| 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()) |
|
|
