# 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. """loading script for the pubchem-07-23-2024 data""" import ijson import datasets _CITATION = """\ @article{Kim:2022:D1373, author = {Kim, Sunghwan and Chen, Jie and Cheng, Tiejun and Gindulyte, Asta and He, Jia and He, Siqian and Li, Qingliang and Shoemaker, Benjamin A and Thiessen, Paul A and Yu, Bo and Zaslavsky, Leonid and Zhang, Jian and Bolton, Evan E}, title = "{PubChem 2023 update}", journal = {Nucleic Acids Research}, volume = {51}, pages = {D1373-D1380}, year = {2022}, doi = {10.1093/nar/gkac956} } """ _DESCRIPTION = """\ PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information \ resource that serves a wide range of use cases. In the past \ two years, a number of changes were made to PubChem. Data from more than 120 \ data sources was added to PubChem. Some major highlights include: the \ integration of Google Patents data into PubChem, which greatly expanded the \ coverage of the PubChem Patent data collection; the creation of the Cell Line \ and Taxonomy data collections, which provide quick and easy access to chemical \ information for a given cell line and taxon, respectively; and the update of \ the bioassay data model. In addition, new functionalities were added to the \ PubChem programmatic access protocols, PUG-REST and PUG-View, including support \ for target-centric data download for a given protein, gene, pathway, cell line, \ and taxon and the addition of the `standardize` option to PUG-REST, which \ returns the standardized form of an input chemical structure. A significant \ update was also made to PubChemRDF. The present paper provides an overview of \ these changes. """ _HOMEPAGE = "https://pubchem.ncbi.nlm.nih.gov" _LICENSE = "https://www.ncbi.nlm.nih.gov/home/about/policies/#data" _BASE_DATA_URL_FORMAT_STR = "https://huggingface.co/datasets/molssiai-hub/pubchem-07-23-2024/resolve/main/data/train/Compound_{range}.json" _CONFIG_NAMES = [ "pubchem-07-23-2024" ] _FEATURE_KEYS = [ 'PUBCHEM_COMPOUND_CID', 'PUBCHEM_COMPOUND_CANONICALIZED', 'PUBCHEM_CACTVS_COMPLEXITY', 'PUBCHEM_CACTVS_HBOND_ACCEPTOR', 'PUBCHEM_CACTVS_HBOND_DONOR', 'PUBCHEM_CACTVS_ROTATABLE_BOND', 'PUBCHEM_CACTVS_SUBSKEYS', 'PUBCHEM_IUPAC_OPENEYE_NAME', 'PUBCHEM_IUPAC_CAS_NAME', 'PUBCHEM_IUPAC_NAME_MARKUP', 'PUBCHEM_IUPAC_NAME', 'PUBCHEM_IUPAC_SYSTEMATIC_NAME', 'PUBCHEM_IUPAC_TRADITIONAL_NAME', 'PUBCHEM_IUPAC_INCHI', 'PUBCHEM_IUPAC_INCHIKEY', 'PUBCHEM_XLOGP3_AA', 'PUBCHEM_EXACT_MASS', 'PUBCHEM_MOLECULAR_FORMULA', 'PUBCHEM_MOLECULAR_WEIGHT', 'PUBCHEM_OPENEYE_CAN_SMILES', 'PUBCHEM_OPENEYE_ISO_SMILES', 'PUBCHEM_CACTVS_TPSA', 'PUBCHEM_MONOISOTOPIC_WEIGHT', 'PUBCHEM_TOTAL_CHARGE', 'PUBCHEM_HEAVY_ATOM_COUNT', 'PUBCHEM_ATOM_DEF_STEREO_COUNT', 'PUBCHEM_ATOM_UDEF_STEREO_COUNT', 'PUBCHEM_BOND_DEF_STEREO_COUNT', 'PUBCHEM_BOND_UDEF_STEREO_COUNT', 'PUBCHEM_ISOTOPIC_ATOM_COUNT', 'PUBCHEM_COMPONENT_COUNT', 'PUBCHEM_CACTVS_TAUTO_COUNT', 'PUBCHEM_COORDINATE_TYPE', 'PUBCHEM_BONDANNOTATIONS', 'COORDS', 'ATOMIC_INDICES', 'ATOMIC_SYMBOLS', 'ATOMIC_NUMBERS', 'ATOMIC_FORMAL_CHARGES', 'BOND_ORDERS', 'PUBCHEM_XLOGP3', 'PUBCHEM_NONSTANDARDBOND', 'PUBCHEM_REFERENCE_STANDARDIZATION' ] _FEATURE_TYPES = datasets.Features( { 'PUBCHEM_COMPOUND_CID': datasets.Value(dtype='string', id=None), 'PUBCHEM_COMPOUND_CANONICALIZED': datasets.Value(dtype='string', id=None), 'PUBCHEM_CACTVS_COMPLEXITY': datasets.Value(dtype='float64', id=None), 'PUBCHEM_CACTVS_HBOND_ACCEPTOR': datasets.Value(dtype='int64', id=None), 'PUBCHEM_CACTVS_HBOND_DONOR': datasets.Value(dtype='int64', id=None), 'PUBCHEM_CACTVS_ROTATABLE_BOND': datasets.Value(dtype='int64', id=None), 'PUBCHEM_CACTVS_SUBSKEYS': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_OPENEYE_NAME': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_CAS_NAME': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_NAME_MARKUP': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_NAME': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_SYSTEMATIC_NAME': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_TRADITIONAL_NAME': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_INCHI': datasets.Value(dtype='string', id=None), 'PUBCHEM_IUPAC_INCHIKEY': datasets.Value(dtype='string', id=None), 'PUBCHEM_XLOGP3_AA': datasets.Value(dtype='float64', id=None), 'PUBCHEM_EXACT_MASS': datasets.Value(dtype='float64', id=None), 'PUBCHEM_MOLECULAR_FORMULA': datasets.Value(dtype='string', id=None), 'PUBCHEM_MOLECULAR_WEIGHT': datasets.Value(dtype='float64', id=None), 'PUBCHEM_OPENEYE_CAN_SMILES': datasets.Value(dtype='string', id=None), 'PUBCHEM_OPENEYE_ISO_SMILES': datasets.Value(dtype='string', id=None), 'PUBCHEM_CACTVS_TPSA': datasets.Value(dtype='float64', id=None), 'PUBCHEM_MONOISOTOPIC_WEIGHT': datasets.Value(dtype='float64', id=None), 'PUBCHEM_TOTAL_CHARGE': datasets.Value(dtype='int64', id=None), 'PUBCHEM_HEAVY_ATOM_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_ATOM_DEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_ATOM_UDEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_BOND_DEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_BOND_UDEF_STEREO_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_ISOTOPIC_ATOM_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_COMPONENT_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_CACTVS_TAUTO_COUNT': datasets.Value(dtype='int64', id=None), 'PUBCHEM_COORDINATE_TYPE': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), 'PUBCHEM_BONDANNOTATIONS': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), 'COORDS': datasets.Sequence(feature=datasets.Value(dtype='float64', id=None), length=-1, id=None), 'ATOMIC_INDICES': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), 'ATOMIC_SYMBOLS': datasets.Sequence(feature=datasets.Value(dtype='string', id=None), length=-1, id=None), 'ATOMIC_NUMBERS': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), 'ATOMIC_FORMAL_CHARGES': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), 'BOND_ORDERS': datasets.Sequence(feature=datasets.Value(dtype='int64', id=None), length=-1, id=None), 'PUBCHEM_XLOGP3': datasets.Value(dtype='string', id=None), 'PUBCHEM_NONSTANDARDBOND': datasets.Value(dtype='string', id=None), 'PUBCHEM_REFERENCE_STANDARDIZATION': datasets.Value(dtype='string', id=None) } ) _ID_RANGES = [ '000000001_000500000', '000500001_001000000', '001000001_001500000', '001500001_002000000', '002000001_002500000', '002500001_003000000', '003000001_003500000', '003500001_004000000', '004000001_004500000', '004500001_005000000', '005000001_005500000', '005500001_006000000', '006000001_006500000', '006500001_007000000', '007000001_007500000', '007500001_008000000', '008000001_008500000', '008500001_009000000', '009000001_009500000', '009500001_010000000', '010000001_010500000', '010500001_011000000', '011000001_011500000', '011500001_012000000', '012000001_012500000', '012500001_013000000', '013000001_013500000', '013500001_014000000', '014000001_014500000', '014500001_015000000', '015000001_015500000', '015500001_016000000', '016000001_016500000', '016500001_017000000', '017000001_017500000', '017500001_018000000', '018000001_018500000', '018500001_019000000', '019000001_019500000', '019500001_020000000', '020000001_020500000', '020500001_021000000', '021000001_021500000', '021500001_022000000', '022000001_022500000', '022500001_023000000', '023000001_023500000', '023500001_024000000', '024000001_024500000', '024500001_025000000', '025000001_025500000', '025500001_026000000', '026000001_026500000', '026500001_027000000', '027000001_027500000', '027500001_028000000', '028000001_028500000', '028500001_029000000', '029000001_029500000', '029500001_030000000', '030000001_030500000', '030500001_031000000', '031000001_031500000', '031500001_032000000', '032000001_032500000', '032500001_033000000', '033000001_033500000', '033500001_034000000', '034000001_034500000', '034500001_035000000', '035000001_035500000', '035500001_036000000', '036000001_036500000', '036500001_037000000', '037000001_037500000', '037500001_038000000', '038000001_038500000', '038500001_039000000', '039000001_039500000', '039500001_040000000', '040000001_040500000', '040500001_041000000', '041000001_041500000', '041500001_042000000', '042000001_042500000', '042500001_043000000', '043000001_043500000', '043500001_044000000', '044000001_044500000', '044500001_045000000', '045000001_045500000', '045500001_046000000', '046000001_046500000', '046500001_047000000', '047000001_047500000', '047500001_048000000', '048000001_048500000', '048500001_049000000', '049000001_049500000', '049500001_050000000', '050000001_050500000', '050500001_051000000', '051000001_051500000', '051500001_052000000', '052000001_052500000', '052500001_053000000', '053000001_053500000', '053500001_054000000', '054000001_054500000', '054500001_055000000', '055000001_055500000', '055500001_056000000', '056000001_056500000', '056500001_057000000', '057000001_057500000', '057500001_058000000', '058000001_058500000', '058500001_059000000', '059000001_059500000', '059500001_060000000', '060000001_060500000', '060500001_061000000', '061000001_061500000', '061500001_062000000', '062000001_062500000', '062500001_063000000', '063000001_063500000', '063500001_064000000', '064000001_064500000', '064500001_065000000', '065000001_065500000', '065500001_066000000', '066000001_066500000', '066500001_067000000', '067000001_067500000', '067500001_068000000', '068000001_068500000', '068500001_069000000', '069000001_069500000', '069500001_070000000', '070000001_070500000', '070500001_071000000', '071000001_071500000', '071500001_072000000', '072000001_072500000', '072500001_073000000', '073000001_073500000', '073500001_074000000', '074000001_074500000', '074500001_075000000', '075000001_075500000', '075500001_076000000', '076000001_076500000', '076500001_077000000', '077000001_077500000', '077500001_078000000', '078000001_078500000', '078500001_079000000', '079000001_079500000', '079500001_080000000', '080000001_080500000', '080500001_081000000', '081000001_081500000', '081500001_082000000', '082000001_082500000', '082500001_083000000', '083000001_083500000', '083500001_084000000', '084000001_084500000', '084500001_085000000', '085000001_085500000', '085500001_086000000', '086000001_086500000', '086500001_087000000', '087000001_087500000', '087500001_088000000', '088000001_088500000', '088500001_089000000', '089000001_089500000', '089500001_090000000', '090000001_090500000', '090500001_091000000', '091000001_091500000', '091500001_092000000', '092000001_092500000', '092500001_093000000', '093000001_093500000', '093500001_094000000', '094000001_094500000', '094500001_095000000', '095000001_095500000', '095500001_096000000', '096000001_096500000', '096500001_097000000', '097000001_097500000', '097500001_098000000', '098000001_098500000', '098500001_099000000', '099000001_099500000', '099500001_100000000', '100000001_100500000', '100500001_101000000', '101000001_101500000', '101500001_102000000', '102000001_102500000', '102500001_103000000', '103000001_103500000', '103500001_104000000', '104000001_104500000', '104500001_105000000', '105000001_105500000', '105500001_106000000', '106000001_106500000', '106500001_107000000', '107000001_107500000', '107500001_108000000', '108000001_108500000', '108500001_109000000', '109000001_109500000', '109500001_110000000', '110000001_110500000', '110500001_111000000', '111000001_111500000', '111500001_112000000', '112000001_112500000', '112500001_113000000', '113000001_113500000', '113500001_114000000', '114000001_114500000', '114500001_115000000', '115000001_115500000', '115500001_116000000', '116000001_116500000', '116500001_117000000', '117000001_117500000', '117500001_118000000', '118000001_118500000', '118500001_119000000', '119000001_119500000', '119500001_120000000', '120000001_120500000', '120500001_121000000', '121000001_121500000', '121500001_122000000', '122000001_122500000', '122500001_123000000', '123000001_123500000', '123500001_124000000', '124000001_124500000', '124500001_125000000', '125000001_125500000', '125500001_126000000', '126000001_126500000', '126500001_127000000', '127000001_127500000', '127500001_128000000', '128000001_128500000', '128500001_129000000', '129000001_129500000', '129500001_130000000', '130000001_130500000', '130500001_131000000', '131000001_131500000', '131500001_132000000', '132000001_132500000', '132500001_133000000', '133000001_133500000', '133500001_134000000', '134000001_134500000', '134500001_135000000', '135000001_135500000', '135500001_136000000', '136000001_136500000', '136500001_137000000', '137000001_137500000', '137500001_138000000', '138000001_138500000', '138500001_139000000', '139000001_139500000', '139500001_140000000', '140000001_140500000', '140500001_141000000', '141000001_141500000', '141500001_142000000', '142000001_142500000', '142500001_143000000', '143000001_143500000', '143500001_144000000', '144000001_144500000', '144500001_145000000', '145000001_145500000', '145500001_146000000', '146000001_146500000', '146500001_147000000', '147000001_147500000', '147500001_148000000', '148000001_148500000', '148500001_149000000', '149000001_149500000', '149500001_150000000', '150000001_150500000', '150500001_151000000', '151000001_151500000', '151500001_152000000', '152000001_152500000', '152500001_153000000', '153000001_153500000', '153500001_154000000', '154000001_154500000', '154500001_155000000', '155000001_155500000', '155500001_156000000', '156000001_156500000', '156500001_157000000', '157000001_157500000', '157500001_158000000', '158000001_158500000', '158500001_159000000', '159000001_159500000', '159500001_160000000', '160000001_160500000', '160500001_161000000', '161000001_161500000', '161500001_162000000', '162000001_162500000', '162500001_163000000', '163000001_163500000', '163500001_164000000', '164000001_164500000', '164500001_165000000', '165000001_165500000', '165500001_166000000', '166000001_166500000', '166500001_167000000', '167000001_167500000', '167500001_168000000', '168000001_168500000', '168500001_169000000', '169000001_169500000', '169500001_170000000', '170000001_170500000', '170500001_171000000', '171000001_171500000', '171500001_172000000' ] class PubChemConfig(datasets.BuilderConfig): """ Configuration class for the PubChem dataset. Args: features (dict): A dictionary specifying the features of the dataset. data_url (str): The URL to download the dataset. url (str): The URL to the dataset homepage. citation (str): The citation for the dataset. **kwargs: Additional keyword arguments. Attributes: version (datasets.Version): The version of the dataset. """ def __init__(self, features, url, citation, id_range, **kwargs): super(PubChemConfig, self).__init__( version=datasets.Version("0.0.0"), **kwargs ) self.features = features self.url = url self.citation = citation self.id_range = id_range class PubChem(datasets.GeneratorBasedBuilder): BUILDER_CONFIG_CLASS = PubChemConfig DEFAULT_CONFIG_NAME = "pubchem-07-23-2024" VERSION = datasets.Version("0.0.0") url = "https://huggingface.co/datasets/molssiai-hub/pubchem-07-23-2024" BUILDER_CONFIGS = [ PubChemConfig( name="pubchem-07-23-2024", description=_DESCRIPTION, features=_FEATURE_KEYS, url=url, citation=_CITATION, id_range=_ID_RANGES, ) ] def _info(self): if self.config.name in _CONFIG_NAMES: features = _FEATURE_TYPES else: raise NotImplementedError("Unknown configuration in _info") return datasets.DatasetInfo( description=_DESCRIPTION, features=features, homepage=_HOMEPAGE, supervised_keys=None, license=_LICENSE, citation=_CITATION, ) def _split_generators(self, dl_manager): if self.config.name in _CONFIG_NAMES: file_list = [] for range in self.config.id_range: file_list.append(_BASE_DATA_URL_FORMAT_STR.format( name=self.config.name, range=range)) else: raise NotImplementedError( "Unknown configuration in _split_generators") return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={ "filepaths": dl_manager.download(sorted(file_list)), }, ) ] def _generate_examples(self, filepaths): if self.config.name in _CONFIG_NAMES: idx = 0 for filepath in filepaths: with open(filepath, "rb") as f: items = ijson.items(f, "item", use_float=True) for data in items: yield idx, data idx += 1 else: raise NotImplementedError( "Unknown configuration in _generate_examples")