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_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