portable_rdock_pipeline/scripts/download_example_smiles.py

from __future__ import annotations

import argparse
import csv
from pathlib import Path


ROOT = Path(__file__).resolve().parents[1]
DEFAULT_SOURCE_CSV = ROOT / "data" / "ligands" / "prelim_set_mdm2_4hg7" / "shared_library_dedup.csv"
DEFAULT_BUNDLED_SMI = ROOT / "data" / "examples" / "example_smiles_1000.smi"


def _write_rows(rows: list[tuple[str, str]], out: Path) -> Path:
    out.parent.mkdir(parents=True, exist_ok=True)
    out.write_text("\n".join(f"{smiles} {ligand_id}" for smiles, ligand_id in rows) + "\n", encoding="utf-8")
    return out


def _read_smi(path: Path, n: int) -> list[tuple[str, str]]:
    rows: list[tuple[str, str]] = []
    for idx, line in enumerate(path.read_text(encoding="utf-8").splitlines()):
        text = line.strip()
        if not text or text.startswith("#"):
            continue
        parts = text.split()
        smiles = parts[0]
        ligand_id = parts[1] if len(parts) > 1 else f"lig_{idx:05d}"
        rows.append((smiles, ligand_id))
        if len(rows) >= n:
            break
    return rows


def _read_csv_rows(path: Path, n: int) -> list[tuple[str, str]]:
    rows: list[tuple[str, str]] = []
    with path.open("r", encoding="utf-8", newline="") as handle:
        reader = csv.DictReader(handle)
        for idx, item in enumerate(reader):
            smiles = str(item.get("smiles", "")).strip()
            ligand_id = str(item.get("ligand_id", "")).strip() or f"lig_{idx:05d}"
            if not smiles:
                continue
            rows.append((smiles, ligand_id))
            if len(rows) >= n:
                break
    return rows


def main() -> int:
    parser = argparse.ArgumentParser(description="Prepare a real 1000-SMILES example file from the public benchmark library in this repo.")
    parser.add_argument("--n", type=int, default=1000)
    parser.add_argument("--out", default=str(DEFAULT_BUNDLED_SMI))
    args = parser.parse_args()

    out = Path(args.out)
    if DEFAULT_SOURCE_CSV.exists():
        rows = _read_csv_rows(DEFAULT_SOURCE_CSV, args.n)
        if len(rows) < args.n:
            raise SystemExit(
                f"Requested {args.n} SMILES but {DEFAULT_SOURCE_CSV} yielded only {len(rows)} rows."
            )
        _write_rows(rows, out)
        print(out)
        return 0

    if DEFAULT_BUNDLED_SMI.exists():
        rows = _read_smi(DEFAULT_BUNDLED_SMI, args.n)
        if len(rows) < args.n:
            raise SystemExit(
                f"Requested {args.n} SMILES but bundled file {DEFAULT_BUNDLED_SMI} contains only {len(rows)} rows."
            )
        _write_rows(rows, out)
        print(out)
        return 0

    raise SystemExit(
        "No real example 1000-SMILES source is available. Expected either "
        f"{DEFAULT_SOURCE_CSV} or {DEFAULT_BUNDLED_SMI}."
    )


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