File size: 2,366 Bytes
504d922 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | from __future__ import annotations
import argparse
import json
import tarfile
import urllib.request
from pathlib import Path
import sys
ROOT = Path(__file__).resolve().parents[1]
if str(ROOT) not in sys.path:
sys.path.insert(0, str(ROOT))
from docking_pipeline.validation import validate_dud
def _resolve_data_dir(data_dir: str, download_url: str | None) -> str:
path = Path(data_dir)
if path.exists() or not download_url:
return str(path)
path.mkdir(parents=True, exist_ok=True)
archive = path / Path(download_url).name
urllib.request.urlretrieve(download_url, archive)
with tarfile.open(archive, "r:*") as tar:
tar.extractall(path)
children = [p for p in path.iterdir() if p.is_dir()]
return str(children[0] if len(children) == 1 else path)
def main() -> int:
parser = argparse.ArgumentParser(description="Run rDock DUD enrichment workflow for one system")
parser.add_argument("--data-dir", required=True, help="Directory containing DUD_rDock_TestSet systems")
parser.add_argument("--system", help="System ID, e.g. hivpr")
parser.add_argument("--out", required=True)
parser.add_argument("--n-runs", type=int, default=100)
parser.add_argument("--jobs", default="auto")
parser.add_argument("--cpu-fraction", type=float, default=0.85)
parser.add_argument("--download-if-missing", action="store_true")
parser.add_argument("--list-systems", action="store_true")
parser.add_argument("--download-url", help="Optional DUD_rDock_TestSet tar.gz URL to fetch when --data-dir is absent")
args = parser.parse_args()
from docking_pipeline.validation import discover_validation_systems, ensure_validation_data
data_dir = ensure_validation_data(
_resolve_data_dir(args.data_dir, args.download_url if args.download_if_missing else None),
"dud",
args.download_url,
args.download_if_missing,
)
if args.list_systems:
print(json.dumps([s.__dict__ for s in discover_validation_systems(data_dir, "dud")], indent=2))
else:
if not args.system:
raise SystemExit("--system is required unless --list-systems is used")
print(json.dumps(validate_dud(data_dir, args.system, args.out, n_runs=args.n_runs, jobs=args.jobs), indent=2))
return 0
if __name__ == "__main__":
raise SystemExit(main())
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