Module molcrawl.protein_sequence.dataset.download_proteingym

Download ProteinGym v1.3 DMS substitution data for fine-tuning.

The downloaded CSV files are saved to save_path so that prepare_proteingym.py can read them directly.

Usage

from molcrawl.protein_sequence.dataset.download_proteingym import download_proteingym download_proteingym("/path/to/proteingym_v1.3")

Functions

def download_proteingym(save_path: str | pathlib.Path) ‑> pathlib.Path

Expand source code

def download_proteingym(save_path: Union[str, Path]) -> Path:
    """
    Download ProteinGym v1.3 DMS substitution CSV files into *save_path*.

    After this function returns, *save_path* will contain:
        DMS_ProteinGym_substitutions/   ← one CSV per assay
        DMS_substitutions.csv           ← reference metadata (one row per assay)

    Args:
        save_path: Destination directory (created if missing).

    Returns:
        Path to the directory containing individual assay CSV files.
    """
    save_path = Path(save_path)
    save_path.mkdir(parents=True, exist_ok=True)

    # --- substitutions zip --------------------------------------------------
    zip_path = save_path / "DMS_ProteinGym_substitutions.zip"
    _download_with_progress(_SUBSTITUTIONS_URL, zip_path)

    csv_dir = save_path / "DMS_ProteinGym_substitutions"
    if not csv_dir.exists():
        logger.info("Extracting %s ...", zip_path)
        with zipfile.ZipFile(zip_path, "r") as zf:
            zf.extractall(save_path)
        logger.info("Extracted to %s", csv_dir)
    else:
        logger.info("Already extracted: %s", csv_dir)

    # --- reference CSV ------------------------------------------------------
    ref_path = save_path / "DMS_substitutions.csv"
    _download_with_progress(_REFERENCE_URL, ref_path)

    return csv_dir

Download ProteinGym v1.3 DMS substitution CSV files into save_path.

After this function returns, save_path will contain: DMS_ProteinGym_substitutions/ ← one CSV per assay DMS_substitutions.csv ← reference metadata (one row per assay)

Args

save_path

Destination directory (created if missing).

Returns

Path to the directory containing individual assay CSV files.