# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """A tiny dataset containing 5 molecule configurations for fast inference example.""" import csv import json import os import torch import datasets # You can copy an official description _DESCRIPTION = """\ This data is a trimmed version of the GEOM Drugs Dataset. """ _HOMEPAGE = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JNGTDF" _LICENSE = "Creative Commons 1.0 Universal: https://creativecommons.org/publicdomain/zero/1.0/" _CITATION = """\ @data{DVN/JNGTDF_2021, author = {Axelrod, Simon and Gomez-Bombarelli, Rafael}, publisher = {Harvard Dataverse}, title = {{GEOM}}, year = {2021}, version = {V4}, doi = {10.7910/DVN/JNGTDF}, url = {https://doi.org/10.7910/DVN/JNGTDF} } """ # TODO: Add link to the official dataset URLs here # The HuggingFace Datasets library doesn't host the datasets but only points to the original files. # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method) _URLS = { "drugs": "https://huggingface.co/datasets/fusing/geodiff-example-data/tree/main/data/molecules.pkl", } class GeoDiffExampleData(datasets.GeneratorBasedBuilder): VERSION = datasets.Version("1.1.0") # This is an example of a dataset with multiple configurations. # If you don't want/need to define several sub-sets in your dataset, # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes. # If you need to make complex sub-parts in the datasets with configurable options # You can create your own builder configuration class to store attribute, inheriting from datasets.BuilderConfig # BUILDER_CONFIG_CLASS = MyBuilderConfig # You will be able to load one or the other configurations in the following list with # data = datasets.load_dataset('my_dataset', 'first_domain') # data = datasets.load_dataset('my_dataset', 'second_domain') BUILDER_CONFIGS = [ datasets.BuilderConfig(name="drugs", version=VERSION, description="This part of my dataset covers a first domain"), ] DEFAULT_CONFIG_NAME = "drugs" # It's not mandatory to have a default configuration. Just use one if it make sense. def _info(self): if self.config.name == "drugs": # This is the name of the configuration selected in BUILDER_CONFIGS above features = datasets.Features( { "num_molecules": 5, #datasets.Value("string"), # These are the features of your dataset like images, labels ... } ) else: raise NotImplementedError("Other Domains Not Added") return datasets.DatasetInfo( # This is the description that will appear on the datasets page. description=_DESCRIPTION, # This defines the different columns of the dataset and their types features=features, # Here we define them above because they are different between the two configurations # If there's a common (input, target) tuple from the features, uncomment supervised_keys line below and # specify them. They'll be used if as_supervised=True in builder.as_dataset. # supervised_keys=("sentence", "label"), # Homepage of the dataset for documentation homepage=_HOMEPAGE, # License for the dataset if available license=_LICENSE, # Citation for the dataset citation=_CITATION, ) def _split_generators(self, dl_manager): # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLS # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files. # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive urls = _URLS[self.config.name] data_dir = dl_manager.download_and_extract(urls) return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, # These kwargs will be passed to _generate_examples gen_kwargs={ "filepath": data_dir, "split": "train", }, ) ] # method parameters are unpacked from `gen_kwargs` as given in `_split_generators` def _generate_examples(self, filepath, split): # TODO: This method handles input defined in _split_generators to yield (key, example) tuples from the dataset. # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example. with open(filepath, encoding="utf-8") as f: data = torch.load(f) yield data