return job_dict._getvalue() def use_single_processor(settings, pdb_monomers, input_pdb_dir_path, pdb_data_dir, mutfile_data_dir, dataset_cases_by_pdb_chain): job_dict = {} for keypair in pdb_monomers: pdb_dir_path = os.path.join(input_pdb_dir_path, '%s.pdb' % keypair[0]) create_input_files(job_dict, settings, pdb_dir_path, pdb_data_dir, mutfile_data_dir, keypair, dataset_cases_by_pdb_chain[keypair]) sys.stdout.write('\n') return job_dict if __name__ == '__main__': import pprint try: arguments = docopt.docopt(__doc__.format(**locals())) except Exception, e: print('Failed while parsing arguments: %s.' % str(e)) sys.exit(1) # Set the PDB input path input_pdb_dir_path = '../../input/pdbs' # Read the settings file settings = rosetta.parse_settings.get_dict() # Read in the dataset file dataset_filepath = arguments['--dataset'][0] dataset_filename = os.path.splitext(os.path.split(dataset_filepath)[1])[0] if not os.path.exists(dataset_filepath): raise Exception('The dataset file %s does not exist.' % dataset_filepath)
f.write("%d%s %s PIKAA A\n" % (pdb_res, insertion_code, chain)) def make_pack_resfile(pack_resfile_path, close_residues_list): with open(pack_resfile_path, "w") as f: f.write(resfile_start) for atom_resnum, atom_insertion_code, atom_chain in close_residues_list: f.write("%d%s %s NATAA\n" % (atom_resnum, atom_insertion_code, atom_chain)) if __name__ == "__main__": import pprint try: arguments = docopt.docopt(__doc__.format(**locals())) except Exception as e: print(("Failed while parsing arguments: %s." % str(e))) sys.exit(1) if arguments.get("--output_directory"): job_output_directory = arguments["--output_directory"][0] if not (os.path.exists(job_output_directory)): raise Exception( "The specified output directory %s does not exist." % output_dir) if arguments.get("--extra_name"): extra_name = arguments["--extra_name"][0] if arguments.get("--number_repeats"):