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_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