trials):
o = standardOptions(Options.firstPassageTime, TEMPERATURE, trials,
ATIME_OUT)
hybridization(o, strand_seq, trials, True)
setSaltGao2006(o)
o.join_concentration = concentration
return o
def getOptions(trials):
o = standardOptions(Options.firstStep, TEMPERATURE, trials, ATIME_OUT)
hybridization(o, strand_seq, trials)
setSaltGao2006(o)
# setArrheniusConstantsDNA23(o)
setArrParams(o, 96)
return o
def getOptions(trials):
o = standardOptions(Literals.first_passage_time, TEMPERATURE, trials,
ATIME_OUT)
hybridization(o, strand_seq, trials, True)
setSaltGao2006(o)
o.join_concentration = concentration
o.DNA23Metropolis()
return o
def getOptions(
trials, settings
): #start_complex_top, start_complex_bot, success_stop_condition, failed_stop_condition
options = standardOptions("First Step", TEMPERATURE, settings.trials,
ATIME_OUT)
hybridization(options, settings.mySeq, settings.trials)
setSaltGao2006(options)
options.output_interval = 1 # print every state, ever
return options