pipeline/dock_batch.py

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())