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Patch 11 #34

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6161ec9
creating fattenhelper.py
nasimzf Jan 2, 2019
5e4b847
update test_string_method.py
nasimzf Jan 2, 2019
104b32f
update builder.py
nasimzf Jan 2, 2019
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251 changes: 171 additions & 80 deletions src/interface/builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -534,6 +534,97 @@ def genAndSavePathsFromString(self, pathway, printMeanTime=False):
print "Size T = %i --- bytesize = %i " % (len(self.protoTransitions), sys.getsizeof (self.protoTransitions))
print "Time = %f" % (time.time() - startTime)


#NZ next three functions ( mergeSet_2, transitionMerge_2, fattenStateSpace_batch) are used to avoid memory leak in fattenStateSpace_batch, starting:
def mergeSet_2(self, this, that):

for key, val in that.iteritems():

this[key] = val;

def transitionMerge_2(self, protoTransitions):

for key, value in protoTransitions.iteritems():

sFrom = key[0]
sTo = key[1]

if sFrom in self.protoSpace and sTo in self.protoSpace:

if not key in self.protoTransitions:
self.protoTransitions[key] = value
self.mergingCounter += 1

def fattenStateSpace_batch(self, start = None , end = None ):
print "using fattenStateSpace_batch from builder.py! "

""" Load up the energy model with a near zero-length simulation """
myOptions = self.optionsFunction(copy.deepcopy(self.optionsArgs))
myOptions.simulation_mode = Literals.trajectory
myOptions.activestatespace = False
myOptions.simulation_time = 0.0000000001
myOptions.start_state = hybridizationString("AAA")[0] #pathway[0]
#
s = SimSystem(myOptions)
s.start()
""" Done setting the energy model """

ogVerb = Builder.verbosity
Builder.verbosity = False
counter = 0


def inspectionSim(inputs):

o1 = standardOptions()
#The next 3 lines ensure the energy of the states are calculated in same condition as state space states. Useful if use fattenstatespace to add new states
o1.sodium = self.options.sodium
o1.magnesium = self.options.magnesium
o1.temperature = self.options.temperature
o1.reuse_energymodel = True
#print "o1.temperature is " , o1.temperature
o1.rate_method = self.options.rate_method
o1.start_state = inputs[0]

return o1
self.tempstatespace = dict()
self.temptransitions = dict()
for key, value in self.protoSpacebackup.iteritems():

if start != None and end != None:
if counter < start :
counter += 1
continue
if counter >= end:
counter +=1
break
ogVerb = True
(seqs, ids, structs) = self.protoSequences[key]

myState = []

for seq, id, struct in zip(seqs, ids, structs):

seqs = seq.split('+')
ids = id.split(',')
myC = makeComplex(seqs, struct, ids)

myState.append(myC)

''' post: myState is the state we want to explore transitions for. '''

myB = Builder(inspectionSim, [myState])
myB.genAndSavePathsFile(inspecting=True)

#self.transitionMerge(myB)
self.mergeSet_2(self.protoTransitions, myB.protoTransitions)

counter += 1
Builder.verbosity = ogVerb




'''
Generates all transitions between states in the statespaces and adds missing transitions
'''
Expand Down Expand Up @@ -681,133 +772,133 @@ def runPaths(optionsF, optionsArgs, space, transitions, initStates, finalStates,
print "Multistrand simulation is now done, time = %.2f" % (time.time() - simTime)

""" load the space """
myFile = open(self.the_dir + str(myOptions.interface.current_seed) + "/protospace.txt", "r")
with open(self.the_dir + str(myOptions.interface.current_seed) + "/protospace.txt", "r") as myFile:

for line in myFile:

uniqueID, energyvals, seqs = self.parseState(line, myOptions._temperature_kelvin, myOptions.join_concentration)

if not uniqueID in sequences:
sequences[uniqueID] = seqs
for line in myFile:

if not uniqueID in space:
uniqueID, energyvals, seqs = self.parseState(line, myOptions._temperature_kelvin, myOptions.join_concentration)

space[uniqueID] = energyvals
if not uniqueID in sequences:
sequences[uniqueID] = seqs

elif not space[uniqueID] == energyvals:
if not uniqueID in space:

print "My hashmap contains " + str(uniqueID) + " with Energy " + str(space[uniqueID]) + " but found: " + str(energyvals)
print "Line = " + line
space[uniqueID] = energyvals

elif not space[uniqueID] == energyvals:

print "My hashmap contains " + str(uniqueID) + " with Energy " + str(space[uniqueID]) + " but found: " + str(energyvals)
print "Line = " + line

""" load the transitions """
myFile = open(self.the_dir + str(myOptions.interface.current_seed) + "/prototransitions.txt", "r")
with open(self.the_dir + str(myOptions.interface.current_seed) + "/prototransitions.txt", "r") as myFile:

index = 0
go_on = True
index = 0
go_on = True

myLines = []
myLines = []

for line in myFile:
myLines.append(line)
for line in myFile:
myLines.append(line)

while go_on:
while go_on:

line1 = myLines[index];
line2 = myLines[index + 1];
line3 = myLines[index + 2];
index = index + 4 # note the whitespace
line1 = myLines[index];
line2 = myLines[index + 1];
line3 = myLines[index + 2];

index = index + 4 # note the whitespace

go_on = len(myLines) > index
go_on = len(myLines) > index

uID1, ev1, seq1 = self.parseState(line2, myOptions._temperature_kelvin, myOptions.join_concentration)
uID2, ev2, seq2 = self.parseState(line3, myOptions._temperature_kelvin, myOptions.join_concentration)
uID1, ev1, seq1 = self.parseState(line2, myOptions._temperature_kelvin, myOptions.join_concentration)
uID2, ev2, seq2 = self.parseState(line3, myOptions._temperature_kelvin, myOptions.join_concentration)

transitionPair = (uID1, uID2)
transitionPair = (uID1, uID2)

if not transitionPair in transitions:
if not transitionPair in transitions:

transitionList = list()
transitionList = list()

n_complex1 = int(line2.split()[0])
n_complex2 = int(line3.split()[0])
n_complex1 = int(line2.split()[0])
n_complex2 = int(line3.split()[0])

if n_complex1 == n_complex2:
transitionList.append(transitiontype.unimolecular)
if n_complex1 == n_complex2:
transitionList.append(transitiontype.unimolecular)

if n_complex1 > n_complex2:
transitionList.append(transitiontype.bimolecularIn)
if n_complex1 > n_complex2:
transitionList.append(transitiontype.bimolecularIn)

if n_complex2 > n_complex1:
transitionList.append(transitiontype.bimolecularOut)
if n_complex2 > n_complex1:
transitionList.append(transitiontype.bimolecularOut)

if myOptions.rate_method == Literals.arrhenius:
# decode the transition and add it
transitionList.extend(codeToDesc(int(float(line1))))
if myOptions.rate_method == Literals.arrhenius:
# decode the transition and add it
transitionList.extend(codeToDesc(int(float(line1))))

transitions[transitionPair] = transitionList
transitions[transitionPair] = transitionList

""" load the initial states """
myFile = open(self.the_dir + str(myOptions.interface.current_seed) + "/protoinitialstates.txt", "r")
with open(self.the_dir + str(myOptions.interface.current_seed) + "/protoinitialstates.txt", "r") as myFile:

myLines = []
myLines = []

for line in myFile:
myLines.append(line)
for line in myFile:
myLines.append(line)

index = 0
go_on = True
index = 0
go_on = True

if len(myLines) == 0:
print "No initial states found!"
if len(myLines) == 0:
print "No initial states found!"

while go_on:
while go_on:

line1 = myLines[index];
line2 = myLines[index + 1];
line1 = myLines[index];
line2 = myLines[index + 1];

index = index + 2 # note the whitespace
go_on = len(myLines) > index
index = index + 2 # note the whitespace
go_on = len(myLines) > index

uID1, ev1, seq1 = self.parseState(line2, myOptions._temperature_kelvin, myOptions.join_concentration)
count = int(line1.split()[0])
uID1, ev1, seq1 = self.parseState(line2, myOptions._temperature_kelvin, myOptions.join_concentration)
count = int(line1.split()[0])

if not uID1 in initStates:
if not uID1 in initStates:

newEntry = InitCountFlux()
newEntry.count = count
newEntry.flux = 777777 # arrType is the flux, and is unique to the initial state
newEntry = InitCountFlux()
newEntry.count = count
newEntry.flux = 777777 # arrType is the flux, and is unique to the initial state

initStates[uID1] = newEntry
initStates[uID1] = newEntry

""" load the final states """
myFile = open(self.the_dir + str(myOptions.interface.current_seed) + "/protofinalstates.txt", "r")
with open(self.the_dir + str(myOptions.interface.current_seed) + "/protofinalstates.txt", "r") as myFile:

myLines = []
myLines = []

for line in myFile:
myLines.append(line)
for line in myFile:
myLines.append(line)

index = 0
go_on = True
index = 0
go_on = True

if len(myLines) == 0:
# raise ValueError("No succesful final states found -- mean first passage time would be infinite ")
go_on = False
if len(myLines) == 0:
# raise ValueError("No succesful final states found -- mean first passage time would be infinite ")
go_on = False

while go_on:
while go_on:

line1 = myLines[index];
line2 = myLines[index + 1];
index = index + 2
line1 = myLines[index];
line2 = myLines[index + 1];
index = index + 2

go_on = len(myLines) > (index + 1)
go_on = len(myLines) > (index + 1)

uID1, ev1, seq1 = self.parseState(line1, myOptions._temperature_kelvin, myOptions.join_concentration)
tag = line2.split()[0]
uID1, ev1, seq1 = self.parseState(line1, myOptions._temperature_kelvin, myOptions.join_concentration)
tag = line2.split()[0]

if not uID1 in finalStates:
finalStates[uID1] = tag
if not uID1 in finalStates:
finalStates[uID1] = tag

""" Now delete the files as they can get quite large """
os.remove(self.the_dir + str(myOptions.interface.current_seed) + "/protospace.txt")
Expand Down
51 changes: 51 additions & 0 deletions tutorials/rare_events_casestudy/fattenhelper.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
import sys
import cPickle as pickle
import gc
import time
from multistrand.builder import Builder
from test_string_method import associationNoInit
print "importing associationNoInit from test_string_method.py in fattenhelper.py "


start = sys.argv[1]
end = sys.argv[2]
pathbuilder = sys.argv[3]
pathspace= sys.argv[4 ]
pathsequences = sys.argv[5]
pathoptions= sys.argv[6]

print "In fattenhelper.py, which uses associationNoInit from test_string_method to initialize a builder. Then it calls fattenStateSpace_batch, etc to fatten states "
#def do(start, end, pathbuilder, pathspace , pathsequences, pathoptions) :
mytime = open ("times.txt", "a")
mytime.write( pathbuilder + " start " + str( start) + "end " + str(end) + "\n" )
st = time.time()

with open(pathoptions , "rb" ) as p:
optionsArg = pickle.load( p)

myBuilder= Builder(associationNoInit, optionsArg )

with open(pathspace , "rb" ) as p:
myBuilder.protoSpacebackup = pickle.load( p)

with open( pathsequences , "rb" ) as p :
myBuilder.protoSequences = pickle.load( p)

mytime.write( "load time " + str( time.time() - st )+"\n")

st = time.time ( )
myBuilder.fattenStateSpace_batch(start = int(start) , end= int( end))

mytime.write( "fatten time time " + str( time.time() - st ) +"\n")

st = time.time()

with open( pathbuilder + "pt" + str(start)+"-" +str(end) , "wb" ) as p:
pickle.dump(myBuilder.protoTransitions, p)


mytime.write( "save time " + str( time.time() - st ) +"\n")
mytime.close()

del myBuilder
gc.collect()
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