pubchem_selfies.py

# 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 os

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
FILES = [
   "data/Compound_021000001_021500000/Compound_021000001_021500000_SELFIES.jsonl.gz",
   "data/Compound_034500001_035000000/Compound_034500001_035000000_SELFIES.jsonl.gz",
   "data/Compound_023500001_024000000/Compound_023500001_024000000_SELFIES.jsonl.gz",
   "data/Compound_151500001_152000000/Compound_151500001_152000000_SELFIES.jsonl.gz",
   "data/Compound_126500001_127000000/Compound_126500001_127000000_SELFIES.jsonl.gz",
   "data/Compound_030500001_031000000/Compound_030500001_031000000_SELFIES.jsonl.gz",
   "data/Compound_061500001_062000000/Compound_061500001_062000000_SELFIES.jsonl.gz",
   "data/Compound_031500001_032000000/Compound_031500001_032000000_SELFIES.jsonl.gz",
   "data/Compound_111000001_111500000/Compound_111000001_111500000_SELFIES.jsonl.gz",
   "data/Compound_058500001_059000000/Compound_058500001_059000000_SELFIES.jsonl.gz",
   "data/Compound_065500001_066000000/Compound_065500001_066000000_SELFIES.jsonl.gz",
   "data/Compound_065000001_065500000/Compound_065000001_065500000_SELFIES.jsonl.gz",
   "data/Compound_039500001_040000000/Compound_039500001_040000000_SELFIES.jsonl.gz",
   "data/Compound_014000001_014500000/Compound_014000001_014500000_SELFIES.jsonl.gz",
   "data/Compound_021500001_022000000/Compound_021500001_022000000_SELFIES.jsonl.gz",
   "data/Compound_081000001_081500000/Compound_081000001_081500000_SELFIES.jsonl.gz",
   "data/Compound_122000001_122500000/Compound_122000001_122500000_SELFIES.jsonl.gz",
   "data/Compound_045000001_045500000/Compound_045000001_045500000_SELFIES.jsonl.gz",
   "data/Compound_017500001_018000000/Compound_017500001_018000000_SELFIES.jsonl.gz",
   "data/Compound_059000001_059500000/Compound_059000001_059500000_SELFIES.jsonl.gz",
   "data/Compound_141000001_141500000/Compound_141000001_141500000_SELFIES.jsonl.gz",
   "data/Compound_129500001_130000000/Compound_129500001_130000000_SELFIES.jsonl.gz",
   "data/Compound_163500001_164000000/Compound_163500001_164000000_SELFIES.jsonl.gz",
   "data/Compound_089000001_089500000/Compound_089000001_089500000_SELFIES.jsonl.gz",
   "data/Compound_077000001_077500000/Compound_077000001_077500000_SELFIES.jsonl.gz",
   "data/Compound_161000001_161500000/Compound_161000001_161500000_SELFIES.jsonl.gz",
   "data/Compound_113000001_113500000/Compound_113000001_113500000_SELFIES.jsonl.gz",
   "data/Compound_040000001_040500000/Compound_040000001_040500000_SELFIES.jsonl.gz",
   "data/Compound_010000001_010500000/Compound_010000001_010500000_SELFIES.jsonl.gz",
   "data/Compound_091500001_092000000/Compound_091500001_092000000_SELFIES.jsonl.gz",
   "data/Compound_154500001_155000000/Compound_154500001_155000000_SELFIES.jsonl.gz",
   "data/Compound_098500001_099000000/Compound_098500001_099000000_SELFIES.jsonl.gz",
   "data/Compound_019000001_019500000/Compound_019000001_019500000_SELFIES.jsonl.gz",
   "data/Compound_064000001_064500000/Compound_064000001_064500000_SELFIES.jsonl.gz",
   "data/Compound_147000001_147500000/Compound_147000001_147500000_SELFIES.jsonl.gz",
   "data/Compound_001500001_002000000/Compound_001500001_002000000_SELFIES.jsonl.gz",
   "data/Compound_137000001_137500000/Compound_137000001_137500000_SELFIES.jsonl.gz",
   "data/Compound_161500001_162000000/Compound_161500001_162000000_SELFIES.jsonl.gz",
   "data/Compound_074000001_074500000/Compound_074000001_074500000_SELFIES.jsonl.gz",
   "data/Compound_133500001_134000000/Compound_133500001_134000000_SELFIES.jsonl.gz",
   "data/Compound_028000001_028500000/Compound_028000001_028500000_SELFIES.jsonl.gz",
   "data/Compound_147500001_148000000/Compound_147500001_148000000_SELFIES.jsonl.gz",
   "data/Compound_159000001_159500000/Compound_159000001_159500000_SELFIES.jsonl.gz",
   "data/Compound_098000001_098500000/Compound_098000001_098500000_SELFIES.jsonl.gz",
   "data/Compound_024000001_024500000/Compound_024000001_024500000_SELFIES.jsonl.gz",
   "data/Compound_043000001_043500000/Compound_043000001_043500000_SELFIES.jsonl.gz",
   "data/Compound_004500001_005000000/Compound_004500001_005000000_SELFIES.jsonl.gz",
   "data/Compound_118000001_118500000/Compound_118000001_118500000_SELFIES.jsonl.gz",
   "data/Compound_104500001_105000000/Compound_104500001_105000000_SELFIES.jsonl.gz",
   "data/Compound_013000001_013500000/Compound_013000001_013500000_SELFIES.jsonl.gz",
   "data/Compound_035500001_036000000/Compound_035500001_036000000_SELFIES.jsonl.gz",
   "data/Compound_129000001_129500000/Compound_129000001_129500000_SELFIES.jsonl.gz",
   "data/Compound_141500001_142000000/Compound_141500001_142000000_SELFIES.jsonl.gz",
   "data/Compound_120500001_121000000/Compound_120500001_121000000_SELFIES.jsonl.gz",
   "data/Compound_066000001_066500000/Compound_066000001_066500000_SELFIES.jsonl.gz",
   "data/Compound_060000001_060500000/Compound_060000001_060500000_SELFIES.jsonl.gz",
   "data/Compound_014500001_015000000/Compound_014500001_015000000_SELFIES.jsonl.gz",
   "data/Compound_159500001_160000000/Compound_159500001_160000000_SELFIES.jsonl.gz",
   "data/Compound_107500001_108000000/Compound_107500001_108000000_SELFIES.jsonl.gz",
   "data/Compound_139500001_140000000/Compound_139500001_140000000_SELFIES.jsonl.gz",
   "data/Compound_088500001_089000000/Compound_088500001_089000000_SELFIES.jsonl.gz",
   "data/Compound_070000001_070500000/Compound_070000001_070500000_SELFIES.jsonl.gz",
   "data/Compound_103000001_103500000/Compound_103000001_103500000_SELFIES.jsonl.gz",
   "data/Compound_063000001_063500000/Compound_063000001_063500000_SELFIES.jsonl.gz",
   "data/Compound_052500001_053000000/Compound_052500001_053000000_SELFIES.jsonl.gz",
   "data/Compound_094000001_094500000/Compound_094000001_094500000_SELFIES.jsonl.gz",
   "data/Compound_091000001_091500000/Compound_091000001_091500000_SELFIES.jsonl.gz",
   "data/Compound_075000001_075500000/Compound_075000001_075500000_SELFIES.jsonl.gz",
   "data/Compound_116500001_117000000/Compound_116500001_117000000_SELFIES.jsonl.gz",
   "data/Compound_164500001_165000000/Compound_164500001_165000000_SELFIES.jsonl.gz",
   "data/Compound_071500001_072000000/Compound_071500001_072000000_SELFIES.jsonl.gz",
   "data/Compound_055000001_055500000/Compound_055000001_055500000_SELFIES.jsonl.gz",
   "data/Compound_027500001_028000000/Compound_027500001_028000000_SELFIES.jsonl.gz",
   "data/Compound_132500001_133000000/Compound_132500001_133000000_SELFIES.jsonl.gz",
   "data/Compound_027000001_027500000/Compound_027000001_027500000_SELFIES.jsonl.gz",
   "data/Compound_132000001_132500000/Compound_132000001_132500000_SELFIES.jsonl.gz",
   "data/Compound_089500001_090000000/Compound_089500001_090000000_SELFIES.jsonl.gz",
   "data/Compound_120000001_120500000/Compound_120000001_120500000_SELFIES.jsonl.gz",
   "data/Compound_088000001_088500000/Compound_088000001_088500000_SELFIES.jsonl.gz",
   "data/Compound_117500001_118000000/Compound_117500001_118000000_SELFIES.jsonl.gz",
   "data/Compound_114000001_114500000/Compound_114000001_114500000_SELFIES.jsonl.gz",
   "data/Compound_049500001_050000000/Compound_049500001_050000000_SELFIES.jsonl.gz",
   "data/Compound_134000001_134500000/Compound_134000001_134500000_SELFIES.jsonl.gz",
   "data/Compound_115000001_115500000/Compound_115000001_115500000_SELFIES.jsonl.gz",
   "data/Compound_143500001_144000000/Compound_143500001_144000000_SELFIES.jsonl.gz",
   "data/Compound_164000001_164500000/Compound_164000001_164500000_SELFIES.jsonl.gz",
   "data/Compound_094500001_095000000/Compound_094500001_095000000_SELFIES.jsonl.gz",
   "data/Compound_072500001_073000000/Compound_072500001_073000000_SELFIES.jsonl.gz",
   "data/Compound_086500001_087000000/Compound_086500001_087000000_SELFIES.jsonl.gz",
   "data/Compound_084000001_084500000/Compound_084000001_084500000_SELFIES.jsonl.gz",
   "data/Compound_148500001_149000000/Compound_148500001_149000000_SELFIES.jsonl.gz",
   "data/Compound_144000001_144500000/Compound_144000001_144500000_SELFIES.jsonl.gz",
   "data/Compound_146000001_146500000/Compound_146000001_146500000_SELFIES.jsonl.gz",
   "data/Compound_054500001_055000000/Compound_054500001_055000000_SELFIES.jsonl.gz",
   "data/Compound_034000001_034500000/Compound_034000001_034500000_SELFIES.jsonl.gz",
   "data/Compound_007000001_007500000/Compound_007000001_007500000_SELFIES.jsonl.gz",
   "data/Compound_056500001_057000000/Compound_056500001_057000000_SELFIES.jsonl.gz",
   "data/Compound_152500001_153000000/Compound_152500001_153000000_SELFIES.jsonl.gz",
   "data/Compound_030000001_030500000/Compound_030000001_030500000_SELFIES.jsonl.gz",
   "data/Compound_031000001_031500000/Compound_031000001_031500000_SELFIES.jsonl.gz",
   "data/Compound_035000001_035500000/Compound_035000001_035500000_SELFIES.jsonl.gz",
   "data/Compound_156500001_157000000/Compound_156500001_157000000_SELFIES.jsonl.gz",
   "data/Compound_036000001_036500000/Compound_036000001_036500000_SELFIES.jsonl.gz",
   "data/Compound_157500001_158000000/Compound_157500001_158000000_SELFIES.jsonl.gz",
   "data/Compound_051500001_052000000/Compound_051500001_052000000_SELFIES.jsonl.gz",
   "data/Compound_144500001_145000000/Compound_144500001_145000000_SELFIES.jsonl.gz",
   "data/Compound_038500001_039000000/Compound_038500001_039000000_SELFIES.jsonl.gz",
   "data/Compound_018500001_019000000/Compound_018500001_019000000_SELFIES.jsonl.gz",
   "data/Compound_149000001_149500000/Compound_149000001_149500000_SELFIES.jsonl.gz",
   "data/Compound_139000001_139500000/Compound_139000001_139500000_SELFIES.jsonl.gz",
   "data/Compound_039000001_039500000/Compound_039000001_039500000_SELFIES.jsonl.gz",
   "data/Compound_102000001_102500000/Compound_102000001_102500000_SELFIES.jsonl.gz",
   "data/Compound_022000001_022500000/Compound_022000001_022500000_SELFIES.jsonl.gz",
   "data/Compound_009500001_010000000/Compound_009500001_010000000_SELFIES.jsonl.gz",
   "data/Compound_086000001_086500000/Compound_086000001_086500000_SELFIES.jsonl.gz",
   "data/Compound_040500001_041000000/Compound_040500001_041000000_SELFIES.jsonl.gz",
   "data/Compound_131500001_132000000/Compound_131500001_132000000_SELFIES.jsonl.gz",
   "data/Compound_095000001_095500000/Compound_095000001_095500000_SELFIES.jsonl.gz",
   "data/Compound_107000001_107500000/Compound_107000001_107500000_SELFIES.jsonl.gz",
   "data/Compound_076500001_077000000/Compound_076500001_077000000_SELFIES.jsonl.gz",
   "data/Compound_013500001_014000000/Compound_013500001_014000000_SELFIES.jsonl.gz",
   "data/Compound_056000001_056500000/Compound_056000001_056500000_SELFIES.jsonl.gz",
   "data/Compound_138000001_138500000/Compound_138000001_138500000_SELFIES.jsonl.gz",
   "data/Compound_162500001_163000000/Compound_162500001_163000000_SELFIES.jsonl.gz",
   "data/Compound_136000001_136500000/Compound_136000001_136500000_SELFIES.jsonl.gz",
   "data/Compound_146500001_147000000/Compound_146500001_147000000_SELFIES.jsonl.gz",
   "data/Compound_007500001_008000000/Compound_007500001_008000000_SELFIES.jsonl.gz",
   "data/Compound_037500001_038000000/Compound_037500001_038000000_SELFIES.jsonl.gz",
   "data/Compound_015000001_015500000/Compound_015000001_015500000_SELFIES.jsonl.gz",
   "data/Compound_106500001_107000000/Compound_106500001_107000000_SELFIES.jsonl.gz",
   "data/Compound_003500001_004000000/Compound_003500001_004000000_SELFIES.jsonl.gz",
   "data/Compound_131000001_131500000/Compound_131000001_131500000_SELFIES.jsonl.gz",
   "data/Compound_102500001_103000000/Compound_102500001_103000000_SELFIES.jsonl.gz",
   "data/Compound_112000001_112500000/Compound_112000001_112500000_SELFIES.jsonl.gz",
   "data/Compound_049000001_049500000/Compound_049000001_049500000_SELFIES.jsonl.gz",
   "data/Compound_041000001_041500000/Compound_041000001_041500000_SELFIES.jsonl.gz",
   "data/Compound_011000001_011500000/Compound_011000001_011500000_SELFIES.jsonl.gz",
   "data/Compound_079500001_080000000/Compound_079500001_080000000_SELFIES.jsonl.gz",
   "data/Compound_105500001_106000000/Compound_105500001_106000000_SELFIES.jsonl.gz",
   "data/Compound_123500001_124000000/Compound_123500001_124000000_SELFIES.jsonl.gz",
   "data/Compound_057000001_057500000/Compound_057000001_057500000_SELFIES.jsonl.gz",
   "data/Compound_110500001_111000000/Compound_110500001_111000000_SELFIES.jsonl.gz",
   "data/Compound_029500001_030000000/Compound_029500001_030000000_SELFIES.jsonl.gz",
   "data/Compound_082000001_082500000/Compound_082000001_082500000_SELFIES.jsonl.gz",
   "data/Compound_087500001_088000000/Compound_087500001_088000000_SELFIES.jsonl.gz",
   "data/Compound_100500001_101000000/Compound_100500001_101000000_SELFIES.jsonl.gz",
   "data/Compound_018000001_018500000/Compound_018000001_018500000_SELFIES.jsonl.gz",
   "data/Compound_114500001_115000000/Compound_114500001_115000000_SELFIES.jsonl.gz",
   "data/Compound_008000001_008500000/Compound_008000001_008500000_SELFIES.jsonl.gz",
   "data/Compound_143000001_143500000/Compound_143000001_143500000_SELFIES.jsonl.gz",
   "data/Compound_142000001_142500000/Compound_142000001_142500000_SELFIES.jsonl.gz",
   "data/Compound_109000001_109500000/Compound_109000001_109500000_SELFIES.jsonl.gz",
   "data/Compound_047000001_047500000/Compound_047000001_047500000_SELFIES.jsonl.gz",
   "data/Compound_077500001_078000000/Compound_077500001_078000000_SELFIES.jsonl.gz",
   "data/Compound_100000001_100500000/Compound_100000001_100500000_SELFIES.jsonl.gz",
   "data/Compound_043500001_044000000/Compound_043500001_044000000_SELFIES.jsonl.gz",
   "data/Compound_029000001_029500000/Compound_029000001_029500000_SELFIES.jsonl.gz",
   "data/Compound_078500001_079000000/Compound_078500001_079000000_SELFIES.jsonl.gz",
   "data/Compound_005000001_005500000/Compound_005000001_005500000_SELFIES.jsonl.gz",
   "data/Compound_153000001_153500000/Compound_153000001_153500000_SELFIES.jsonl.gz",
   "data/Compound_004000001_004500000/Compound_004000001_004500000_SELFIES.jsonl.gz",
   "data/Compound_072000001_072500000/Compound_072000001_072500000_SELFIES.jsonl.gz",
   "data/Compound_045500001_046000000/Compound_045500001_046000000_SELFIES.jsonl.gz",
   "data/Compound_050000001_050500000/Compound_050000001_050500000_SELFIES.jsonl.gz",
   "data/Compound_115500001_116000000/Compound_115500001_116000000_SELFIES.jsonl.gz",
   "data/Compound_155500001_156000000/Compound_155500001_156000000_SELFIES.jsonl.gz",
   "data/Compound_025500001_026000000/Compound_025500001_026000000_SELFIES.jsonl.gz",
   "data/Compound_106000001_106500000/Compound_106000001_106500000_SELFIES.jsonl.gz",
   "data/Compound_075500001_076000000/Compound_075500001_076000000_SELFIES.jsonl.gz",
   "data/Compound_062500001_063000000/Compound_062500001_063000000_SELFIES.jsonl.gz",
   "data/Compound_155000001_155500000/Compound_155000001_155500000_SELFIES.jsonl.gz",
   "data/Compound_105000001_105500000/Compound_105000001_105500000_SELFIES.jsonl.gz",
   "data/Compound_097500001_098000000/Compound_097500001_098000000_SELFIES.jsonl.gz",
   "data/Compound_005500001_006000000/Compound_005500001_006000000_SELFIES.jsonl.gz",
   "data/Compound_127500001_128000000/Compound_127500001_128000000_SELFIES.jsonl.gz",
   "data/Compound_135500001_136000000/Compound_135500001_136000000_SELFIES.jsonl.gz",
   "data/Compound_020000001_020500000/Compound_020000001_020500000_SELFIES.jsonl.gz",
   "data/Compound_135000001_135500000/Compound_135000001_135500000_SELFIES.jsonl.gz",
   "data/Compound_068000001_068500000/Compound_068000001_068500000_SELFIES.jsonl.gz",
   "data/Compound_026000001_026500000/Compound_026000001_026500000_SELFIES.jsonl.gz",
   "data/Compound_099500001_100000000/Compound_099500001_100000000_SELFIES.jsonl.gz",
   "data/Compound_158000001_158500000/Compound_158000001_158500000_SELFIES.jsonl.gz",
   "data/Compound_069000001_069500000/Compound_069000001_069500000_SELFIES.jsonl.gz",
   "data/Compound_078000001_078500000/Compound_078000001_078500000_SELFIES.jsonl.gz",
   "data/Compound_066500001_067000000/Compound_066500001_067000000_SELFIES.jsonl.gz",
   "data/Compound_076000001_076500000/Compound_076000001_076500000_SELFIES.jsonl.gz",
   "data/Compound_009000001_009500000/Compound_009000001_009500000_SELFIES.jsonl.gz",
   "data/Compound_117000001_117500000/Compound_117000001_117500000_SELFIES.jsonl.gz",
   "data/Compound_055500001_056000000/Compound_055500001_056000000_SELFIES.jsonl.gz",
   "data/Compound_012500001_013000000/Compound_012500001_013000000_SELFIES.jsonl.gz",
   "data/Compound_011500001_012000000/Compound_011500001_012000000_SELFIES.jsonl.gz",
   "data/Compound_015500001_016000000/Compound_015500001_016000000_SELFIES.jsonl.gz",
   "data/Compound_092000001_092500000/Compound_092000001_092500000_SELFIES.jsonl.gz",
   "data/Compound_008500001_009000000/Compound_008500001_009000000_SELFIES.jsonl.gz",
   "data/Compound_000000001_000500000/Compound_000000001_000500000_SELFIES.jsonl.gz",
   "data/Compound_151000001_151500000/Compound_151000001_151500000_SELFIES.jsonl.gz",
   "data/Compound_082500001_083000000/Compound_082500001_083000000_SELFIES.jsonl.gz",
   "data/Compound_012000001_012500000/Compound_012000001_012500000_SELFIES.jsonl.gz",
   "data/Compound_057500001_058000000/Compound_057500001_058000000_SELFIES.jsonl.gz",
   "data/Compound_103500001_104000000/Compound_103500001_104000000_SELFIES.jsonl.gz",
   "data/Compound_067500001_068000000/Compound_067500001_068000000_SELFIES.jsonl.gz",
   "data/Compound_108000001_108500000/Compound_108000001_108500000_SELFIES.jsonl.gz",
   "data/Compound_046500001_047000000/Compound_046500001_047000000_SELFIES.jsonl.gz",
   "data/Compound_017000001_017500000/Compound_017000001_017500000_SELFIES.jsonl.gz",
   "data/Compound_058000001_058500000/Compound_058000001_058500000_SELFIES.jsonl.gz",
   "data/Compound_079000001_079500000/Compound_079000001_079500000_SELFIES.jsonl.gz",
   "data/Compound_062000001_062500000/Compound_062000001_062500000_SELFIES.jsonl.gz",
   "data/Compound_145000001_145500000/Compound_145000001_145500000_SELFIES.jsonl.gz",
   "data/Compound_163000001_163500000/Compound_163000001_163500000_SELFIES.jsonl.gz",
   "data/Compound_067000001_067500000/Compound_067000001_067500000_SELFIES.jsonl.gz",
   "data/Compound_083000001_083500000/Compound_083000001_083500000_SELFIES.jsonl.gz",
   "data/Compound_068500001_069000000/Compound_068500001_069000000_SELFIES.jsonl.gz",
   "data/Compound_020500001_021000000/Compound_020500001_021000000_SELFIES.jsonl.gz",
   "data/Compound_046000001_046500000/Compound_046000001_046500000_SELFIES.jsonl.gz",
   "data/Compound_096500001_097000000/Compound_096500001_097000000_SELFIES.jsonl.gz",
   "data/Compound_081500001_082000000/Compound_081500001_082000000_SELFIES.jsonl.gz",
   "data/Compound_108500001_109000000/Compound_108500001_109000000_SELFIES.jsonl.gz",
   "data/Compound_085500001_086000000/Compound_085500001_086000000_SELFIES.jsonl.gz",
   "data/Compound_119000001_119500000/Compound_119000001_119500000_SELFIES.jsonl.gz",
   "data/Compound_090500001_091000000/Compound_090500001_091000000_SELFIES.jsonl.gz",
   "data/Compound_036500001_037000000/Compound_036500001_037000000_SELFIES.jsonl.gz",
   "data/Compound_130500001_131000000/Compound_130500001_131000000_SELFIES.jsonl.gz",
   "data/Compound_121500001_122000000/Compound_121500001_122000000_SELFIES.jsonl.gz",
   "data/Compound_113500001_114000000/Compound_113500001_114000000_SELFIES.jsonl.gz",
   "data/Compound_145500001_146000000/Compound_145500001_146000000_SELFIES.jsonl.gz",
   "data/Compound_041500001_042000000/Compound_041500001_042000000_SELFIES.jsonl.gz",
   "data/Compound_083500001_084000000/Compound_083500001_084000000_SELFIES.jsonl.gz",
   "data/Compound_052000001_052500000/Compound_052000001_052500000_SELFIES.jsonl.gz",
   "data/Compound_140500001_141000000/Compound_140500001_141000000_SELFIES.jsonl.gz",
   "data/Compound_154000001_154500000/Compound_154000001_154500000_SELFIES.jsonl.gz",
   "data/Compound_044000001_044500000/Compound_044000001_044500000_SELFIES.jsonl.gz",
   "data/Compound_002000001_002500000/Compound_002000001_002500000_SELFIES.jsonl.gz",
   "data/Compound_010500001_011000000/Compound_010500001_011000000_SELFIES.jsonl.gz",
   "data/Compound_073000001_073500000/Compound_073000001_073500000_SELFIES.jsonl.gz",
   "data/Compound_048500001_049000000/Compound_048500001_049000000_SELFIES.jsonl.gz",
   "data/Compound_032000001_032500000/Compound_032000001_032500000_SELFIES.jsonl.gz",
   "data/Compound_026500001_027000000/Compound_026500001_027000000_SELFIES.jsonl.gz",
   "data/Compound_112500001_113000000/Compound_112500001_113000000_SELFIES.jsonl.gz",
   "data/Compound_069500001_070000000/Compound_069500001_070000000_SELFIES.jsonl.gz",
   "data/Compound_110000001_110500000/Compound_110000001_110500000_SELFIES.jsonl.gz",
   "data/Compound_156000001_156500000/Compound_156000001_156500000_SELFIES.jsonl.gz",
   "data/Compound_037000001_037500000/Compound_037000001_037500000_SELFIES.jsonl.gz",
   "data/Compound_130000001_130500000/Compound_130000001_130500000_SELFIES.jsonl.gz",
   "data/Compound_051000001_051500000/Compound_051000001_051500000_SELFIES.jsonl.gz",
   "data/Compound_093500001_094000000/Compound_093500001_094000000_SELFIES.jsonl.gz",
   "data/Compound_149500001_150000000/Compound_149500001_150000000_SELFIES.jsonl.gz",
   "data/Compound_158500001_159000000/Compound_158500001_159000000_SELFIES.jsonl.gz",
   "data/Compound_074500001_075000000/Compound_074500001_075000000_SELFIES.jsonl.gz",
   "data/Compound_053500001_054000000/Compound_053500001_054000000_SELFIES.jsonl.gz",
   "data/Compound_160500001_161000000/Compound_160500001_161000000_SELFIES.jsonl.gz",
   "data/Compound_022500001_023000000/Compound_022500001_023000000_SELFIES.jsonl.gz",
   "data/Compound_118500001_119000000/Compound_118500001_119000000_SELFIES.jsonl.gz",
   "data/Compound_025000001_025500000/Compound_025000001_025500000_SELFIES.jsonl.gz",
   "data/Compound_128500001_129000000/Compound_128500001_129000000_SELFIES.jsonl.gz",
   "data/Compound_080500001_081000000/Compound_080500001_081000000_SELFIES.jsonl.gz",
   "data/Compound_080000001_080500000/Compound_080000001_080500000_SELFIES.jsonl.gz",
   "data/Compound_101000001_101500000/Compound_101000001_101500000_SELFIES.jsonl.gz",
   "data/Compound_136500001_137000000/Compound_136500001_137000000_SELFIES.jsonl.gz",
   "data/Compound_033500001_034000000/Compound_033500001_034000000_SELFIES.jsonl.gz",
   "data/Compound_048000001_048500000/Compound_048000001_048500000_SELFIES.jsonl.gz",
   "data/Compound_032500001_033000000/Compound_032500001_033000000_SELFIES.jsonl.gz",
   "data/Compound_093000001_093500000/Compound_093000001_093500000_SELFIES.jsonl.gz",
   "data/Compound_123000001_123500000/Compound_123000001_123500000_SELFIES.jsonl.gz",
   "data/Compound_133000001_133500000/Compound_133000001_133500000_SELFIES.jsonl.gz",
   "data/Compound_090000001_090500000/Compound_090000001_090500000_SELFIES.jsonl.gz",
   "data/Compound_042500001_043000000/Compound_042500001_043000000_SELFIES.jsonl.gz",
   "data/Compound_127000001_127500000/Compound_127000001_127500000_SELFIES.jsonl.gz",
   "data/Compound_125000001_125500000/Compound_125000001_125500000_SELFIES.jsonl.gz",
   "data/Compound_138500001_139000000/Compound_138500001_139000000_SELFIES.jsonl.gz",
   "data/Compound_001000001_001500000/Compound_001000001_001500000_SELFIES.jsonl.gz",
   "data/Compound_099000001_099500000/Compound_099000001_099500000_SELFIES.jsonl.gz",
   "data/Compound_002500001_003000000/Compound_002500001_003000000_SELFIES.jsonl.gz",
   "data/Compound_019500001_020000000/Compound_019500001_020000000_SELFIES.jsonl.gz",
   "data/Compound_047500001_048000000/Compound_047500001_048000000_SELFIES.jsonl.gz",
   "data/Compound_097000001_097500000/Compound_097000001_097500000_SELFIES.jsonl.gz",
   "data/Compound_070500001_071000000/Compound_070500001_071000000_SELFIES.jsonl.gz",
   "data/Compound_125500001_126000000/Compound_125500001_126000000_SELFIES.jsonl.gz",
   "data/Compound_064500001_065000000/Compound_064500001_065000000_SELFIES.jsonl.gz",
   "data/Compound_157000001_157500000/Compound_157000001_157500000_SELFIES.jsonl.gz",
   "data/Compound_087000001_087500000/Compound_087000001_087500000_SELFIES.jsonl.gz",
   "data/Compound_071000001_071500000/Compound_071000001_071500000_SELFIES.jsonl.gz",
   "data/Compound_119500001_120000000/Compound_119500001_120000000_SELFIES.jsonl.gz",
   "data/Compound_044500001_045000000/Compound_044500001_045000000_SELFIES.jsonl.gz",
   "data/Compound_016000001_016500000/Compound_016000001_016500000_SELFIES.jsonl.gz",
   "data/Compound_095500001_096000000/Compound_095500001_096000000_SELFIES.jsonl.gz",
   "data/Compound_092500001_093000000/Compound_092500001_093000000_SELFIES.jsonl.gz",
   "data/Compound_000500001_001000000/Compound_000500001_001000000_SELFIES.jsonl.gz",
   "data/Compound_059500001_060000000/Compound_059500001_060000000_SELFIES.jsonl.gz",
   "data/Compound_016500001_017000000/Compound_016500001_017000000_SELFIES.jsonl.gz",
   "data/Compound_061000001_061500000/Compound_061000001_061500000_SELFIES.jsonl.gz",
   "data/Compound_101500001_102000000/Compound_101500001_102000000_SELFIES.jsonl.gz",
   "data/Compound_028500001_029000000/Compound_028500001_029000000_SELFIES.jsonl.gz",
   "data/Compound_042000001_042500000/Compound_042000001_042500000_SELFIES.jsonl.gz",
   "data/Compound_152000001_152500000/Compound_152000001_152500000_SELFIES.jsonl.gz",
   "data/Compound_122500001_123000000/Compound_122500001_123000000_SELFIES.jsonl.gz",
   "data/Compound_150500001_151000000/Compound_150500001_151000000_SELFIES.jsonl.gz",
   "data/Compound_142500001_143000000/Compound_142500001_143000000_SELFIES.jsonl.gz",
   "data/Compound_162000001_162500000/Compound_162000001_162500000_SELFIES.jsonl.gz",
   "data/Compound_053000001_053500000/Compound_053000001_053500000_SELFIES.jsonl.gz",
   "data/Compound_104000001_104500000/Compound_104000001_104500000_SELFIES.jsonl.gz",
   "data/Compound_084500001_085000000/Compound_084500001_085000000_SELFIES.jsonl.gz",
   "data/Compound_140000001_140500000/Compound_140000001_140500000_SELFIES.jsonl.gz",
   "data/Compound_160000001_160500000/Compound_160000001_160500000_SELFIES.jsonl.gz",
   "data/Compound_126000001_126500000/Compound_126000001_126500000_SELFIES.jsonl.gz",
   "data/Compound_153500001_154000000/Compound_153500001_154000000_SELFIES.jsonl.gz",
   "data/Compound_134500001_135000000/Compound_134500001_135000000_SELFIES.jsonl.gz",
   "data/Compound_063500001_064000000/Compound_063500001_064000000_SELFIES.jsonl.gz",
   "data/Compound_109500001_110000000/Compound_109500001_110000000_SELFIES.jsonl.gz",
   "data/Compound_137500001_138000000/Compound_137500001_138000000_SELFIES.jsonl.gz",
   "data/Compound_085000001_085500000/Compound_085000001_085500000_SELFIES.jsonl.gz",
   "data/Compound_024500001_025000000/Compound_024500001_025000000_SELFIES.jsonl.gz",
   "data/Compound_116000001_116500000/Compound_116000001_116500000_SELFIES.jsonl.gz",
   "data/Compound_006000001_006500000/Compound_006000001_006500000_SELFIES.jsonl.gz",
   "data/Compound_128000001_128500000/Compound_128000001_128500000_SELFIES.jsonl.gz",
   "data/Compound_121000001_121500000/Compound_121000001_121500000_SELFIES.jsonl.gz",
   "data/Compound_150000001_150500000/Compound_150000001_150500000_SELFIES.jsonl.gz",
   "data/Compound_124000001_124500000/Compound_124000001_124500000_SELFIES.jsonl.gz",
   "data/Compound_111500001_112000000/Compound_111500001_112000000_SELFIES.jsonl.gz",
   "data/Compound_148000001_148500000/Compound_148000001_148500000_SELFIES.jsonl.gz",
   "data/Compound_006500001_007000000/Compound_006500001_007000000_SELFIES.jsonl.gz",
   "data/Compound_033000001_033500000/Compound_033000001_033500000_SELFIES.jsonl.gz",
   "data/Compound_096000001_096500000/Compound_096000001_096500000_SELFIES.jsonl.gz",
   "data/Compound_038000001_038500000/Compound_038000001_038500000_SELFIES.jsonl.gz",
   "data/Compound_124500001_125000000/Compound_124500001_125000000_SELFIES.jsonl.gz",
   "data/Compound_050500001_051000000/Compound_050500001_051000000_SELFIES.jsonl.gz",
   "data/Compound_003000001_003500000/Compound_003000001_003500000_SELFIES.jsonl.gz",
   "data/Compound_073500001_074000000/Compound_073500001_074000000_SELFIES.jsonl.gz",
   "data/Compound_023000001_023500000/Compound_023000001_023500000_SELFIES.jsonl.gz",
   "data/Compound_060500001_061000000/Compound_060500001_061000000_SELFIES.jsonl.gz",
   "data/Compound_054000001_054500000/Compound_054000001_054500000_SELFIES.jsonl.gz"
]

class PubchemSelfies(datasets.GeneratorBasedBuilder):
    """A dataset of PubChem molecules represented as SELFIES."""

    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="A dataset of PubChem molecules represented as SELFIES."
    )

    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):
        downloaded_files = dl_manager.download(FILES)

        train_len = int(len(downloaded_files) * 0.8)
        valid_len = int(len(downloaded_files) * 0.1)

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                # These kwargs will be passed to _generate_examples
                gen_kwargs={
                    "subdirs": downloaded_files[:train_len],
                    "split": "train",
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.VALIDATION,
                # These kwargs will be passed to _generate_examples
                gen_kwargs={
                    "subdirs": downloaded_files[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": downloaded_files[-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 filepath in subdirs:
            with gzip.open(open(filepath, "rb"), "rt", encoding="utf-8") as f:
                for row_idx, row in enumerate(f):
                    data = json.loads(row)
                    properties = data["molecules"][0]["properties"]
                    key = f"{os.path.basename(filepath)}_{row_idx}"
                    yield key, {
                        "PUBCHEM_COMPOUND_CID": properties["PUBCHEM_COMPOUND_CID"],
                        "PUBCHEM_OPENEYE_CAN_SMILES": properties[
                            "PUBCHEM_OPENEYE_CAN_SMILES"
                        ],
                        "CAN_SELFIES": properties["CAN_SELFIES"],
                    }