Source code for torchdrug.datasets.tox21

import os

from torchdrug import data, utils
from torchdrug.core import Registry as R
from torchdrug.utils import doc


[docs]@R.register("datasets.Tox21") @doc.copy_args(data.MoleculeDataset.load_csv, ignore=("smiles_field", "target_fields")) class Tox21(data.MoleculeDataset): """ Qualitative toxicity measurements on 12 biological targets, including nuclear receptors and stress response pathways. Statistics: - #Molecule: 7,831 - #Classification task: 12 Parameters: path (str): path to store the dataset verbose (int, optional): output verbose level **kwargs """ url = "http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/tox21.csv.gz" md5 = "2882d69e70bba0fec14995f26787cc25" target_fields = ["NR-AR", "NR-AR-LBD", "NR-AhR", "NR-Aromatase", "NR-ER", "NR-ER-LBD", "NR-PPAR-gamma", "SR-ARE", "SR-ATAD5", "SR-HSE", "SR-MMP", "SR-p53"] def __init__(self, path, verbose=1, **kwargs): path = os.path.expanduser(path) if not os.path.exists(path): os.makedirs(path) self.path = path zip_file = utils.download(self.url, path, md5=self.md5) csv_file = utils.extract(zip_file) self.load_csv(csv_file, smiles_field="smiles", target_fields=self.target_fields, verbose=verbose, **kwargs)