def doFirstPassageTimeAssocation(seq, concentrations, T=20, numOfRuns=500):
# for each concentration z, do one "first passage time" run for association, and get k_eff(z)
Result = []
times = list()
for concentration in concentrations:
myRates = first_passage_association(seq,
numOfRuns,
concentration=concentration,
T=T)
keff = myRates.log10KEff(concentration)
myBootstrap = Bootstrap(myRates, concentration)
low, high = myBootstrap.ninetyFivePercentiles()
logStd = myBootstrap.logStd()
Result.append((keff, np.log10(low), np.log10(high), logStd))
times.append((np.log10(myMultistrand.runTime), 0.0, 0.0))
print "keff = %g /M/s at %s" % (keff,
concentration_string(concentration))
print
return Result, times
def doFirstStepMode(seq, concentrations, T=20.0, numOfRuns=500):
# track time for each kind of simulation, using time.time(), which has units of second
# do one "first step mode" run, get k1, k2, etc, from which z_crit and k_eff(z) can be computed
myMultistrand = first_step_simulation(seq, numOfRuns, T=T)
myRates = myMultistrand.results
# print myRates.dataset
time2 = time.time()
print str(myRates)
FSResult = list()
for z in concentrations:
kEff = myRates.kEff(z)
myBootstrap = Bootstrap(myRates,
N=BOOTSTRAP_RESAMPLE,
concentration=z,
computek1=False)
low, high = myBootstrap.ninetyFivePercentiles()
logStd = myBootstrap.logStd()
print "keff = %g /M/s at %s" % (kEff, concentration_string(z))
myResult = (np.log10(kEff), np.log10(low), np.log10(high), logStd)
FSResult.append(myResult)
print
# call NUPACK for pfunc dG of the reaction, calculate krev based on keff
print "Calculating dissociate rate constant based on NUPACK partition function energies and first step mode k_eff..."
dG_top = nupack.pfunc([seq], T=T)
dG_bot = nupack.pfunc([Strand(sequence=seq).C.sequence], T=T)
dG_duplex = nupack.pfunc([seq, Strand(sequence=seq).C.sequence], T=T)
RT = 1.987e-3 * (273.15 + T)
time3 = time.time()
time_nupack = time3 - time2
krev_nupack = kEff * np.exp((dG_duplex - dG_top - dG_bot) / RT)
print "krev = %g /s (%g seconds)" % (krev_nupack, time_nupack)
times = list()
for i in concentrations:
myTime = (np.log10(myMultistrand.runTime), 0.0, 0.0)
times.append(myTime)
return FSResult, times
def fluffyPlot(ax, seqs, concentrations):
myXTicks = list()
for conc in concentrations:
myXTicks.append(concentration_string(conc))
plt.xticks(rotation=-40)
plt.xticks(np.log10(concentrations), myXTicks)
plt.gca().invert_xaxis()
ax.set_xlabel('Concentration')
# Shrink current axis by 20%
box = ax.get_position()
ax.set_position(
[box.x0, box.y0 + box.height * 0.2, box.width * 0.8, 0.8 * box.height])
ax.legend(seqs, loc='center left', bbox_to_anchor=(1, 0.5))
def first_passage_association(strand_seq, trials, concentration, T=20.0):
print "Running first passage time simulations for association of %s at %s..." % (
strand_seq, concentration_string(concentration))
def getOptions(trials):
o = standardOptions(Options.firstPassageTime, TEMPERATURE, trials,
ATIME_OUT)
hybridization(o, strand_seq, trials, True)
setSaltGao2006(o)
o.join_concentration = concentration
return o
myMultistrand.setOptionsFactory1(getOptions, trials)
myMultistrand.setPassageMode()
myMultistrand.run()
return myMultistrand.results
def doFirstPassageTimeAssocation(seq, concentrations, T=20, numOfRuns=500):
# for each concentration z, do one "first passage time" run for association, and get k_eff(z)
Result = []
times = list()
for concentration in concentrations:
if len(seq) > 10 and concentration < 1e-5:
keff = 5.5
low = 1e+5
high = 1e+6
logStd = -1.0
else:
myMultistrand = first_passage_association(
seq, numOfRuns, concentration=concentration, T=T)
myRates = myMultistrand.results
# print myRates.dataset
keff = myRates.log10KEff(concentration)
myBootstrap = Bootstrap(myRates,
N=BOOTSTRAP_RESAMPLE,
concentration=concentration)
low, high = myBootstrap.ninetyFivePercentiles()
logStd = myBootstrap.logStd()
Result.append((keff, np.log10(low), np.log10(high), logStd))
times.append((np.log10(myMultistrand.runTime), 0.0, 0.0))
print "keff = %g /M/s at %s" % (keff, concentration_string(concentration))
return Result, times
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