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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 | from __future__ import annotations
import argparse
import json
from pathlib import Path
import sys
ROOT_DIR = Path(__file__).resolve().parents[1]
if str(ROOT_DIR) not in sys.path:
sys.path.insert(0, str(ROOT_DIR))
import pandas as pd
from libs.docking.backend_rdock import RDockBackend
from libs.utils.config import load_config
def main() -> int:
parser = argparse.ArgumentParser(description="Dock one batch of ligands")
parser.add_argument("--config", default="configs/default.yaml")
parser.add_argument("--ligands", required=True, help="CSV with ligand_id,smiles")
parser.add_argument("--output", default="results/dock_batch.csv")
parser.add_argument("--allow-mock", action="store_true")
args = parser.parse_args()
cfg = load_config(args.config)
root = Path(__file__).resolve().parents[1]
backend = RDockBackend()
target_path = root / cfg["data"]["target_path"]
target_ctx = backend.prepare_target(target_path, root / "results/dock_batch_target")
lig_df = pd.read_csv(args.ligands)
work = root / "results/dock_batch_work"
files = [backend.prepare_ligand(str(r.ligand_id), str(r.smiles), work) for r in lig_df.itertuples(index=False)]
results = backend.dock(target_ctx, files, work / "docking", allow_mock=args.allow_mock)
parsed = backend.parse_results(results)
out = root / args.output
out.parent.mkdir(parents=True, exist_ok=True)
pd.DataFrame(parsed).to_csv(out, index=False)
print(json.dumps({"output": str(out), "rows": len(parsed)}, indent=2))
return 0
if __name__ == "__main__":
raise SystemExit(main())
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