def main():
"""
Simple main that creates the proteins, mutates the protein, calculates pKa values, and prints pKa files
"""
# I. preliminaries
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
version = propka.makeVersion(label=options.version_label)
# creating protein object and calculating reference folding energy
myProtein = Protein(pdbfile=pdbfiles[0], options=options)
myProtein.calculatePKA(version=version, options=options)
dG_ref = myProtein.calculateFoldingEnergy(options=options)
# creating a dictionary with atom objects needed for e.g. alignment mutations
atoms = mutate.makeCompositeAtomsDictionary(protein=myProtein, pdbfiles=pdbfiles, options=options)
# II. making mutations and calculating the folding energy
for mutation in options.mutations:
pka_print(mutation)
newProtein = mutate.makeMutatedProtein(myProtein, atoms=atoms, mutation=mutation, options=options)
# calculating pKa values for ionizable residues
newProtein.calculatePKA(version=version, options=options)
newProtein.writePKA(options=options)
dG_mut = newProtein.calculateFoldingEnergy(options=options)
pka_print("staliblization:")
pka_print("%8.2lf %6.2lf %s" % (dG_ref, dG_ref-dG_ref, "WT"))
pka_print("%8.2lf %6.2lf %s" % (dG_mut, dG_mut-dG_ref, "Mutant"))
newProtein.writePDB(hydrogens=True, options=options)
def makeMutant(self, mutation=None, atoms=None, version=None, options=None):
"""
mutates the protein according to 'mutation' using 'method'
"""
import Source.mutate as mutate
newProtein = mutate.makeMutatedProtein(self, mutation=mutation, atoms=atoms, options=options)
return newProtein
def main():
"""
Simple main that creates the proteins, mutates the protein, calculates pKa values, and prints pKa files
"""
# I. preliminaries
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
version = propka.makeVersion(label=options.version_label)
# creating protein object and calculating reference folding energy
myProtein = Protein(pdbfile=pdbfiles[0], options=options)
myProtein.calculatePKA(version=version, options=options)
dG_ref = myProtein.calculateFoldingEnergy(options=options)
# creating a dictionary with atom objects needed for e.g. alignment mutations
atoms = mutate.makeCompositeAtomsDictionary(protein=myProtein,
pdbfiles=pdbfiles,
options=options)
# II. making mutations and calculating the folding energy
for mutation in options.mutations:
print(mutation)
newProtein = mutate.makeMutatedProtein(myProtein,
atoms=atoms,
mutation=mutation,
options=options)
# calculating pKa values for ionizable residues
newProtein.calculatePKA(version=version, options=options)
newProtein.writePKA(options=options)
dG_mut = newProtein.calculateFoldingEnergy(options=options)
print("staliblization:")
print("%8.2lf %6.2lf %s" % (dG_ref, dG_ref - dG_ref, "WT"))
print("%8.2lf %6.2lf %s" % (dG_mut, dG_mut - dG_ref, "Mutant"))
newProtein.writePDB(hydrogens=True, options=options)