def doReactionAssociation(arguments, output=True):
stdOptions = standardOptions()
stdOptions.simulation_mode = Literals.trajectory
stdOptions.num_simulations = arguments[0]
stdOptions.temperature = arguments[1]
stdOptions.join_concentration = arguments[2]
seq = arguments[3]
hybridization(stdOptions, seq, doFirstPassage=True)
if len(arguments) > 4:
stdOptions.sodium = arguments[4]
stdOptions.magnesium = arguments[5]
if output:
stdOptions.output_interval = 1
stdOptions.simulation_time = A_TIME_OUT
stdOptions.simulation_mode = Literals.trajectory
i = 65
for state in stdOptions.start_state:
for strand in state.strand_list:
strand.id = i
i += 1
return stdOptions
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 test1(unusedargs):
o1 = standardOptions()
hybridization(o1, "CCC")
o1.simulation_mode = Literals.first_passage_time
return o1
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, material):
o = standardOptions(Options.firstStep,
tempIn=25.0,
trials=200,
timeOut=0.1)
hybridization(o, strand_seq, trials)
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, material, temperature=25.0, sodium=1.0):
o = standardOptions(Literals.first_step,
tempIn=temperature,
trials=200,
timeOut=1.0)
o.sodium = sodium
hybridization(o, strand_seq, trials)
o.DNA23Metropolis()
# setArrParams(o, 92) # the best DNA23 parameter set
return o
def doSims(strandSeq, numTraj=2):
o1 = standardOptions()
o1.num_simulations = numTraj
o1.output_interval = 1
hybridization(o1, strandSeq)
o1.initial_seed = 1777
s = SimSystem(o1)
s.start()
printTrajectory(o1)
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
def getOptions(trials):
o = standardOptions(tempIn=float(form_f['temperature']), timeOut=A_TIME_OUT)
o.num_simulations = TRIALS
hybridization(o, strand_seq, trials)
o.sodium = form_f['sodium']
o.magnesium = form_f['magnesium']
o.concentration = 1.0E-9
if "RNA" == form_f['substrate']:
o.substrate_type = Literals.substrateRNA
return o
def doSims(strandSeq, numTraj=2):
o1 = standardOptions()
o1.num_simulations = numTraj
o1.output_interval = 1
o1.simulation_time = ATIME_OUT
# o1.substrate_type = Options.substrateRNA
hybridization(o1, strandSeq )
o1.initial_seed = 1777+6
s = SimSystem(o1)
s.start()
printTrajectory(o1)
def doReaction(arguments):
stdOptions = standardOptions()
stdOptions.output_interval = 1
stdOptions.simulation_mode = Literals.trajectory
stdOptions.join_concentration = 0.001
stdOptions.simulation_time = 400.0
stdOptions.num_simulations = arguments[0]
stdOptions.temperature = arguments[2]
toggle = arguments[3]
if toggle == str_association:
hybridization(stdOptions, arguments[1], myTrials=arguments[0], doFirstPassage=True)
elif toggle == str_hairpin_closing:
hairpinclosing(stdOptions, arguments[1], "TTTTT")
elif toggle == str_threeway_strand_displacement:
threewayDisplacement(stdOptions, "ACTACG", "AACATGAAGTA", myTrials=arguments[0])
elif toggle == str_dissociation:
dissociation(stdOptions, arguments[1], myTrials=arguments[0])
""" Make sure that multistrand IDs equal, everytime.
This is required for correctly combining multiple runs.
The Multistrand behavior makes sense,
but not for this specific use case. """
i = 65
for complex in stdOptions.start_state:
for strand in complex.strand_list:
strand.id = i
i += 1
stdOptions.DNA23Metropolis()
return stdOptions