def main():
""" Entry point for the aizynthcli command
"""
args = _get_arguments()
if args.nproc:
return _multiprocess_smiles(args)
multi_smiles = os.path.exists(args.smiles)
file_level_logging = logging.DEBUG if args.log_to_file else None
setup_logger(logging.INFO, file_level_logging)
finder = AiZynthFinder(configfile=args.config)
_select_stocks(finder, args)
finder.expansion_policy.select(args.policy
or finder.expansion_policy.items[0])
try:
finder.filter_policy.select(args.policy)
except KeyError:
pass
if multi_smiles:
_process_multi_smiles(args.smiles, finder, args.output)
else:
_process_single_smiles(args.smiles, finder, args.output)
def _multiprocess_smiles(args: argparse.Namespace) -> None:
def create_cmd(index, filename):
cmd_args = [
"aizynthcli",
"--smiles",
filename,
"--config",
args.config,
"--output",
hdf_files[index - 1],
]
if args.policy:
cmd_args.extend(["--policy", args.policy])
if args.stocks:
cmd_args.append("--stocks")
cmd_args.extend(args.stocks)
if args.cluster:
cmd_args.append("--cluster")
return cmd_args
if not os.path.exists(args.smiles):
raise ValueError(
"For multiprocessing execution the --smiles argument needs to be a filename"
)
setup_logger(logging.INFO)
filenames = split_file(args.smiles, args.nproc)
hdf_files = [tempfile.mktemp(suffix=".hdf") for _ in range(args.nproc)]
start_processes(filenames, "aizynthcli", create_cmd)
if not all(os.path.exists(filename) for filename in hdf_files):
raise FileNotFoundError(
"Not all output files produced. Please check the individual log files: 'aizynthcli*.log'"
)
cat_hdf_files(hdf_files, args.output or "output.hdf5")
def __init__(self, configfile, setup=True):
setup_logger(logging.INFO)
self.finder = AiZynthFinder(configfile=configfile)
self._input = dict()
self._output = dict()
self._buttons = dict()
if setup:
self.setup()
def __init__(self, configfile: str, setup: bool = True) -> None:
setup_logger(logging.INFO)
self.finder = AiZynthFinder(configfile=configfile)
self._input: StrDict = dict()
self._output: StrDict = dict()
self._buttons: StrDict = dict()
if setup:
self.setup()
def __init__(self, configfile: str, setup: bool = True) -> None:
# pylint: disable=used-before-assignment
setup_logger(logging.INFO)
self.finder = AiZynthFinder(configfile=configfile)
self._input: StrDict = dict()
self._output: StrDict = dict()
self._buttons: StrDict = dict()
if setup:
self.setup()
def main():
""" Entry point for the aizynthcli command
"""
args = _get_arguments()
multi_smiles = os.path.exists(args.smiles)
file_level_logging = logging.DEBUG if args.log_to_file else None
setup_logger(logging.INFO, file_level_logging)
finder = AiZynthFinder(configfile=args.config)
_select_stocks(finder, args)
finder.policy.select_policy(args.policy
or finder.policy.available_policies()[0])
if multi_smiles:
_process_multi_smiles(args.smiles, finder, args.output)
else:
_process_single_smiles(args.smiles, finder, args.output)
def main() -> None:
"""Entry point for the aizynthcli command"""
args = _get_arguments()
if args.nproc:
_multiprocess_smiles(args)
return
multi_smiles = os.path.exists(args.smiles)
file_level_logging = logging.DEBUG if args.log_to_file else None
setup_logger(logging.INFO, file_level_logging)
finder = AiZynthFinder(configfile=args.config)
_select_stocks(finder, args)
finder.expansion_policy.select(args.policy
or finder.expansion_policy.items[0])
finder.filter_policy.select(args.filter)
func = _process_multi_smiles if multi_smiles else _process_single_smiles
func(args.smiles, finder, args.output, args.cluster,
args.route_distance_model)