diff --git a/pacs/utils/fit.py b/pacs/utils/fit.py index 71df367..3a49021 100644 --- a/pacs/utils/fit.py +++ b/pacs/utils/fit.py @@ -1,5 +1,4 @@ import multiprocessing as mp -import subprocess from pathlib import Path from pacs.models.settings import MDsettings @@ -55,7 +54,7 @@ def fit_mdtraj(settings: MDsettings, trj_file: str, out_file: str) -> None: parent = Path(trj_file).parent stem = Path(trj_file).stem fit_trj_file = ( - f"{parent}/{stem}_fit{ext}" if out_file == None else f"{parent}/{out_file}" + f"{parent}/{stem}_fit{ext}" if out_file is None else f"{parent}/{out_file}" ) ref_structure = settings.reference diff --git a/pacs/utils/genfeature/genfeat.py b/pacs/utils/genfeature/genfeat.py index cab064e..33ef2cb 100644 --- a/pacs/utils/genfeature/genfeat.py +++ b/pacs/utils/genfeature/genfeat.py @@ -22,7 +22,7 @@ def save(self, cycle: int, replica: int, features: np.ndarray) -> None: features, ) LOGGER.info( - f"feature of trial{self.trial:03}cycle{cycle:03}replica{replica:03} was saved at {self.output_directory}/" + f"feature of trial{self.trial:03}cycle{cycle:03}replica{replica:03} was saved at {self.output_directory}/" # noqa B950 ) def prepare(self) -> None: @@ -43,7 +43,7 @@ def cal_parallel(self, calc_feature, *args, **kwargs) -> None: exit(1) cycle = re.findall(r"(\d+)", str(path))[1] replica = re.findall(r"(\d+)", str(path))[2] - trj_path = f"./trial{self.trial:03}/cycle{cycle:03}/replica{replica:03}/{self.trj_filename}" + trj_path = f"./trial{self.trial:03}/cycle{cycle:03}/replica{replica:03}/{self.trj_filename}" # noqa B950 future = executor.submit(calc_feature, trj_path, *args, **kwargs) job_dict_list.append( diff --git a/pacs/utils/parser.py b/pacs/utils/parser.py index e7795ae..035435b 100644 --- a/pacs/utils/parser.py +++ b/pacs/utils/parser.py @@ -160,7 +160,7 @@ def parse(self) -> MDsettings: "--keep_selection", type=str, required=True, - help='selection of molecules to be retained in trajectory files. (e.g. "not water")', + help='selection to be retained in trajectory files. (e.g. "not water")', ) parser_rmmol_mdtraj.add_argument( "-e",