GOOD.data.good_datasets.orig_zinc

The original 250k ZINC dataset from the ZINC database and the “Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules” paper

Classes

ZINC(root, name[, transform, pre_transform, ...])

The ZINC dataset from the ZINC database and the "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules" paper, containing about 250,000 molecular graphs with up to 38 heavy atoms.
class GOOD.data.good_datasets.orig_zinc.ZINC(root, name, transform=None, pre_transform=None, pre_filter=None, subset=False)[source]

Bases: InMemoryDataset

The ZINC dataset from the ZINC database and the “Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules” paper, containing about 250,000 molecular graphs with up to 38 heavy atoms. The task is to regress a synthetic computed property dubbed as the constrained solubility.

Parameters

  • root (string) – Root directory where the dataset should be saved.

  • subset (boolean, optional) – If set to True, will only load a subset of the dataset (12,000 molecular graphs), following the “Benchmarking Graph Neural Networks” paper. (default: False)

  • split (string, optional) – If "train", loads the training dataset. If "val", loads the validation dataset. If "test", loads the test dataset. (default: "train")

  • transform (callable, optional) – A function/transform that takes in an torch_geometric.data.Data object and returns a transformed version. The data object will be transformed before every access. (default: None)

  • pre_transform (callable, optional) – A function/transform that takes in an torch_geometric.data.Data object and returns a transformed version. The data object will be transformed before being saved to disk. (default: None)

  • pre_filter (callable, optional) – A function that takes in an torch_geometric.data.Data object and returns a boolean value, indicating whether the data object should be included in the final dataset. (default: None)

download()[source]

Downloads the dataset to the self.raw_dir folder.

process()[source]

Processes the dataset to the self.processed_dir folder.

property processed_file_names

The name of the files in the self.processed_dir folder that must be present in order to skip processing.

property raw_file_names

The name of the files in the self.raw_dir folder that must be present in order to skip downloading.