model.SummarySites()
model.WriteJobFiles()
model.CalculateElectrostaticEnergies()
mcModel = MCModelDefault()
model.DefineMCModel(mcModel)
curves = TitrationCurves(model, curveSampling=0.5)
curves.CalculateCurves()
curves.WriteCurves(directory=curveDir)
curves.CalculateHalfpKs()
models[label] = [model, curves]
logFile.Text("\n*** pK1/2 values for the old model ***\n")
model, curves = models["old"]
curves.PrintHalfpKs()
logFile.Text("\n*** pK1/2 values for the new model ***\n")
model, curves = models["new"]
curves.PrintHalfpKs()
# End of script
logFile.Footer()
# Table from the paper Miteva et al. Nucleic Acids Research, 2005, 33, p. W372-375
# residue pKintr pKcalc pKbashford pKexper
# earlierResults = (
# ( "NTR" , 998 , 5.6 , 5.1 , 6.4 , 7.8 , 8.0 ),
# ( "HIS" , 15 , 3.5 , 2.4 , 4.0 , 5.8 , 5.8 ),
# ( "GLU" , 7 , 5.5 , 3.2 , 2.1 , 2.6 , 2.6 ),
# ( "GLU" , 35 , 6.5 , 5.7 , 6.3 , 6.1 , 6.1 ),
("PRTA", "CYS", 80),
("PRTA", "CYS", 76),
("PRTA", "CYS", 94),
("PRTA", "ARG", 0),
)
cem.Initialize(excludeResidues=exclusions, includeTermini=True)
cem.Summary()
cem.SummarySites()
cem.WriteJobFiles()
cem.CalculateElectrostaticEnergies(calculateETA=False)
cem.CalculateProbabilities(pH=7.0)
cem.SummaryProbabilities()
curves = TitrationCurves(cem)
curves.CalculateCurves()
curves.WriteCurves(directory="curves_analytic")
curves.PrintHalfpKs(decimalPlaces=1)
sampling = MCModelDefault()
cem.DefineMCModel(sampling)
cem.CalculateProbabilities(pH=7.0)
cem.SummaryProbabilities()
mcc = TitrationCurves(cem)
mcc.CalculateCurves()
mcc.WriteCurves(directory="curves_mc")
mcc.PrintHalfpKs(decimalPlaces=1)