def main():
"""
This is the main that just performs the determinant search
"""
# I. preliminaries
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
version = propka.makeVersion(label=options.version_label)
# creating protein object
myProtein = Protein(pdbfile=pdbfiles[0], options=options)
# creating a dictionary with atom objects needed for e.g. alignment mutations
atoms = makeCompositeAtomsDictionary(protein=myProtein,
pdbfiles=pdbfiles,
options=options)
# II. optimise 'single-site' mutation and selecting the good determinants
mutations = []
for mutation in options.mutations:
# II.a. combinatorial search of 'determinants' for each site
best_mutation = myProtein.optimizeMutationDeterminants(
atoms=atoms, mutation=mutation, version=version, options=options)
if best_mutation != None:
mutations.append(best_mutation)
def main():
"""
This is the main that just performs the determinant search
"""
# I. preliminaries
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
version = propka.makeVersion(label=options.version_label)
# creating protein object
myProtein = Protein(pdbfile=pdbfiles[0], options=options)
# creating a dictionary with atom objects needed for e.g. alignment mutations
atoms = makeCompositeAtomsDictionary(protein=myProtein, pdbfiles=pdbfiles, options=options)
# II. optimise 'single-site' mutation and selecting the good determinants
mutations = []
for mutation in options.mutations:
# II.a. combinatorial search of 'determinants' for each site
best_mutation = myProtein.optimizeMutationDeterminants(atoms=atoms, mutation=mutation, version=version, options=options)
if best_mutation != None:
mutations.append( best_mutation )
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 main():
"""
This is a tailor-made propka-executable for propka's GUI, but also useful for commandline execution
"""
# I. preliminaries
# loading options, flaggs and arguments; making a version object
options, pdbfiles = lib.loadOptions()
version = propka.makeVersion(label=options.version_label)
# creating the protein object
myProtein = Protein(pdbfile=pdbfiles[0], options=options)
# creating a dictionary with atom objects needed for e.g. alignment mutations
atoms = makeCompositeAtomsDictionary(protein=myProtein,
pdbfiles=pdbfiles,
options=options)
# II. optimise 'single-site' mutation and selecting the good determinants
mutations = []
for mutation in options.mutations:
# II.a. combinatorial search of 'determinants' for each site
best_mutation = myProtein.optimizeMutationDeterminants(
atoms=atoms, mutation=mutation, version=version, options=options)
if best_mutation != None:
mutations.append(best_mutation)
# III. combinatorial search of single-site mutations with their resulting 'determinants'
if len(mutations) > 0:
best_mutation = myProtein.optimizeMultipleMutations(
mutations=mutations, atoms=atoms, version=version, options=options)
else:
print("Could not find any mutation combination more stable than WT\n")
sys.exit(8)
def main():
"""
This is a tailor-made propka-executable for propka's GUI, but also useful for commandline execution
"""
# I. preliminaries
# loading options, flaggs and arguments; making a version object
options, pdbfiles = lib.loadOptions()
version = propka.makeVersion(label=options.version_label)
# creating the protein object
myProtein = Protein(pdbfile=pdbfiles[0], options=options)
# creating a dictionary with atom objects needed for e.g. alignment mutations
atoms = makeCompositeAtomsDictionary(protein=myProtein, pdbfiles=pdbfiles, options=options)
# II. optimise 'single-site' mutation and selecting the good determinants
mutations = []
for mutation in options.mutations:
# II.a. combinatorial search of 'determinants' for each site
best_mutation = myProtein.optimizeMutationDeterminants(atoms=atoms, mutation=mutation, version=version, options=options)
if best_mutation != None:
mutations.append( best_mutation )
# III. combinatorial search of single-site mutations with their resulting 'determinants'
if len(mutations) > 0:
best_mutation = myProtein.optimizeMultipleMutations(mutations=mutations, atoms=atoms, version=version, options=options)
else:
pka_print("Could not find any mutation combination more stable than WT\n")
sys.exit(8)
def main():
"""
Simple main that creates the proteins, protonates them, and prints new pdb files with hydrogen atoms
"""
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
for pdbfile in pdbfiles:
# creating protein object
myProtein = Protein(pdbfile=pdbfile, options=options)
filename = "%s_new.pdb" % (myProtein.name)
myProtein.writePDB(filename=filename, hydrogens=True)
def main():
"""
Simple main that creates the proteins, protonates them, and prints new pdb files with hydrogen atoms
"""
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
for pdbfile in pdbfiles:
# creating protein object
myProtein = Protein(pdbfile=pdbfile, options=options)
filename = "%s_new.pdb" % (myProtein.name)
myProtein.writePDB(filename=filename, hydrogens=True)
def main():
"""
Simple main that creates the proteins, calculates pKa values, and prints pKa files
"""
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
for pdbfile in pdbfiles:
# creating protein object
myProtein = Protein(pdbfile=pdbfile, options=options)
# calculating pKa values for ionizable residues
myProtein.calculatePKA(options=options)
# printing pka file
myProtein.writePKA(options=options)
def main():
"""
Simple main that creates the proteins, calculates pKa values, and prints pKa files
"""
# loading options, flaggs and arguments
options, pdbfiles = lib.loadOptions()
for pdbfile in pdbfiles:
# creating protein object
myProtein = Protein(pdbfile=pdbfile, options=options)
# calculating pKa values for ionizable residues
myProtein.calculatePKA(options=options)
# printing pka file
myProtein.writePKA(options=options)
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)
