pdb_protein_ligand_complexes.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 complex coordinates."""

import huggingface_hub
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/pdb_protein_ligand_complexes},
author={Jens Glaser, ORNL
},
year={2022}
}
"""

# TODO: Add description of the dataset here
# You can copy an official description
_DESCRIPTION = """\
A dataset to fine-tune language models on protein-ligand complex structures
"""

# 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)
_URL = "https://huggingface.co/datasets/jglaser/pdb_protein_ligand_complexes/resolve/main/"
_data_dir = "data/"
_file_names = {'default': _data_dir+'pdb.parquet'}

_URLs = {name: _URL+_file_names[name] for name in _file_names}


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

    VERSION = datasets.Version("1.0.0")

    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(
            {
                "pdb_id": datasets.Value("string"),
                "lig_id": datasets.Value("string"),
                "seq": datasets.Value("string"),
                "smiles": datasets.Value("string"),
                "ligand_xyz": datasets.Sequence(datasets.Sequence(datasets.Value('float32'))),
                "receptor_xyz": datasets.Sequence(datasets.Sequence(datasets.Value('float32'))),
                # 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
        files = dl_manager.download_and_extract(_URLs)

        return [
            datasets.SplitGenerator(
                # These kwargs will be passed to _generate_examples
                name=datasets.Split.TRAIN,
                gen_kwargs={
                    'filepath': files["default"],
                },
            ),

        ]

    def _generate_tables(
        self, filepath
    ):
        from pyarrow import fs
        local = fs.LocalFileSystem()

        for i, f in enumerate([filepath]):
            yield i, pq.read_table(f,filesystem=local)