def computeHittingTimes(settings, reverse=False):
myMultistrand = MergeSim()
myMultistrand.setNumOfThreads(NUM_PROCESS)
if settings.type == enum_yurke2:
myMultistrand.setOptionsFactory1(simulationYurke2, settings.nTrials)
if settings.type == enum_bonnet:
myMultistrand.setOptionsFactory2(simulationHairpin, settings.nTrials,
reverse)
if settings.type == enum_flamm:
myMultistrand.setOptionsFactory1(simulationFlamm2000, settings.nTrials)
if settings.type == enum_yurke:
myMultistrand.setOptionsFactory1(simulationYurke, settings.nTrials)
if settings.type == enum_rickettsia:
myMultistrand.setOptionsFactory1(simulationRickettsia,
12 * settings.nTrials)
myMultistrand.setTerminationCriteria(terminationCount=settings.nTrials)
if settings.type == enum_bonnet or settings.type == enum_yurke2:
myMultistrand.setPassageMode() # using the pre-set success / fail
if settings.type == enum_flamm or settings.type == enum_yurke or settings.type == enum_rickettsia:
# non-first stepping mode, no need to store trajectory information
myMultistrand.setPassageMode()
myMultistrand.run()
return myMultistrand.results
def first_step_simulation(form_f):
strand_seq = form_f['sequence']
print ("Running first step mode simulations for %s (with Boltzmann sampling)..." % (strand_seq))
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
MergeSimSettings.max_trials = MAX_TRIALS
myMultistrand = MergeSim()
myMultistrand.setOptionsFactory1(getOptions, TRIALS)
myMultistrand.setTerminationCriteria(int(form_f["trajectories"]))
myMultistrand.settings.timeOut = max(WALL_TIME_TIMEOUT, form_f["trajectories"])
myMultistrand.run()
return myMultistrand
def computeRate(selector):
myMultistrand = MergeSim()
myMultistrand.setOptionsFactory2(genOptions, NUMOFPATHS, selector)
myMultistrand.setNumOfThreads(NUMOFTHREADS)
myMultistrand.setTerminationCriteria(TERMINATIONCRIT)
myMultistrand.setLeakMode() # the new leak object -- faster bootstrapping.
myMultistrand.printTrajectory()
return 0.0, 0.0, 0.0
myMultistrand.run()
myFSR = myMultistrand.results
low, high = myFSR.doBootstrap()
return myFSR.k1(), low, high
def first_passage_association(strand_seq, trials, concentration, T=20.0):
thisMS = MergeSim()
thisMS.setNumOfThreads(8)
print "Running first passage time simulations for association of %s at %s..." % (
strand_seq, concentration_string(concentration))
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
thisMS.setOptionsFactory1(getOptions, trials)
thisMS.setPassageMode()
thisMS.run()
return thisMS
def first_step_simulation(strand_seq, trials, T=20.0):
myMS = MergeSim()
myMS.setNumOfThreads(8)
print(
"Running first step mode simulations for %s (with Boltzmann sampling)..."
% (strand_seq))
def getOptions(trials):
o = standardOptions(Literals.first_step, TEMPERATURE, trials,
ATIME_OUT)
hybridization(o, strand_seq, trials)
setSaltGao2006(o)
o.DNA23Metropolis()
return o
myMS.setOptionsFactory1(getOptions, trials)
myMS.setFirstStepMode() # ensure the right results object is set.
# myMultistrand.setLeakMode()
myMS.setTerminationCriteria(terminationCount=trials)
myMS.run()
return myMS