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 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 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 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)