binding_affinity.py

# coding=utf-8
# 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.
"""TODO: A dataset of protein sequences, ligand SMILES and binding affinities."""

import huggingface_hub
import pandas as pd
import os
import pyarrow.parquet as pq
import datasets


# TODO: Add BibTeX citation
# Find for instance the citation on arxiv or on the dataset repo/website
_CITATION = """\
@InProceedings{huggingface:dataset,
title = {jglaser/binding_affinity},
author={Jens Glaser, ORNL
},
year={2021}
}
"""

# TODO: Add description of the dataset here
# You can copy an official description
_DESCRIPTION = """\
A dataset to refine language models on protein-ligand binding affinity prediction.
"""

# TODO: Add a link to an official homepage for the dataset here
_HOMEPAGE = ""

# TODO: Add the licence for the dataset here if you can find it
_LICENSE = "BSD two-clause"

# TODO: Add link to the official dataset URLs here
# The HuggingFace dataset library don't host the datasets but only point to the original files
# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
_URLs = {
    'default': ["https://huggingface.co/datasets/jglaser/binding_affinity/resolve/main/data/all.parquet"],
}


# TODO: Name of the dataset usually match the script name with CamelCase instead of snake_case
class BindingAffinity(datasets.ArrowBasedBuilder):
    """List of protein sequences, ligand SMILES and binding affinities."""

    VERSION = datasets.Version("1.0.0")

    # 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="first_domain", version=VERSION, description="This part of my dataset covers a first domain"),
    #    datasets.BuilderConfig(name="second_domain", version=VERSION, description="This part of my dataset covers a second domain"),
    #]

    #DEFAULT_CONFIG_NAME = "affinities"  # It's not mandatory to have a default configuration. Just use one if it make sense.

    def _info(self):
        # TODO: This method specifies the datasets.DatasetInfo object which contains informations and typings for the dataset
        #if self.config.name == "first_domain":  # This is the name of the configuration selected in BUILDER_CONFIGS above
        #    features = datasets.Features(
        #        {
        #            "sentence": datasets.Value("string"),
        #             "option1": datasets.Value("string"),
        #            "answer": datasets.Value("string")
        #            # These are the features of your dataset like images, labels ...
        #        }
        #    )
        #else:  # This is an example to show how to have different features for "first_domain" and "second_domain"
        features = datasets.Features(
            {
                "affinity_uM": datasets.Value("float"),
                "neg_log10_affinity_M": datasets.Value("float"),
                # These are the features of your dataset like images, labels ...
            }
        )
        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,
            # specify them here. They'll be used if as_supervised=True in
            # builder.as_dataset.
            supervised_keys=None,
            # 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):
        """Returns SplitGenerators."""
        # 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
        my_urls = _URLs[self.config.name]
        files = dl_manager.download_and_extract(my_urls)
        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                # These kwargs will be passed to _generate_examples
                gen_kwargs={
                    "filepath": files[0],
                    "split": "train",
                },
            ),
#            datasets.SplitGenerator(
#                name=datasets.Split.TEST,
#                # These kwargs will be passed to _generate_examples
#                gen_kwargs={
#                    "filepath": os.path.join(data_dir, "test.parquet"),
#                    "split": "test"
#                },
#            ),
#            datasets.SplitGenerator(
#                name=datasets.Split.VALIDATION,
#                # These kwargs will be passed to _generate_examples
#                gen_kwargs={
#                    "filepath": os.path.join(data_dir, "dev.parquet"),
#                    "split": "dev",
#                },
#            ),
        ]

    def _generate_examples(
        self, filepath, split  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
    ):
        """ Yields examples as (key, example) tuples. """
        # This method handles input defined in _split_generators to yield (key, example) tuples from the dataset.
        # The `key` is here for legacy reason (tfds) and is not important in itself.

        df = pd.read_parquet(filepath)
        for k, row in df.iterrows():
            yield k, {
                "seq": row["seq"],
                "smiles": row["smiles"],
                "neg_log10_affinity_M": row["neg_log10_affinity_M"],
                "affinity_uM": row["affinity_uM"],
            }

    def _generate_tables(
        self, filepath, split  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
    ):
        df = pq.read_table(filepath)
        yield split, df