Module molcrawl.compounds.utils.general

Functions

def combine_datasets(raw_data_dir: str, output_dir: str)

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def combine_datasets(raw_data_dir: str, output_dir: str):
    """
    Combine all datasets to generate OrganiX13

    Args:
        raw_data_dir: raw data directory
        output_dir: Integrated data output directory
    """
    combine_all(raw_data_dir, output_dir)

Combine all datasets to generate OrganiX13

Args

raw_data_dir

raw data directory

output_dir

Integrated data output directory

def download_additional_datasets(raw_data_dir: str)

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def download_additional_datasets(raw_data_dir: str):
    """Alias ​​for backwards compatibility. Please use download_llamol_datasets."""
    download_llamol_datasets(raw_data_dir)

Alias ​​for backwards compatibility. Please use download_llamol_datasets.

def download_datasets(raw_data_dir: str, output_dir: str)

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def download_datasets(raw_data_dir: str, output_dir: str):
    """
    Download and integrate all datasets (for legacy compatibility)

    Args:
        raw_data_dir: raw data storage directory
        output_dir: Integrated data output directory
    """
    download_zinc20(raw_data_dir)
    download_opv(raw_data_dir)
    download_llamol_datasets(raw_data_dir)
    combine_datasets(raw_data_dir, output_dir)

Download and integrate all datasets (for legacy compatibility)

Args

raw_data_dir

raw data storage directory

output_dir

Integrated data output directory

def download_llamol_datasets(raw_data_dir: str)

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def download_llamol_datasets(raw_data_dir: str):
    """
    LlaMol dataset (download from Fraunhofer-SCAI/llamol repository)

    Args:
        raw_data_dir: raw data storage directory (COMPOUNDS_DIR)
    """
    # Save in data/Fraunhofer-SCAI-llamol directory
    llamol_dir = os.path.join(raw_data_dir, "data", "Fraunhofer-SCAI-llamol")
    os.makedirs(llamol_dir, exist_ok=True)

    # Check the integrity of existing parquet files
    _verify_llamol_parquet_files(llamol_dir)

    download_datasets_from_repo(llamol_dir)

    # Create marker file
    data_dir = os.path.join(raw_data_dir, "data")
    marker_file = Path(data_dir) / "llamol_download.marker"
    marker_file.touch()

LlaMol dataset (download from Fraunhofer-SCAI/llamol repository)

Args

raw_data_dir

raw data storage directory (COMPOUNDS_DIR)

def download_opv(raw_data_dir: str)

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def download_opv(raw_data_dir: str):
    """
    Download OPV dataset

    Args:
        raw_data_dir: raw data storage directory (COMPOUNDS_DIR)
    """
    # save to data/opv directory
    opv_dir = os.path.join(raw_data_dir, "data", "opv")
    os.makedirs(opv_dir, exist_ok=True)

    OPV(opv_dir)

    # Create marker file
    data_dir = os.path.join(raw_data_dir, "data")
    marker_file = Path(data_dir) / "opv_download.marker"
    marker_file.touch()

Download OPV dataset

Args

raw_data_dir

raw data storage directory (COMPOUNDS_DIR)

def download_zinc20(raw_data_dir: str)

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def download_zinc20(raw_data_dir: str):
    """
    Download and convert ZINC20 dataset

    Args:
        raw_data_dir: raw data storage directory (COMPOUNDS_DIR)
    """
    download_zinc_files()
    # Save to data/zinc20 directory
    zinc_save_path = os.path.join(raw_data_dir, "data", "zinc20")
    convert_zinc_to_parquet(zinc_save_path)

    # Create marker file
    data_dir = os.path.join(raw_data_dir, "data")
    os.makedirs(data_dir, exist_ok=True)
    marker_file = Path(data_dir) / "zinc20_download.marker"
    marker_file.touch()

Download and convert ZINC20 dataset

Args

raw_data_dir

raw data storage directory (COMPOUNDS_DIR)