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"):