def timings(settings):
output = ResultsHybridization()
for i in range(NUM_OF_REPEATS):
startTime = time.time()
myBuilder = Builder(settings.function, settings.arguments)
if DO_CONVERGENCE:
myBuilder.genUntilConvergence(CONVERGENCE_CRIT)
else:
myBuilder.genAndSavePathsFile()
builderRate = BuilderRate(myBuilder)
output.buildTime.append(time.time() - startTime)
startTime = time.time()
output.rates.append(
np.log10(1.0 /
builderRate.averageTimeFromInitial(bimolecular=True)))
output.matrixTime.append(time.time() - startTime)
output.nStates.append(builderRate.n_states)
output.nTransitions.append(builderRate.n_transitions)
return output
"""Produce the required plots here"""
def genAndPrint(numOfPaths, toggle):
simulation_temperature = 50.0
print "Building the statespace from traces for reaction: " + toggle + " at T = %.1f C " % simulation_temperature
myBuilder = Builder(doReaction, [numOfPaths, test8mer, simulation_temperature, toggle])
myBuilder.genAndSavePathsFile()
myBuilder.genAndSavePathsFile()
print myBuilder
builderRate = BuilderRate(myBuilder)
if not (toggle == str_dissociation or toggle == str_threeway_strand_displacement):
time = builderRate.averageTimeFromInitial(bimolecular=False)
print "\nRate = %.2f /s \n" % (1.0 / time)
else:
time = builderRate.averageTimeFromInitial(bimolecular=True)
print "\nRate = %.2f /M/s \n" % (1.0 / time)
""" 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 main():
b = Builder(test0, [])
b.genAndSavePathsFile(inspecting=True)
print b
b = Builder(test1, [])
b.genAndSavePathsFile(inspecting=True)
print b
def call_Builder(self, num_simulations):
myBuilder = Builder(doReaction, [
num_simulations, self.simulation_time, self.reaction_type,
self.dataset_type, self.strands_list, self.sodium, self.magnesium,
self.kinetic_parameters_simulation, self.bimolecular_reaction,
self.temperature, self.temperature_change,
self.join_concentration_change, self.join_concentration,
rate_method, self.use_initialfinalfrompathway, self.startStates
])
start_time = timeit.default_timer()
if self.num_simulations > 0:
myBuilder.genAndSavePathsFile(
supplyInitialState=self.startStates[0])
builderpath = self.dataset_path + "/" + myenums.Permanent_Folder.MYBUILDER.value + "/" + myenums.Permanent_Folder.MYBUILDER.value + str(
self.docID)
lenp = len(myBuilder.protoSpace)
start = 0
myBuilder.protoSpacebackup = copy.deepcopy(myBuilder.protoSpace)
pathuniqueid = builderpath + myenums.EDITIONAL.UNIQUEID.value
with open(pathuniqueid, "wb") as p:
pickle.dump(myBuilder.uniqueID_number, p)
pathspace = builderpath + myenums.EDITIONAL.PROTOSPACEBACKUP.value
with open(pathspace, "wb") as p:
pickle.dump(myBuilder.protoSpacebackup, p)
pathsequences = builderpath + myenums.EDITIONAL.PROTOSEQUENCES.value
with open(pathsequences, "wb") as p:
pickle.dump(myBuilder.protoSequences, p)
pathoptions = builderpath + myenums.EDITIONAL.PATHOPTIONS.value
with open(pathoptions, "wb") as p:
pickle.dump(myBuilder.optionsArgs, p)
batchsize = 2000
while start < lenp:
st = timeit.default_timer()
end = min(lenp, start + batchsize)
print "progress ", str(end), " / ", str(lenp), self.docID
# There was some memory leak issues when I used the fattenStateSpace function in builder.py, so I added fatten helper to avoid the memory issues by saving intermediate results, restarting Multistrand, and restoring the intermediate results
command = [
"python", "fattenhelper.py",
str(start),
str(end), builderpath, pathspace, pathsequences,
pathoptions, pathuniqueid
]
shell = call(command)
ft = timeit.default_timer()
#print "making fatten state space time" , ft-st
del shell
with open(
builderpath + myenums.EDITIONAL.TEMPSTATESPACE.value +
str(start) + "-" + str(end), "rb") as p:
tempstatespace = pickle.load(p)
with open(
builderpath + myenums.EDITIONAL.TEMPTRANSITIONS.value +
str(start) + "-" + str(end), "rb") as p:
temptransitions = pickle.load(p)
os.remove(builderpath +
myenums.EDITIONAL.TEMPSTATESPACE.value + str(start) +
"-" + str(end))
os.remove(builderpath +
myenums.EDITIONAL.TEMPTRANSITIONS.value +
str(start) + "-" + str(end))
myBuilder.mergeSet(myBuilder.protoSpace, tempstatespace)
myBuilder.mergeSet(myBuilder.protoTransitions_FPEI,
temptransitions)
start = end
with open(pathuniqueid, "rb") as p:
myBuilder.uniqueID_number = pickle.load(p)
os.remove(pathuniqueid)
os.remove(pathspace)
os.remove(pathsequences)
os.remove(pathoptions)
del myBuilder.protoSpacebackup
del myBuilder.uniqueID_number
print "Statistics: ", "statespace: ", len(
myBuilder.protoSpace), "finalstates: ", len(
myBuilder.protoFinalStates), "initialstates: ", len(
myBuilder.protoInitialStates)
return myBuilder