| 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()) |
|
|
