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Changing prints to python3 style
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Ryan McGee authored and Ryan McGee committed Mar 5, 2020
1 parent a210a65 commit 2c6fbe3
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Showing 3 changed files with 57 additions and 57 deletions.
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50 changes: 25 additions & 25 deletions pycrobe/betalactamase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -351,7 +351,7 @@ def run(self, time, dt, inoculums, media, temp, noise_r=0.0, downsample_output_d
N[t+1] = N[t] + dN*dt
N[t+1] = numpy.clip(N[t+1], a_min=0, a_max=None)

dB = -delta_B*B[t] - r[t]*B[t] - epsilon_B*(B[t] - Bext[t]) + alpha_B*( (B_max - B[t]) / (k_alpha + (B_max - B[t])) )
dB = -delta_B*B[t] - numpy.maximum((r[t]-l[t]), 0)*B[t] - epsilon_B*(B[t] - Bext[t]) + alpha_B*( (B_max - B[t]) / (k_alpha + (B_max - B[t])) )
B[t+1] = B[t] + dB*dt
B[t+1] = numpy.clip(B[t+1], a_min=0, a_max=None)

Expand Down Expand Up @@ -399,30 +399,30 @@ def run(self, time, dt, inoculums, media, temp, noise_r=0.0, downsample_output_d
d_Bext[t+1] = (Vmax_Bext * Aext[t+1])/(k_Bext + Aext[t+1])


# print "N["+str(t)+"] = " + str(N[t])
# print "r["+str(t)+"] = " + str(r[t])
# print "l["+str(t)+"] = " + str(l[t])
# print "r-l["+str(t)+"] = " + str(r[t]-l[t])
# print "B["+str(t)+"] = " + str(B[t])
# print str(l[t]*(1-xi_B)*B[t]*Vol*N[t])
# print "Bext["+str(t)+"] = " + str(Bext[t])
# print "A["+str(t)+"] = " + str(A[t])
# print "Aext["+str(t)+"] = " + str(Aext[t])
# print "d_B["+str(t)+"] = " + str(d_B[t])
# print "d_Bext["+str(t)+"] = " + str(d_Bext[t])
# print "S["+str(t)+"] = " + str(S[t])
# print "------------------------------"
# print "N["+str(t+1)+"] = " + str(N[t+1])
# print "r["+str(t+1)+"] = " + str(r[t+1])
# print "l["+str(t+1)+"] = " + str(l[t+1])
# print "B["+str(t+1)+"] = " + str(B[t+1])
# print "Bext["+str(t+1)+"] = " + str(Bext[t+1])
# print "A["+str(t+1)+"] = " + str(A[t+1])
# print "Aext["+str(t+1)+"] = " + str(Aext[t+1])
# print "d_B["+str(t+1)+"] = " + str(d_B[t+1])
# print "d_Bext["+str(t+1)+"] = " + str(d_Bext[t+1])
# print "S["+str(t+1)+"] = " + str(S[t+1])
# print "=============================="
# print("N["+str(t)+"] = " + str(N[t]))
# print("r["+str(t)+"] = " + str(r[t]))
# print("l["+str(t)+"] = " + str(l[t]))
# print("r-l["+str(t)+"] = " + str(r[t]-l[t]))
# print("B["+str(t)+"] = " + str(B[t]))
# print(str(l[t]*(1-xi_B)*B[t]*Vol*N[t]))
# print("Bext["+str(t)+"] = " + str(Bext[t]))
# print("A["+str(t)+"] = " + str(A[t]))
# print("Aext["+str(t)+"] = " + str(Aext[t]))
# print("d_B["+str(t)+"] = " + str(d_B[t]))
# print("d_Bext["+str(t)+"] = " + str(d_Bext[t]))
# print("S["+str(t)+"] = " + str(S[t]))
# print("------------------------------")
# print("N["+str(t+1)+"] = " + str(N[t+1]))
# print("r["+str(t+1)+"] = " + str(r[t+1]))
# print("l["+str(t+1)+"] = " + str(l[t+1]))
# print("B["+str(t+1)+"] = " + str(B[t+1]))
# print("Bext["+str(t+1)+"] = " + str(Bext[t+1]))
# print("A["+str(t+1)+"] = " + str(A[t+1]))
# print("Aext["+str(t+1)+"] = " + str(Aext[t+1]))
# print("d_B["+str(t+1)+"] = " + str(d_B[t+1]))
# print("d_Bext["+str(t+1)+"] = " + str(d_Bext[t+1]))
# print("S["+str(t+1)+"] = " + str(S[t+1]))
# print("==============================")


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down
64 changes: 32 additions & 32 deletions pycrobe/standard.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,21 +220,21 @@ def add(self, added_media):

def info(self):
if(self.nutrient is not None):
print "\tNutrient " + self.nutrient.name + ":\n" + "\t\tconcentration\t= " + ("%.2E" % self.nutrient.concentration) + " ug/mL"
print("\tNutrient " + self.nutrient.name + ":\n" + "\t\tconcentration\t= " + ("%.2E" % self.nutrient.concentration) + " ug/mL")
else:
print "\t(no nutrient)"
print("\t(no nutrient)")
#----------
if(len(self.drugs)>0):
for drug in self.drugs:
print "\tDrug " + drug.name + ":\n" + "\t\tconcentration\t= " + ("%.3f" % drug.concentration) + " ug/mL"
print("\tDrug " + drug.name + ":\n" + "\t\tconcentration\t= " + ("%.3f" % drug.concentration) + " ug/mL")
else:
print "\t(no drugs)"
print("\t(no drugs)")
#----------
if(len(self.solutes)>0):
for solute in self.solutes:
print "\tSolute " + solute.name + ":\n" + "\t\tconcentration\t= " + (("%.3f" % solute.concentration) if solute.concentration>0.001 else ("%.2E" % solute.concentration)) + " ug/mL"
print("\tSolute " + solute.name + ":\n" + "\t\tconcentration\t= " + (("%.3f" % solute.concentration) if solute.concentration>0.001 else ("%.2E" % solute.concentration)) + " ug/mL")
else:
print "\t(no other solutes)"
print("\t(no other solutes)")



Expand Down Expand Up @@ -462,14 +462,14 @@ def run(self, time, dt, inoculums, media, temp, noise_r=0.0, downsample_output_d
growthPhase[i] = 'exponential'


# print "N["+str(t)+"] = " + str(N[t])
# print "r["+str(t)+"] = " + str(r[t])
# print "S["+str(t)+"] = " + str(S[t])
# print "------------------------------"
# print "N["+str(t+1)+"] = " + str(N[t+1])
# print "r["+str(t+1)+"] = " + str(r[t+1])
# print "S["+str(t+1)+"] = " + str(S[t+1])
# print "=============================="
# print("N["+str(t)+"] = " + str(N[t]))
# print("r["+str(t)+"] = " + str(r[t]))
# print("S["+str(t)+"] = " + str(S[t]))
# print("------------------------------")
# print("N["+str(t+1)+"] = " + str(N[t+1]))
# print("r["+str(t+1)+"] = " + str(r[t+1]))
# print("S["+str(t+1)+"] = " + str(S[t+1]))
# print("==============================")


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -726,18 +726,18 @@ def totalCellDensity(self):


def info(self):
print "Culture " + self.name + ":"
print "--------------------------------"
print "\tVolume\t\t\t= " + ("%.3f" % self.totalVolume()) + " mL"
print "\tDensity\t\t\t= " + ( '%.2E' % Decimal(str( self.totalCellDensity() )) ) + " cfu/mL"
print "\tTotal CellCount\t= " + ( '%.2E' % Decimal(str( self.totalCellCount() )) ) + " cfu"
print("Culture " + self.name + ":")
print("--------------------------------")
print("\tVolume\t\t\t= " + ("%.3f" % self.totalVolume()) + " mL")
print("\tDensity\t\t\t= " + ( '%.2E' % Decimal(str( self.totalCellDensity() )) ) + " cfu/mL")
print("\tTotal CellCount\t= " + ( '%.2E' % Decimal(str( self.totalCellCount() )) ) + " cfu")
#----------
if(len(self.inoculums)>0):
inoculumDensities = self.getInoculumDensities()
for inoculum in self.inoculums:
print "\tInoculum " + inoculum.strain.name + ":\n" + "\t\tdensity\t\t= " + ( '%.2E' % Decimal(str( inoculumDensities[inoculum.strain.name] )) )+" cfu/mL" + "\n\t\tcell count\t= " + ( '%.2E' % Decimal(str( inoculum.cellCount )) )+" cfu" + "\n\t\tfrequency\t= " + ( '%.4f' % self.getInoculumFrequencies()[inoculum.strain.name] ) + "" + "\n\t\tgrowthPhase\t= " + inoculum.growthPhase
print("\tInoculum " + inoculum.strain.name + ":\n" + "\t\tdensity\t\t= " + ( '%.2E' % Decimal(str( inoculumDensities[inoculum.strain.name] )) )+" cfu/mL" + "\n\t\tcell count\t= " + ( '%.2E' % Decimal(str( inoculum.cellCount )) )+" cfu" + "\n\t\tfrequency\t= " + ( '%.4f' % self.getInoculumFrequencies()[inoculum.strain.name] ) + "" + "\n\t\tgrowthPhase\t= " + inoculum.growthPhase)
else:
print "\t(no inoculums)"
print("\t(no inoculums)")
#----------
self.media.info()

Expand Down Expand Up @@ -783,12 +783,12 @@ def incubate(self, cultures, time, dt, record_growth_curves=False):
for c, culture in enumerate(cultures):
culture.incubate(time=dt, dt=dt, temp=effectiveTemps[c])

print "N["+str(t)+"] = " + str(culture.inoculums[0].cellCount)
print "r["+str(t)+"] = " + str(culture.inoculums[0].growthRate)
print "phase["+str(t)+"] = " + str(culture.inoculums[0].growthPhase)
print "timer["+str(t)+"] = " + str(culture.inoculums[0].growthCycleTimer)
print "END INCUBATOR T = "+str(t)
print "------------------------------"
print("N["+str(t)+"] = " + str(culture.inoculums[0].cellCount))
print("r["+str(t)+"] = " + str(culture.inoculums[0].growthRate))
print("phase["+str(t)+"] = " + str(culture.inoculums[0].growthPhase))
print("timer["+str(t)+"] = " + str(culture.inoculums[0].growthCycleTimer))
print("END INCUBATOR T = "+str(t))
print("------------------------------")
if(culture.media.nutrient.concentration <= 1e-1):
culture.info()
exit()
Expand Down Expand Up @@ -898,13 +898,13 @@ def totalColonyCount(self):


def info(self):
print "AgarPlate " + self.name + ":"
print "--------------------------------"
print "\tTotal Colonies = " + str(self.totalColonyCount())
print("AgarPlate " + self.name + ":")
print("--------------------------------")
print("\tTotal Colonies = " + str(self.totalColonyCount()))
for marker in numpy.unique([inoculum.strain.marker for inoculum in self.inoculums]):
print "\tMarker " + marker + ":\n" + "\t\tcell count\t= " + str( self.getColonyCounts()[marker] )
print("\tMarker " + marker + ":\n" + "\t\tcell count\t= " + str( self.getColonyCounts()[marker] ))
# for inoculum in self.inoculums:
# print "\tInoculum " + inoculum.strain.name + ":\n" + "\t\tcell count\t= " + str( self.getColonyCounts()[inoculum.strain.marker] )
# print("\tInoculum " + inoculum.strain.name + ":\n" + "\t\tcell count\t= " + str( self.getColonyCounts()[inoculum.strain.marker] ))


##################################################
Expand Down

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