def statespace_threewaybm(form_f):
strand_seq = form_f['sequence']
ltoehold = form_f['ltoehold']
rtoehold = form_f['rtoehold']
''' do not set the initial state -- allow builder to do this '''
def getOptions(arguments):
o = standardOptions()
o.simulation_mode = Literals.trajectory
o.num_simulations = B_MULT * form_f["trajectories"]
o.sodium = form_f['sodium']
o.magnesium = form_f['magnesium']
o.temperature = float(form_f['temperature'])
o.simulation_time = BUILDER_TIMEOUT
o.join_concentration = BUILDER_CONC
if "RNA" == form_f['substrate']:
o.substrate_type = Literals.substrateRNA
endComplex = arguments[0]
stopSuccess = StopCondition(Literals.success, [(endComplex, Literals.exact_macrostate, 0)])
o.stop_conditions = [stopSuccess]
return o
startStates = threewaybmString(ltoehold, strand_seq, rtoehold)
endState = startStates[-1]
Builder.verbosity = True
myBuilder = Builder(getOptions, [endState[0]])
''' setting the precision to just 2 states will ensure the builder stops after a single iteration. '''
startTime = time.time()
myBuilder.genAndSavePathsFromString(startStates[:(len(startStates) - 1)])
# myBuilder.fattenStateSpace()
buildTime = time.time() - startTime
bRate = BuilderRate(myBuilder)
return bRate , buildTime
def genAndPrint(numOfPaths, toggle):
global sumTime
print "Building the statespace from traces for reaction: " + toggle
startStates = getString([toggle, test15mer])
endState = startStates[-1]
myBuilder = Builder(getOptions, [endState[0]])
''' setting the precision to just 2 states will ensure the builder stops after a single iteration. '''
startTime = time.time()
# Builder.verbosity = False
myBuilder.genAndSavePathsFromString(startStates[:(len(startStates) - 1)])
# Builder.verbosity = True
myBuilder.fattenStateSpace()
buildTime = time.time() - startTime
print "Build time was %.2f s" % buildTime
sumTime += buildTime
print myBuilder
builderRate = BuilderRate(myBuilder)
if not (toggle == str_dissociation
or toggle == str_threeway_strand_displacement):
compTime = builderRate.averageTimeFromInitial(bimolecular=False)
print "\nRate = %.2f /s \n" % (1.0 / compTime)
else:
compTime = builderRate.averageTimeFromInitial(bimolecular=True)
print "\nRate = %.2f /M/s \n" % (1.0 / compTime)
""" Fields you could look at: """
if False:
print builderRate.stateIndex
print builderRate.rate_matrix_csr.toarray()
print "Initial States"
print builderRate.initial_states
print "Final States"
print builderRate.final_states
print str(builderRate)
times = builderRate.averageTime()
print str(times)
def timings(seq, nTrials, deltaPruning=None):
output = ResultsHybridization()
def association_comparison(seq, endComplex):
return Settings(associationNoInit,
[nTrials, suyamaT, suyamaC, endComplex],
enum_hybridization, title_hybridization)
if EXP_TOGGLE == 1:
startStates = hybridizationString(seq)
if EXP_TOGGLE == 2:
startStates = threewaybmString("A", seq, "ACTAGG")
if EXP_TOGGLE == 3:
startStates = dissociationString(seq)
endState = startStates[-1]
sett = association_comparison(seq, endState[0])
for i in range(NUM_OF_REPEATS):
startTime = time.time()
BuilderRate.solveToggle = 0
myBuilder = Builder(sett.function, sett.arguments)
Builder.verbosity = True
myBuilder.genAndSavePathsFromString(startStates[:(len(startStates) -
1)])
print myBuilder
myBuilder.fattenStateSpace()
print myBuilder
# myBuilder.genUntilConvergenceWithInitialState(10000, startStates[:(len(startStates) - 1)], printMeanTime=True)
if not deltaPruning == None:
print "Going to delta prune with %.2E" % deltaPruning
myBuilder.deltaPruning(deltaPruning, printCount=True)
maxRange = 1
if TEST_RATE_LIMIT:
maxRange = 5
for i in range(maxRange):
builderRate = BuilderRate(myBuilder)
builderRate.rateLimit = builderRate.rateLimit * (10**i)
if i == (maxRange - 1):
builderRate.rateLimit = 0.0
print "rateLimit = " + str(builderRate.rateLimit)
builderRate.setMatrix()
output.buildTime.append(time.time() - startTime)
startTime = time.time()
biCheck = (EXP_TOGGLE == 1 or EXP_TOGGLE == 2)
output.rates.append(
np.log10(
1.0 /
builderRate.averageTimeFromInitial(bimolecular=biCheck)))
pruned_mfpt = builderRate.averageTimeFromInitial(bimolecular=False)
print "Rate = %.2E, MFPT = %.2E, compute_time = %.2f \n\n " % (
output.rates[-1], pruned_mfpt, output.buildTime[-1])
output.matrixTime.append(time.time() - startTime)
output.nStates.append(len(builderRate.statespace))
return output