pipeline/prepare_target.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))

from libs.docking.backend_rdock import RDockBackend
from libs.utils.config import load_config


def main() -> int:
    parser = argparse.ArgumentParser(description="Prepare target structure for docking")
    parser.add_argument("--config", default="configs/default.yaml")
    parser.add_argument("--work-dir", default="results/target_prep")
    args = parser.parse_args()

    cfg = load_config(args.config)
    root = Path(__file__).resolve().parents[1]
    backend = RDockBackend()
    target_path = root / cfg["data"]["target_path"]
    context = backend.prepare_target(target_path, root / args.work_dir)
    print(json.dumps({k: str(v) for k, v in context.items()}, indent=2))
    return 0


if __name__ == "__main__":
    raise SystemExit(main())