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sha256:c3530f2e243c446a057f971dc6f1fe37d6c7683bc2f862a1aa41039505877d8c +size 365453420 diff --git a/dataset_infos.json b/dataset_infos.json new file mode 100644 index 0000000000000000000000000000000000000000..6c6a9925a5db996a7caf865522e8e09c3cfdbf3c --- /dev/null +++ b/dataset_infos.json @@ -0,0 +1 @@ +{"default": {"description": "This dataset contains ~100M molecules from PubChem, with their SMILES and SELFIES representations.\n", "citation": "@ARTICLE{Kim2016-sz,\n title = \"{PubChem} Substance and Compound databases\",\n author = \"Kim, Sunghwan and Thiessen, Paul A and Bolton, Evan E and Chen,\n Jie and Fu, Gang and Gindulyte, Asta and Han, Lianyi and He,\n Jane and He, Siqian and Shoemaker, Benjamin A and Wang, Jiyao\n and Yu, Bo and Zhang, Jian and Bryant, Stephen H\",\n abstract = \"PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public\n repository for information on chemical substances and their\n biological activities, launched in 2004 as a component of the\n Molecular Libraries Roadmap Initiatives of the US National\n Institutes of Health (NIH). For the past 11 years, PubChem has\n grown to a sizable system, serving as a chemical information\n resource for the scientific research community. PubChem consists\n of three inter-linked databases, Substance, Compound and\n BioAssay. The Substance database contains chemical information\n deposited by individual data contributors to PubChem, and the\n Compound database stores unique chemical structures extracted\n from the Substance database. Biological activity data of\n chemical substances tested in assay experiments are contained in\n the BioAssay database. This paper provides an overview of the\n PubChem Substance and Compound databases, including data sources\n and contents, data organization, data submission using PubChem\n Upload, chemical structure standardization, web-based interfaces\n for textual and non-textual searches, and programmatic access.\n It also gives a brief description of PubChem3D, a resource\n derived from theoretical three-dimensional structures of\n compounds in PubChem, as well as PubChemRDF, Resource\n Description Framework (RDF)-formatted PubChem data for data\n sharing, analysis and integration with information contained in\n other databases.\",\n journal = \"Nucleic Acids Res.\",\n publisher = \"Oxford University Press (OUP)\",\n volume = 44,\n number = \"D1\",\n pages = \"D1202--13\",\n month = jan,\n year = 2016,\n language = \"en\"\n}\n", "homepage": "https://pubchem.ncbi.nlm.nih.gov/", "license": "", "features": {"PUBCHEM_COMPOUND_CID": {"dtype": "int32", "id": null, "_type": "Value"}, "CAN_SELFIES": {"dtype": "string", "id": null, "_type": "Value"}, "PUBCHEM_OPENEYE_CAN_SMILES": {"dtype": "string", "id": null, "_type": "Value"}}, "post_processed": null, "supervised_keys": null, "task_templates": null, "builder_name": "pubchem_selfies", "config_name": "default", "version": {"version_str": "1.1.0", "description": null, "major": 1, "minor": 1, "patch": 0}, "splits": {"train": {"name": "train", "num_bytes": 25852352277, "num_examples": 88568896, "dataset_name": "pubchem_selfies"}, "validation": {"name": "validation", "num_bytes": 3150855470, "num_examples": 11385090, "dataset_name": "pubchem_selfies"}, "test": {"name": "test", "num_bytes": 3520482172, "num_examples": 11044290, "dataset_name": "pubchem_selfies"}}, "download_checksums": {}, "download_size": 0, "post_processing_size": null, "dataset_size": 32523689919, "size_in_bytes": 32523689919}} \ No newline at end of file diff --git a/pubchem_selfies.py b/pubchem_selfies.py new file mode 100644 index 0000000000000000000000000000000000000000..8f592b27abeeec7d4d0bc7d60b099fe50cd0f1c8 --- /dev/null +++ b/pubchem_selfies.py @@ -0,0 +1,486 @@ +# 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: File Description""" + +import json +import glob +import gzip + +import datasets + +# Using https://www.bibtex.com/c/doi-to-bibtex-converter/ (doi: 10.1093/nar/gkv951) +_CITATION = """\ +@ARTICLE{Kim2016-sz, + title = "{PubChem} Substance and Compound databases", + author = "Kim, Sunghwan and Thiessen, Paul A and Bolton, Evan E and Chen, + Jie and Fu, Gang and Gindulyte, Asta and Han, Lianyi and He, + Jane and He, Siqian and Shoemaker, Benjamin A and Wang, Jiyao + and Yu, Bo and Zhang, Jian and Bryant, Stephen H", + abstract = "PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public + repository for information on chemical substances and their + biological activities, launched in 2004 as a component of the + Molecular Libraries Roadmap Initiatives of the US National + Institutes of Health (NIH). For the past 11 years, PubChem has + grown to a sizable system, serving as a chemical information + resource for the scientific research community. PubChem consists + of three inter-linked databases, Substance, Compound and + BioAssay. The Substance database contains chemical information + deposited by individual data contributors to PubChem, and the + Compound database stores unique chemical structures extracted + from the Substance database. Biological activity data of + chemical substances tested in assay experiments are contained in + the BioAssay database. This paper provides an overview of the + PubChem Substance and Compound databases, including data sources + and contents, data organization, data submission using PubChem + Upload, chemical structure standardization, web-based interfaces + for textual and non-textual searches, and programmatic access. + It also gives a brief description of PubChem3D, a resource + derived from theoretical three-dimensional structures of + compounds in PubChem, as well as PubChemRDF, Resource + Description Framework (RDF)-formatted PubChem data for data + sharing, analysis and integration with information contained in + other databases.", + journal = "Nucleic Acids Res.", + publisher = "Oxford University Press (OUP)", + volume = 44, + number = "D1", + pages = "D1202--13", + month = jan, + year = 2016, + language = "en" +} +""" + +# You can copy an official description +_DESCRIPTION = """\ +This dataset contains ~100M molecules from PubChem, with their SMILES and SELFIES representations. +""" + +_HOMEPAGE = "https://pubchem.ncbi.nlm.nih.gov/" + +_LICENSE = "Open Data Commons Open Database License" + +# this list of files has been preshuffled so we can use the same splits everytime +SUBDIRS = [ + "data/Compound_039000001_039500000", + "data/Compound_019500001_020000000", + "data/Compound_152500001_153000000", + "data/Compound_089000001_089500000", + "data/Compound_031500001_032000000", + "data/Compound_145500001_146000000", + "data/Compound_123500001_124000000", + "data/Compound_037500001_038000000", + "data/Compound_030500001_031000000", + "data/Compound_006500001_007000000", + "data/Compound_068500001_069000000", + "data/Compound_093000001_093500000", + "data/Compound_164000001_164500000", + "data/Compound_049000001_049500000", + "data/Compound_037000001_037500000", + "data/Compound_084500001_085000000", + "data/Compound_142500001_143000000", + "data/Compound_138500001_139000000", + "data/Compound_046000001_046500000", + "data/Compound_036000001_036500000", + "data/Compound_013500001_014000000", + "data/Compound_024500001_025000000", + "data/Compound_079500001_080000000", + "data/Compound_110000001_110500000", + "data/Compound_098500001_099000000", + "data/Compound_078500001_079000000", + "data/Compound_030000001_030500000", + "data/Compound_074500001_075000000", + "data/Compound_000000001_000500000", + "data/Compound_094500001_095000000", + "data/Compound_043500001_044000000", + "data/Compound_016000001_016500000", + "data/Compound_120000001_120500000", + "data/Compound_071000001_071500000", + "data/Compound_083500001_084000000", + "data/Compound_075000001_075500000", + "data/Compound_089500001_090000000", + "data/Compound_135000001_135500000", + "data/Compound_140000001_140500000", + "data/Compound_143500001_144000000", + "data/Compound_087500001_088000000", + "data/Compound_064500001_065000000", + "data/Compound_022500001_023000000", + "data/Compound_122000001_122500000", + "data/Compound_050000001_050500000", + "data/Compound_067500001_068000000", + "data/Compound_149500001_150000000", + "data/Compound_049500001_050000000", + "data/Compound_073000001_073500000", + "data/Compound_050500001_051000000", + "data/Compound_072000001_072500000", + "data/Compound_157000001_157500000", + "data/Compound_147500001_148000000", + "data/Compound_132000001_132500000", + "data/Compound_020500001_021000000", + "data/Compound_151500001_152000000", + "data/Compound_010000001_010500000", + "data/Compound_048000001_048500000", + "data/Compound_113500001_114000000", + "data/Compound_042500001_043000000", + "data/Compound_162000001_162500000", + "data/Compound_069500001_070000000", + "data/Compound_076000001_076500000", + "data/Compound_017500001_018000000", + "data/Compound_085000001_085500000", + "data/Compound_107500001_108000000", + "data/Compound_004500001_005000000", + "data/Compound_163000001_163500000", + "data/Compound_100000001_100500000", + "data/Compound_009500001_010000000", + "data/Compound_154500001_155000000", + "data/Compound_153500001_154000000", + "data/Compound_009000001_009500000", + "data/Compound_076500001_077000000", + "data/Compound_134500001_135000000", + "data/Compound_092000001_092500000", + "data/Compound_136500001_137000000", + "data/Compound_153000001_153500000", + "data/Compound_011500001_012000000", + "data/Compound_115500001_116000000", + "data/Compound_085500001_086000000", + "data/Compound_090500001_091000000", + "data/Compound_035500001_036000000", + "data/Compound_012000001_012500000", + "data/Compound_060500001_061000000", + "data/Compound_149000001_149500000", + "data/Compound_116000001_116500000", + "data/Compound_138000001_138500000", + "data/Compound_129500001_130000000", + "data/Compound_077000001_077500000", + "data/Compound_084000001_084500000", + "data/Compound_066500001_067000000", + "data/Compound_003500001_004000000", + "data/Compound_142000001_142500000", + "data/Compound_000500001_001000000", + "data/Compound_032500001_033000000", + "data/Compound_070000001_070500000", + "data/Compound_057000001_057500000", + "data/Compound_051000001_051500000", + "data/Compound_054500001_055000000", + "data/Compound_041000001_041500000", + "data/Compound_003000001_003500000", + "data/Compound_002000001_002500000", + "data/Compound_104000001_104500000", + "data/Compound_019000001_019500000", + "data/Compound_105000001_105500000", + "data/Compound_028000001_028500000", + "data/Compound_080500001_081000000", + "data/Compound_026500001_027000000", + "data/Compound_027500001_028000000", + "data/Compound_161000001_161500000", + "data/Compound_092500001_093000000", + "data/Compound_145000001_145500000", + "data/Compound_096500001_097000000", + "data/Compound_074000001_074500000", + "data/Compound_108500001_109000000", + "data/Compound_057500001_058000000", + "data/Compound_102000001_102500000", + "data/Compound_043000001_043500000", + "data/Compound_129000001_129500000", + "data/Compound_104500001_105000000", + "data/Compound_075500001_076000000", + "data/Compound_121000001_121500000", + "data/Compound_127500001_128000000", + "data/Compound_105500001_106000000", + "data/Compound_038000001_038500000", + "data/Compound_096000001_096500000", + "data/Compound_005500001_006000000", + "data/Compound_064000001_064500000", + "data/Compound_150000001_150500000", + "data/Compound_139000001_139500000", + "data/Compound_063000001_063500000", + "data/Compound_101500001_102000000", + "data/Compound_018000001_018500000", + "data/Compound_034000001_034500000", + "data/Compound_033500001_034000000", + "data/Compound_059000001_059500000", + "data/Compound_022000001_022500000", + "data/Compound_004000001_004500000", + "data/Compound_133500001_134000000", + "data/Compound_052000001_052500000", + "data/Compound_001500001_002000000", + "data/Compound_130000001_130500000", + "data/Compound_082500001_083000000", + "data/Compound_083000001_083500000", + "data/Compound_117500001_118000000", + "data/Compound_156000001_156500000", + "data/Compound_051500001_052000000", + "data/Compound_047000001_047500000", + "data/Compound_059500001_060000000", + "data/Compound_014000001_014500000", + "data/Compound_097000001_097500000", + "data/Compound_041500001_042000000", + "data/Compound_110500001_111000000", + "data/Compound_056000001_056500000", + "data/Compound_078000001_078500000", + "data/Compound_128000001_128500000", + "data/Compound_035000001_035500000", + "data/Compound_045000001_045500000", + "data/Compound_116500001_117000000", + "data/Compound_073500001_074000000", + "data/Compound_018500001_019000000", + "data/Compound_081500001_082000000", + "data/Compound_109000001_109500000", + "data/Compound_133000001_133500000", + "data/Compound_112000001_112500000", + "data/Compound_093500001_094000000", + "data/Compound_044500001_045000000", + "data/Compound_025000001_025500000", + "data/Compound_017000001_017500000", + "data/Compound_069000001_069500000", + "data/Compound_144500001_145000000", + "data/Compound_137500001_138000000", + "data/Compound_063500001_064000000", + "data/Compound_095500001_096000000", + "data/Compound_055000001_055500000", + "data/Compound_002500001_003000000", + "data/Compound_088000001_088500000", + "data/Compound_033000001_033500000", + "data/Compound_008000001_008500000", + "data/Compound_163500001_164000000", + "data/Compound_155500001_156000000", + "data/Compound_113000001_113500000", + "data/Compound_120500001_121000000", + "data/Compound_094000001_094500000", + "data/Compound_155000001_155500000", + "data/Compound_008500001_009000000", + "data/Compound_055500001_056000000", + "data/Compound_045500001_046000000", + "data/Compound_005000001_005500000", + "data/Compound_100500001_101000000", + "data/Compound_088500001_089000000", + "data/Compound_139500001_140000000", + "data/Compound_148500001_149000000", + "data/Compound_160500001_161000000", + "data/Compound_141000001_141500000", + "data/Compound_131000001_131500000", + "data/Compound_015000001_015500000", + "data/Compound_061000001_061500000", + "data/Compound_144000001_144500000", + "data/Compound_031000001_031500000", + "data/Compound_023000001_023500000", + "data/Compound_156500001_157000000", + "data/Compound_152000001_152500000", + "data/Compound_154000001_154500000", + "data/Compound_140500001_141000000", + "data/Compound_114000001_114500000", + "data/Compound_068000001_068500000", + "data/Compound_103000001_103500000", + "data/Compound_071500001_072000000", + "data/Compound_158000001_158500000", + "data/Compound_091000001_091500000", + "data/Compound_012500001_013000000", + "data/Compound_042000001_042500000", + "data/Compound_020000001_020500000", + "data/Compound_159000001_159500000", + "data/Compound_087000001_087500000", + "data/Compound_107000001_107500000", + "data/Compound_034500001_035000000", + "data/Compound_072500001_073000000", + "data/Compound_150500001_151000000", + "data/Compound_047500001_048000000", + "data/Compound_029500001_030000000", + "data/Compound_126500001_127000000", + "data/Compound_061500001_062000000", + "data/Compound_058000001_058500000", + "data/Compound_136000001_136500000", + "data/Compound_117000001_117500000", + "data/Compound_123000001_123500000", + "data/Compound_162500001_163000000", + "data/Compound_134000001_134500000", + "data/Compound_124000001_124500000", + "data/Compound_135500001_136000000", + "data/Compound_036500001_037000000", + "data/Compound_118500001_119000000", + "data/Compound_161500001_162000000", + "data/Compound_056500001_057000000", + "data/Compound_067000001_067500000", + "data/Compound_039500001_040000000", + "data/Compound_102500001_103000000", + "data/Compound_125000001_125500000", + "data/Compound_062000001_062500000", + "data/Compound_001000001_001500000", + "data/Compound_025500001_026000000", + "data/Compound_122500001_123000000", + "data/Compound_048500001_049000000", + "data/Compound_111500001_112000000", + "data/Compound_053000001_053500000", + "data/Compound_032000001_032500000", + "data/Compound_130500001_131000000", + "data/Compound_016500001_017000000", + "data/Compound_109500001_110000000", + "data/Compound_011000001_011500000", + "data/Compound_027000001_027500000", + "data/Compound_044000001_044500000", + "data/Compound_080000001_080500000", + "data/Compound_058500001_059000000", + "data/Compound_119000001_119500000", + "data/Compound_021500001_022000000", + "data/Compound_126000001_126500000", + "data/Compound_066000001_066500000", + "data/Compound_095000001_095500000", + "data/Compound_021000001_021500000", + "data/Compound_077500001_078000000", + "data/Compound_010500001_011000000", + "data/Compound_141500001_142000000", + "data/Compound_098000001_098500000", + "data/Compound_132500001_133000000", + "data/Compound_159500001_160000000", + "data/Compound_065500001_066000000", + "data/Compound_060000001_060500000", + "data/Compound_128500001_129000000", + "data/Compound_081000001_081500000", + "data/Compound_114500001_115000000", + "data/Compound_112500001_113000000", + "data/Compound_148000001_148500000", + "data/Compound_040500001_041000000", + "data/Compound_099000001_099500000", + "data/Compound_053500001_054000000", + "data/Compound_040000001_040500000", + "data/Compound_029000001_029500000", + "data/Compound_052500001_053000000", + "data/Compound_164500001_165000000", + "data/Compound_108000001_108500000", + "data/Compound_062500001_063000000", + "data/Compound_082000001_082500000", + "data/Compound_146000001_146500000", + "data/Compound_023500001_024000000", + "data/Compound_121500001_122000000", + "data/Compound_111000001_111500000", + "data/Compound_103500001_104000000", + "data/Compound_024000001_024500000", + "data/Compound_079000001_079500000", + "data/Compound_127000001_127500000", + "data/Compound_090000001_090500000", + "data/Compound_028500001_029000000", + "data/Compound_015500001_016000000", + "data/Compound_158500001_159000000", + "data/Compound_086000001_086500000", + "data/Compound_091500001_092000000", + "data/Compound_137000001_137500000", + "data/Compound_007500001_008000000", + "data/Compound_124500001_125000000", + "data/Compound_106000001_106500000", + "data/Compound_119500001_120000000", + "data/Compound_101000001_101500000", + "data/Compound_106500001_107000000", + "data/Compound_131500001_132000000", + "data/Compound_086500001_087000000", + "data/Compound_146500001_147000000", + "data/Compound_046500001_047000000", + "data/Compound_006000001_006500000", + "data/Compound_097500001_098000000", + "data/Compound_151000001_151500000", + "data/Compound_125500001_126000000", + "data/Compound_099500001_100000000", + "data/Compound_118000001_118500000", + "data/Compound_013000001_013500000", + "data/Compound_115000001_115500000", + "data/Compound_070500001_071000000", + "data/Compound_054000001_054500000", + "data/Compound_026000001_026500000", + "data/Compound_160000001_160500000", + "data/Compound_143000001_143500000", + "data/Compound_014500001_015000000", + "data/Compound_157500001_158000000", + "data/Compound_007000001_007500000", + "data/Compound_038500001_039000000", + "data/Compound_065000001_065500000", + "data/Compound_147000001_147500000", +] + + +class PubchemSelfies(datasets.GeneratorBasedBuilder): + """TODO: Short description of my dataset.""" + + VERSION = datasets.Version("1.1.0") + + # You will be able to load one or the other configurations in the following list with + BUILDER_CONFIG = datasets.BuilderConfig( + version=VERSION, description="" + ) # TODO: Short description of my dataset. + + def _info(self): + 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=datasets.Features( + { + "PUBCHEM_COMPOUND_CID": datasets.Value("int32"), + "CAN_SELFIES": datasets.Value("string"), + "PUBCHEM_OPENEYE_CAN_SMILES": datasets.Value("string"), + } + ), + # 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): + train_len = int(len(SUBDIRS) * 0.8) + valid_len = int(len(SUBDIRS) * 0.1) + + return [ + datasets.SplitGenerator( + name=datasets.Split.TRAIN, + # These kwargs will be passed to _generate_examples + gen_kwargs={ + "subdirs": SUBDIRS[:train_len], + "split": "train", + }, + ), + datasets.SplitGenerator( + name=datasets.Split.VALIDATION, + # These kwargs will be passed to _generate_examples + gen_kwargs={ + "subdirs": SUBDIRS[train_len : train_len + valid_len], + "split": "valid", + }, + ), + datasets.SplitGenerator( + name=datasets.Split.TEST, + # These kwargs will be passed to _generate_examples + gen_kwargs={ + "subdirs": SUBDIRS[-valid_len:], + "split": "test", + }, + ), + ] + + # method parameters are unpacked from `gen_kwargs` as given in `_split_generators` + def _generate_examples(self, subdirs, split): + # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example. + for subdir in subdirs: + filepath = f"{subdir}/{subdir.split('/')[-1]}_SELFIES.jsonl.gz" + with gzip.open(filepath, mode="rt") as f: + rows = f.readlines() + for key, row in enumerate(rows): + data = json.loads(row) + properties = data["molecules"][0]["properties"] + yield key, { + "PUBCHEM_COMPOUND_CID": properties["PUBCHEM_COMPOUND_CID"], + "PUBCHEM_OPENEYE_CAN_SMILES": properties[ + "PUBCHEM_OPENEYE_CAN_SMILES" + ], + "CAN_SELFIES": properties["CAN_SELFIES"], + }