--- a +++ b/torchdrug/datasets/zinc250k.py @@ -0,0 +1,37 @@ +import os + +from torchdrug import data, utils +from torchdrug.core import Registry as R + + +@R.register("datasets.ZINC250k") +@utils.copy_args(data.MoleculeDataset.load_csv, ignore=("smiles_field", "target_fields")) +class ZINC250k(data.MoleculeDataset): + """ + Subset of ZINC compound database for virtual screening. + + Statistics: + - #Molecule: 498,910 + - #Regression task: 2 + + Parameters: + path (str): path to store the dataset + verbose (int, optional): output verbose level + **kwargs + """ + + url = "https://raw.githubusercontent.com/aspuru-guzik-group/chemical_vae/master/models/zinc_properties/" \ + "250k_rndm_zinc_drugs_clean_3.csv" + md5 = "b59078b2b04c6e9431280e3dc42048d5" + target_fields = ["logP", "qed"] + + def __init__(self, path, verbose=1, **kwargs): + path = os.path.expanduser(path) + if not os.path.exists(path): + os.makedirs(path) + self.path = path + + file_name = utils.download(self.url, path, md5=self.md5) + + self.load_csv(file_name, smiles_field="smiles", target_fields=self.target_fields, + verbose=verbose, **kwargs) \ No newline at end of file