zpn commited on
Commit
34ad093
1 Parent(s): fc7d02c

feat: data loading

Browse files
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pubchem_selfies.py CHANGED
@@ -72,349 +72,348 @@ _HOMEPAGE = "https://pubchem.ncbi.nlm.nih.gov/"
72
  _LICENSE = "Open Data Commons Open Database License"
73
 
74
  # this list of files has been preshuffled so we can use the same splits everytime
75
- SUBDIRS = [
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- "data/Compound_039000001_039500000",
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- "data/Compound_019500001_020000000",
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- "data/Compound_031500001_032000000",
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- "data/Compound_123500001_124000000",
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- "data/Compound_037500001_038000000",
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- "data/Compound_030500001_031000000",
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- "data/Compound_006500001_007000000",
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- "data/Compound_068500001_069000000",
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- "data/Compound_093000001_093500000",
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- "data/Compound_164000001_164500000",
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- "data/Compound_049000001_049500000",
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- "data/Compound_037000001_037500000",
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- "data/Compound_084500001_085000000",
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- "data/Compound_142500001_143000000",
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- "data/Compound_138500001_139000000",
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- "data/Compound_046000001_046500000",
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- "data/Compound_036000001_036500000",
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- "data/Compound_013500001_014000000",
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- "data/Compound_024500001_025000000",
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- "data/Compound_079500001_080000000",
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- "data/Compound_110000001_110500000",
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- "data/Compound_098500001_099000000",
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- "data/Compound_078500001_079000000",
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- "data/Compound_030000001_030500000",
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- "data/Compound_074500001_075000000",
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- "data/Compound_000000001_000500000",
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- "data/Compound_094500001_095000000",
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- "data/Compound_043500001_044000000",
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- "data/Compound_016000001_016500000",
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- "data/Compound_120000001_120500000",
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- "data/Compound_071000001_071500000",
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- "data/Compound_083500001_084000000",
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- "data/Compound_075000001_075500000",
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- "data/Compound_089500001_090000000",
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- "data/Compound_135000001_135500000",
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- "data/Compound_140000001_140500000",
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- "data/Compound_143500001_144000000",
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- "data/Compound_087500001_088000000",
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- "data/Compound_064500001_065000000",
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- "data/Compound_022500001_023000000",
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- "data/Compound_122000001_122500000",
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- "data/Compound_050000001_050500000",
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- "data/Compound_149500001_150000000",
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- "data/Compound_049500001_050000000",
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- "data/Compound_073000001_073500000",
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- "data/Compound_050500001_051000000",
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- "data/Compound_072000001_072500000",
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- "data/Compound_157000001_157500000",
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- "data/Compound_132000001_132500000",
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- "data/Compound_020500001_021000000",
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- "data/Compound_010000001_010500000",
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- "data/Compound_048000001_048500000",
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- "data/Compound_042500001_043000000",
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- "data/Compound_162000001_162500000",
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- "data/Compound_069500001_070000000",
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- "data/Compound_076000001_076500000",
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- "data/Compound_017500001_018000000",
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- "data/Compound_085000001_085500000",
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- "data/Compound_107500001_108000000",
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- "data/Compound_004500001_005000000",
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- "data/Compound_163000001_163500000",
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- "data/Compound_100000001_100500000",
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- "data/Compound_009500001_010000000",
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- "data/Compound_154500001_155000000",
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- "data/Compound_153500001_154000000",
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- "data/Compound_009000001_009500000",
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- "data/Compound_076500001_077000000",
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- "data/Compound_134500001_135000000",
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- "data/Compound_092000001_092500000",
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- "data/Compound_060500001_061000000",
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- "data/Compound_138000001_138500000",
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- "data/Compound_129500001_130000000",
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- "data/Compound_077000001_077500000",
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- "data/Compound_084000001_084500000",
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- "data/Compound_000500001_001000000",
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- "data/Compound_070000001_070500000",
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- "data/Compound_041000001_041500000",
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- "data/Compound_003000001_003500000",
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- "data/Compound_002000001_002500000",
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- "data/Compound_104000001_104500000",
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- "data/Compound_019000001_019500000",
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- "data/Compound_105000001_105500000",
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- "data/Compound_028000001_028500000",
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- "data/Compound_080500001_081000000",
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- "data/Compound_026500001_027000000",
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- "data/Compound_027500001_028000000",
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- "data/Compound_161000001_161500000",
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- "data/Compound_145000001_145500000",
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- "data/Compound_096500001_097000000",
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- "data/Compound_074000001_074500000",
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- "data/Compound_108500001_109000000",
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- "data/Compound_057500001_058000000",
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- "data/Compound_102000001_102500000",
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- "data/Compound_043000001_043500000",
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- "data/Compound_129000001_129500000",
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- "data/Compound_104500001_105000000",
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- "data/Compound_075500001_076000000",
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- "data/Compound_121000001_121500000",
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- "data/Compound_105500001_106000000",
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- "data/Compound_038000001_038500000",
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- "data/Compound_096000001_096500000",
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- "data/Compound_034000001_034500000",
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- "data/Compound_059000001_059500000",
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- "data/Compound_052000001_052500000",
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- "data/Compound_130000001_130500000",
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- "data/Compound_082500001_083000000",
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- "data/Compound_083000001_083500000",
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- "data/Compound_156000001_156500000",
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- "data/Compound_047000001_047500000",
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- "data/Compound_059500001_060000000",
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- "data/Compound_014000001_014500000",
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- "data/Compound_097000001_097500000",
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- "data/Compound_041500001_042000000",
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- "data/Compound_110500001_111000000",
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- "data/Compound_056000001_056500000",
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- "data/Compound_078000001_078500000",
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- "data/Compound_111000001_111500000",
366
- "data/Compound_103500001_104000000",
367
- "data/Compound_024000001_024500000",
368
- "data/Compound_079000001_079500000",
369
- "data/Compound_127000001_127500000",
370
- "data/Compound_090000001_090500000",
371
- "data/Compound_028500001_029000000",
372
- "data/Compound_015500001_016000000",
373
- "data/Compound_158500001_159000000",
374
- "data/Compound_086000001_086500000",
375
- "data/Compound_091500001_092000000",
376
- "data/Compound_137000001_137500000",
377
- "data/Compound_007500001_008000000",
378
- "data/Compound_124500001_125000000",
379
- "data/Compound_106000001_106500000",
380
- "data/Compound_119500001_120000000",
381
- "data/Compound_101000001_101500000",
382
- "data/Compound_106500001_107000000",
383
- "data/Compound_131500001_132000000",
384
- "data/Compound_086500001_087000000",
385
- "data/Compound_146500001_147000000",
386
- "data/Compound_046500001_047000000",
387
- "data/Compound_006000001_006500000",
388
- "data/Compound_097500001_098000000",
389
- "data/Compound_151000001_151500000",
390
- "data/Compound_125500001_126000000",
391
- "data/Compound_099500001_100000000",
392
- "data/Compound_118000001_118500000",
393
- "data/Compound_013000001_013500000",
394
- "data/Compound_115000001_115500000",
395
- "data/Compound_070500001_071000000",
396
- "data/Compound_054000001_054500000",
397
- "data/Compound_026000001_026500000",
398
- "data/Compound_160000001_160500000",
399
- "data/Compound_143000001_143500000",
400
- "data/Compound_014500001_015000000",
401
- "data/Compound_157500001_158000000",
402
- "data/Compound_007000001_007500000",
403
- "data/Compound_038500001_039000000",
404
- "data/Compound_065000001_065500000",
405
- "data/Compound_147000001_147500000",
406
  ]
407
 
408
-
409
  class PubchemSelfies(datasets.GeneratorBasedBuilder):
410
- """TODO: Short description of my dataset."""
411
 
412
  VERSION = datasets.Version("1.1.0")
413
 
414
  # You will be able to load one or the other configurations in the following list with
415
  BUILDER_CONFIG = datasets.BuilderConfig(
416
- version=VERSION, description=""
417
- ) # TODO: Short description of my dataset.
418
 
419
  def _info(self):
420
  return datasets.DatasetInfo(
@@ -431,21 +430,23 @@ class PubchemSelfies(datasets.GeneratorBasedBuilder):
431
  # Homepage of the dataset for documentation
432
  homepage=_HOMEPAGE,
433
  # License for the dataset if available
434
- # license=_LICENSE,
435
  # Citation for the dataset
436
  citation=_CITATION,
437
  )
438
 
439
  def _split_generators(self, dl_manager):
440
- train_len = int(len(SUBDIRS) * 0.8)
441
- valid_len = int(len(SUBDIRS) * 0.1)
 
 
442
 
443
  return [
444
  datasets.SplitGenerator(
445
  name=datasets.Split.TRAIN,
446
  # These kwargs will be passed to _generate_examples
447
  gen_kwargs={
448
- "subdirs": SUBDIRS[:train_len],
449
  "split": "train",
450
  },
451
  ),
@@ -453,7 +454,7 @@ class PubchemSelfies(datasets.GeneratorBasedBuilder):
453
  name=datasets.Split.VALIDATION,
454
  # These kwargs will be passed to _generate_examples
455
  gen_kwargs={
456
- "subdirs": SUBDIRS[train_len : train_len + valid_len],
457
  "split": "valid",
458
  },
459
  ),
@@ -461,7 +462,7 @@ class PubchemSelfies(datasets.GeneratorBasedBuilder):
461
  name=datasets.Split.TEST,
462
  # These kwargs will be passed to _generate_examples
463
  gen_kwargs={
464
- "subdirs": SUBDIRS[-valid_len:],
465
  "split": "test",
466
  },
467
  ),
@@ -470,8 +471,7 @@ class PubchemSelfies(datasets.GeneratorBasedBuilder):
470
  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
471
  def _generate_examples(self, subdirs, split):
472
  # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
473
- for subdir in subdirs:
474
- filepath = f"{subdir}/{subdir.split('/')[-1]}_SELFIES.jsonl.gz"
475
  with gzip.open(filepath, mode="rt") as f:
476
  rows = f.readlines()
477
  for key, row in enumerate(rows):
 
72
  _LICENSE = "Open Data Commons Open Database License"
73
 
74
  # this list of files has been preshuffled so we can use the same splits everytime
75
+ FILES = [
76
+ "data/Compound_021000001_021500000/Compound_021000001_021500000_SELFIES.jsonl.gz",
77
+ "data/Compound_034500001_035000000/Compound_034500001_035000000_SELFIES.jsonl.gz",
78
+ "data/Compound_023500001_024000000/Compound_023500001_024000000_SELFIES.jsonl.gz",
79
+ "data/Compound_151500001_152000000/Compound_151500001_152000000_SELFIES.jsonl.gz",
80
+ "data/Compound_126500001_127000000/Compound_126500001_127000000_SELFIES.jsonl.gz",
81
+ "data/Compound_030500001_031000000/Compound_030500001_031000000_SELFIES.jsonl.gz",
82
+ "data/Compound_061500001_062000000/Compound_061500001_062000000_SELFIES.jsonl.gz",
83
+ "data/Compound_031500001_032000000/Compound_031500001_032000000_SELFIES.jsonl.gz",
84
+ "data/Compound_111000001_111500000/Compound_111000001_111500000_SELFIES.jsonl.gz",
85
+ "data/Compound_058500001_059000000/Compound_058500001_059000000_SELFIES.jsonl.gz",
86
+ "data/Compound_065500001_066000000/Compound_065500001_066000000_SELFIES.jsonl.gz",
87
+ "data/Compound_065000001_065500000/Compound_065000001_065500000_SELFIES.jsonl.gz",
88
+ "data/Compound_039500001_040000000/Compound_039500001_040000000_SELFIES.jsonl.gz",
89
+ "data/Compound_014000001_014500000/Compound_014000001_014500000_SELFIES.jsonl.gz",
90
+ "data/Compound_021500001_022000000/Compound_021500001_022000000_SELFIES.jsonl.gz",
91
+ "data/Compound_081000001_081500000/Compound_081000001_081500000_SELFIES.jsonl.gz",
92
+ "data/Compound_122000001_122500000/Compound_122000001_122500000_SELFIES.jsonl.gz",
93
+ "data/Compound_045000001_045500000/Compound_045000001_045500000_SELFIES.jsonl.gz",
94
+ "data/Compound_017500001_018000000/Compound_017500001_018000000_SELFIES.jsonl.gz",
95
+ "data/Compound_059000001_059500000/Compound_059000001_059500000_SELFIES.jsonl.gz",
96
+ "data/Compound_141000001_141500000/Compound_141000001_141500000_SELFIES.jsonl.gz",
97
+ "data/Compound_129500001_130000000/Compound_129500001_130000000_SELFIES.jsonl.gz",
98
+ "data/Compound_163500001_164000000/Compound_163500001_164000000_SELFIES.jsonl.gz",
99
+ "data/Compound_089000001_089500000/Compound_089000001_089500000_SELFIES.jsonl.gz",
100
+ "data/Compound_077000001_077500000/Compound_077000001_077500000_SELFIES.jsonl.gz",
101
+ "data/Compound_161000001_161500000/Compound_161000001_161500000_SELFIES.jsonl.gz",
102
+ "data/Compound_113000001_113500000/Compound_113000001_113500000_SELFIES.jsonl.gz",
103
+ "data/Compound_040000001_040500000/Compound_040000001_040500000_SELFIES.jsonl.gz",
104
+ "data/Compound_010000001_010500000/Compound_010000001_010500000_SELFIES.jsonl.gz",
105
+ "data/Compound_091500001_092000000/Compound_091500001_092000000_SELFIES.jsonl.gz",
106
+ "data/Compound_154500001_155000000/Compound_154500001_155000000_SELFIES.jsonl.gz",
107
+ "data/Compound_098500001_099000000/Compound_098500001_099000000_SELFIES.jsonl.gz",
108
+ "data/Compound_019000001_019500000/Compound_019000001_019500000_SELFIES.jsonl.gz",
109
+ "data/Compound_064000001_064500000/Compound_064000001_064500000_SELFIES.jsonl.gz",
110
+ "data/Compound_147000001_147500000/Compound_147000001_147500000_SELFIES.jsonl.gz",
111
+ "data/Compound_001500001_002000000/Compound_001500001_002000000_SELFIES.jsonl.gz",
112
+ "data/Compound_137000001_137500000/Compound_137000001_137500000_SELFIES.jsonl.gz",
113
+ "data/Compound_161500001_162000000/Compound_161500001_162000000_SELFIES.jsonl.gz",
114
+ "data/Compound_074000001_074500000/Compound_074000001_074500000_SELFIES.jsonl.gz",
115
+ "data/Compound_133500001_134000000/Compound_133500001_134000000_SELFIES.jsonl.gz",
116
+ "data/Compound_028000001_028500000/Compound_028000001_028500000_SELFIES.jsonl.gz",
117
+ "data/Compound_147500001_148000000/Compound_147500001_148000000_SELFIES.jsonl.gz",
118
+ "data/Compound_159000001_159500000/Compound_159000001_159500000_SELFIES.jsonl.gz",
119
+ "data/Compound_098000001_098500000/Compound_098000001_098500000_SELFIES.jsonl.gz",
120
+ "data/Compound_024000001_024500000/Compound_024000001_024500000_SELFIES.jsonl.gz",
121
+ "data/Compound_043000001_043500000/Compound_043000001_043500000_SELFIES.jsonl.gz",
122
+ "data/Compound_004500001_005000000/Compound_004500001_005000000_SELFIES.jsonl.gz",
123
+ "data/Compound_118000001_118500000/Compound_118000001_118500000_SELFIES.jsonl.gz",
124
+ "data/Compound_104500001_105000000/Compound_104500001_105000000_SELFIES.jsonl.gz",
125
+ "data/Compound_013000001_013500000/Compound_013000001_013500000_SELFIES.jsonl.gz",
126
+ "data/Compound_035500001_036000000/Compound_035500001_036000000_SELFIES.jsonl.gz",
127
+ "data/Compound_129000001_129500000/Compound_129000001_129500000_SELFIES.jsonl.gz",
128
+ "data/Compound_141500001_142000000/Compound_141500001_142000000_SELFIES.jsonl.gz",
129
+ "data/Compound_120500001_121000000/Compound_120500001_121000000_SELFIES.jsonl.gz",
130
+ "data/Compound_066000001_066500000/Compound_066000001_066500000_SELFIES.jsonl.gz",
131
+ "data/Compound_060000001_060500000/Compound_060000001_060500000_SELFIES.jsonl.gz",
132
+ "data/Compound_014500001_015000000/Compound_014500001_015000000_SELFIES.jsonl.gz",
133
+ "data/Compound_159500001_160000000/Compound_159500001_160000000_SELFIES.jsonl.gz",
134
+ "data/Compound_107500001_108000000/Compound_107500001_108000000_SELFIES.jsonl.gz",
135
+ "data/Compound_139500001_140000000/Compound_139500001_140000000_SELFIES.jsonl.gz",
136
+ "data/Compound_088500001_089000000/Compound_088500001_089000000_SELFIES.jsonl.gz",
137
+ "data/Compound_070000001_070500000/Compound_070000001_070500000_SELFIES.jsonl.gz",
138
+ "data/Compound_103000001_103500000/Compound_103000001_103500000_SELFIES.jsonl.gz",
139
+ "data/Compound_063000001_063500000/Compound_063000001_063500000_SELFIES.jsonl.gz",
140
+ "data/Compound_052500001_053000000/Compound_052500001_053000000_SELFIES.jsonl.gz",
141
+ "data/Compound_094000001_094500000/Compound_094000001_094500000_SELFIES.jsonl.gz",
142
+ "data/Compound_091000001_091500000/Compound_091000001_091500000_SELFIES.jsonl.gz",
143
+ "data/Compound_075000001_075500000/Compound_075000001_075500000_SELFIES.jsonl.gz",
144
+ "data/Compound_116500001_117000000/Compound_116500001_117000000_SELFIES.jsonl.gz",
145
+ "data/Compound_164500001_165000000/Compound_164500001_165000000_SELFIES.jsonl.gz",
146
+ "data/Compound_071500001_072000000/Compound_071500001_072000000_SELFIES.jsonl.gz",
147
+ "data/Compound_055000001_055500000/Compound_055000001_055500000_SELFIES.jsonl.gz",
148
+ "data/Compound_027500001_028000000/Compound_027500001_028000000_SELFIES.jsonl.gz",
149
+ "data/Compound_132500001_133000000/Compound_132500001_133000000_SELFIES.jsonl.gz",
150
+ "data/Compound_027000001_027500000/Compound_027000001_027500000_SELFIES.jsonl.gz",
151
+ "data/Compound_132000001_132500000/Compound_132000001_132500000_SELFIES.jsonl.gz",
152
+ "data/Compound_089500001_090000000/Compound_089500001_090000000_SELFIES.jsonl.gz",
153
+ "data/Compound_120000001_120500000/Compound_120000001_120500000_SELFIES.jsonl.gz",
154
+ "data/Compound_088000001_088500000/Compound_088000001_088500000_SELFIES.jsonl.gz",
155
+ "data/Compound_117500001_118000000/Compound_117500001_118000000_SELFIES.jsonl.gz",
156
+ "data/Compound_114000001_114500000/Compound_114000001_114500000_SELFIES.jsonl.gz",
157
+ "data/Compound_049500001_050000000/Compound_049500001_050000000_SELFIES.jsonl.gz",
158
+ "data/Compound_134000001_134500000/Compound_134000001_134500000_SELFIES.jsonl.gz",
159
+ "data/Compound_115000001_115500000/Compound_115000001_115500000_SELFIES.jsonl.gz",
160
+ "data/Compound_143500001_144000000/Compound_143500001_144000000_SELFIES.jsonl.gz",
161
+ "data/Compound_164000001_164500000/Compound_164000001_164500000_SELFIES.jsonl.gz",
162
+ "data/Compound_094500001_095000000/Compound_094500001_095000000_SELFIES.jsonl.gz",
163
+ "data/Compound_072500001_073000000/Compound_072500001_073000000_SELFIES.jsonl.gz",
164
+ "data/Compound_086500001_087000000/Compound_086500001_087000000_SELFIES.jsonl.gz",
165
+ "data/Compound_084000001_084500000/Compound_084000001_084500000_SELFIES.jsonl.gz",
166
+ "data/Compound_148500001_149000000/Compound_148500001_149000000_SELFIES.jsonl.gz",
167
+ "data/Compound_144000001_144500000/Compound_144000001_144500000_SELFIES.jsonl.gz",
168
+ "data/Compound_146000001_146500000/Compound_146000001_146500000_SELFIES.jsonl.gz",
169
+ "data/Compound_054500001_055000000/Compound_054500001_055000000_SELFIES.jsonl.gz",
170
+ "data/Compound_034000001_034500000/Compound_034000001_034500000_SELFIES.jsonl.gz",
171
+ "data/Compound_007000001_007500000/Compound_007000001_007500000_SELFIES.jsonl.gz",
172
+ "data/Compound_056500001_057000000/Compound_056500001_057000000_SELFIES.jsonl.gz",
173
+ "data/Compound_152500001_153000000/Compound_152500001_153000000_SELFIES.jsonl.gz",
174
+ "data/Compound_030000001_030500000/Compound_030000001_030500000_SELFIES.jsonl.gz",
175
+ "data/Compound_031000001_031500000/Compound_031000001_031500000_SELFIES.jsonl.gz",
176
+ "data/Compound_035000001_035500000/Compound_035000001_035500000_SELFIES.jsonl.gz",
177
+ "data/Compound_156500001_157000000/Compound_156500001_157000000_SELFIES.jsonl.gz",
178
+ "data/Compound_036000001_036500000/Compound_036000001_036500000_SELFIES.jsonl.gz",
179
+ "data/Compound_157500001_158000000/Compound_157500001_158000000_SELFIES.jsonl.gz",
180
+ "data/Compound_051500001_052000000/Compound_051500001_052000000_SELFIES.jsonl.gz",
181
+ "data/Compound_144500001_145000000/Compound_144500001_145000000_SELFIES.jsonl.gz",
182
+ "data/Compound_038500001_039000000/Compound_038500001_039000000_SELFIES.jsonl.gz",
183
+ "data/Compound_018500001_019000000/Compound_018500001_019000000_SELFIES.jsonl.gz",
184
+ "data/Compound_149000001_149500000/Compound_149000001_149500000_SELFIES.jsonl.gz",
185
+ "data/Compound_139000001_139500000/Compound_139000001_139500000_SELFIES.jsonl.gz",
186
+ "data/Compound_039000001_039500000/Compound_039000001_039500000_SELFIES.jsonl.gz",
187
+ "data/Compound_102000001_102500000/Compound_102000001_102500000_SELFIES.jsonl.gz",
188
+ "data/Compound_022000001_022500000/Compound_022000001_022500000_SELFIES.jsonl.gz",
189
+ "data/Compound_009500001_010000000/Compound_009500001_010000000_SELFIES.jsonl.gz",
190
+ "data/Compound_086000001_086500000/Compound_086000001_086500000_SELFIES.jsonl.gz",
191
+ "data/Compound_040500001_041000000/Compound_040500001_041000000_SELFIES.jsonl.gz",
192
+ "data/Compound_131500001_132000000/Compound_131500001_132000000_SELFIES.jsonl.gz",
193
+ "data/Compound_095000001_095500000/Compound_095000001_095500000_SELFIES.jsonl.gz",
194
+ "data/Compound_107000001_107500000/Compound_107000001_107500000_SELFIES.jsonl.gz",
195
+ "data/Compound_076500001_077000000/Compound_076500001_077000000_SELFIES.jsonl.gz",
196
+ "data/Compound_013500001_014000000/Compound_013500001_014000000_SELFIES.jsonl.gz",
197
+ "data/Compound_056000001_056500000/Compound_056000001_056500000_SELFIES.jsonl.gz",
198
+ "data/Compound_138000001_138500000/Compound_138000001_138500000_SELFIES.jsonl.gz",
199
+ "data/Compound_162500001_163000000/Compound_162500001_163000000_SELFIES.jsonl.gz",
200
+ "data/Compound_136000001_136500000/Compound_136000001_136500000_SELFIES.jsonl.gz",
201
+ "data/Compound_146500001_147000000/Compound_146500001_147000000_SELFIES.jsonl.gz",
202
+ "data/Compound_007500001_008000000/Compound_007500001_008000000_SELFIES.jsonl.gz",
203
+ "data/Compound_037500001_038000000/Compound_037500001_038000000_SELFIES.jsonl.gz",
204
+ "data/Compound_015000001_015500000/Compound_015000001_015500000_SELFIES.jsonl.gz",
205
+ "data/Compound_106500001_107000000/Compound_106500001_107000000_SELFIES.jsonl.gz",
206
+ "data/Compound_003500001_004000000/Compound_003500001_004000000_SELFIES.jsonl.gz",
207
+ "data/Compound_131000001_131500000/Compound_131000001_131500000_SELFIES.jsonl.gz",
208
+ "data/Compound_102500001_103000000/Compound_102500001_103000000_SELFIES.jsonl.gz",
209
+ "data/Compound_112000001_112500000/Compound_112000001_112500000_SELFIES.jsonl.gz",
210
+ "data/Compound_049000001_049500000/Compound_049000001_049500000_SELFIES.jsonl.gz",
211
+ "data/Compound_041000001_041500000/Compound_041000001_041500000_SELFIES.jsonl.gz",
212
+ "data/Compound_011000001_011500000/Compound_011000001_011500000_SELFIES.jsonl.gz",
213
+ "data/Compound_079500001_080000000/Compound_079500001_080000000_SELFIES.jsonl.gz",
214
+ "data/Compound_105500001_106000000/Compound_105500001_106000000_SELFIES.jsonl.gz",
215
+ "data/Compound_123500001_124000000/Compound_123500001_124000000_SELFIES.jsonl.gz",
216
+ "data/Compound_057000001_057500000/Compound_057000001_057500000_SELFIES.jsonl.gz",
217
+ "data/Compound_110500001_111000000/Compound_110500001_111000000_SELFIES.jsonl.gz",
218
+ "data/Compound_029500001_030000000/Compound_029500001_030000000_SELFIES.jsonl.gz",
219
+ "data/Compound_082000001_082500000/Compound_082000001_082500000_SELFIES.jsonl.gz",
220
+ "data/Compound_087500001_088000000/Compound_087500001_088000000_SELFIES.jsonl.gz",
221
+ "data/Compound_100500001_101000000/Compound_100500001_101000000_SELFIES.jsonl.gz",
222
+ "data/Compound_018000001_018500000/Compound_018000001_018500000_SELFIES.jsonl.gz",
223
+ "data/Compound_114500001_115000000/Compound_114500001_115000000_SELFIES.jsonl.gz",
224
+ "data/Compound_008000001_008500000/Compound_008000001_008500000_SELFIES.jsonl.gz",
225
+ "data/Compound_143000001_143500000/Compound_143000001_143500000_SELFIES.jsonl.gz",
226
+ "data/Compound_142000001_142500000/Compound_142000001_142500000_SELFIES.jsonl.gz",
227
+ "data/Compound_109000001_109500000/Compound_109000001_109500000_SELFIES.jsonl.gz",
228
+ "data/Compound_047000001_047500000/Compound_047000001_047500000_SELFIES.jsonl.gz",
229
+ "data/Compound_077500001_078000000/Compound_077500001_078000000_SELFIES.jsonl.gz",
230
+ "data/Compound_100000001_100500000/Compound_100000001_100500000_SELFIES.jsonl.gz",
231
+ "data/Compound_043500001_044000000/Compound_043500001_044000000_SELFIES.jsonl.gz",
232
+ "data/Compound_029000001_029500000/Compound_029000001_029500000_SELFIES.jsonl.gz",
233
+ "data/Compound_078500001_079000000/Compound_078500001_079000000_SELFIES.jsonl.gz",
234
+ "data/Compound_005000001_005500000/Compound_005000001_005500000_SELFIES.jsonl.gz",
235
+ "data/Compound_153000001_153500000/Compound_153000001_153500000_SELFIES.jsonl.gz",
236
+ "data/Compound_004000001_004500000/Compound_004000001_004500000_SELFIES.jsonl.gz",
237
+ "data/Compound_072000001_072500000/Compound_072000001_072500000_SELFIES.jsonl.gz",
238
+ "data/Compound_045500001_046000000/Compound_045500001_046000000_SELFIES.jsonl.gz",
239
+ "data/Compound_050000001_050500000/Compound_050000001_050500000_SELFIES.jsonl.gz",
240
+ "data/Compound_115500001_116000000/Compound_115500001_116000000_SELFIES.jsonl.gz",
241
+ "data/Compound_155500001_156000000/Compound_155500001_156000000_SELFIES.jsonl.gz",
242
+ "data/Compound_025500001_026000000/Compound_025500001_026000000_SELFIES.jsonl.gz",
243
+ "data/Compound_106000001_106500000/Compound_106000001_106500000_SELFIES.jsonl.gz",
244
+ "data/Compound_075500001_076000000/Compound_075500001_076000000_SELFIES.jsonl.gz",
245
+ "data/Compound_062500001_063000000/Compound_062500001_063000000_SELFIES.jsonl.gz",
246
+ "data/Compound_155000001_155500000/Compound_155000001_155500000_SELFIES.jsonl.gz",
247
+ "data/Compound_105000001_105500000/Compound_105000001_105500000_SELFIES.jsonl.gz",
248
+ "data/Compound_097500001_098000000/Compound_097500001_098000000_SELFIES.jsonl.gz",
249
+ "data/Compound_005500001_006000000/Compound_005500001_006000000_SELFIES.jsonl.gz",
250
+ "data/Compound_127500001_128000000/Compound_127500001_128000000_SELFIES.jsonl.gz",
251
+ "data/Compound_135500001_136000000/Compound_135500001_136000000_SELFIES.jsonl.gz",
252
+ "data/Compound_020000001_020500000/Compound_020000001_020500000_SELFIES.jsonl.gz",
253
+ "data/Compound_135000001_135500000/Compound_135000001_135500000_SELFIES.jsonl.gz",
254
+ "data/Compound_068000001_068500000/Compound_068000001_068500000_SELFIES.jsonl.gz",
255
+ "data/Compound_026000001_026500000/Compound_026000001_026500000_SELFIES.jsonl.gz",
256
+ "data/Compound_099500001_100000000/Compound_099500001_100000000_SELFIES.jsonl.gz",
257
+ "data/Compound_158000001_158500000/Compound_158000001_158500000_SELFIES.jsonl.gz",
258
+ "data/Compound_069000001_069500000/Compound_069000001_069500000_SELFIES.jsonl.gz",
259
+ "data/Compound_078000001_078500000/Compound_078000001_078500000_SELFIES.jsonl.gz",
260
+ "data/Compound_066500001_067000000/Compound_066500001_067000000_SELFIES.jsonl.gz",
261
+ "data/Compound_076000001_076500000/Compound_076000001_076500000_SELFIES.jsonl.gz",
262
+ "data/Compound_009000001_009500000/Compound_009000001_009500000_SELFIES.jsonl.gz",
263
+ "data/Compound_117000001_117500000/Compound_117000001_117500000_SELFIES.jsonl.gz",
264
+ "data/Compound_055500001_056000000/Compound_055500001_056000000_SELFIES.jsonl.gz",
265
+ "data/Compound_012500001_013000000/Compound_012500001_013000000_SELFIES.jsonl.gz",
266
+ "data/Compound_011500001_012000000/Compound_011500001_012000000_SELFIES.jsonl.gz",
267
+ "data/Compound_015500001_016000000/Compound_015500001_016000000_SELFIES.jsonl.gz",
268
+ "data/Compound_092000001_092500000/Compound_092000001_092500000_SELFIES.jsonl.gz",
269
+ "data/Compound_008500001_009000000/Compound_008500001_009000000_SELFIES.jsonl.gz",
270
+ "data/Compound_000000001_000500000/Compound_000000001_000500000_SELFIES.jsonl.gz",
271
+ "data/Compound_151000001_151500000/Compound_151000001_151500000_SELFIES.jsonl.gz",
272
+ "data/Compound_082500001_083000000/Compound_082500001_083000000_SELFIES.jsonl.gz",
273
+ "data/Compound_012000001_012500000/Compound_012000001_012500000_SELFIES.jsonl.gz",
274
+ "data/Compound_057500001_058000000/Compound_057500001_058000000_SELFIES.jsonl.gz",
275
+ "data/Compound_103500001_104000000/Compound_103500001_104000000_SELFIES.jsonl.gz",
276
+ "data/Compound_067500001_068000000/Compound_067500001_068000000_SELFIES.jsonl.gz",
277
+ "data/Compound_108000001_108500000/Compound_108000001_108500000_SELFIES.jsonl.gz",
278
+ "data/Compound_046500001_047000000/Compound_046500001_047000000_SELFIES.jsonl.gz",
279
+ "data/Compound_017000001_017500000/Compound_017000001_017500000_SELFIES.jsonl.gz",
280
+ "data/Compound_058000001_058500000/Compound_058000001_058500000_SELFIES.jsonl.gz",
281
+ "data/Compound_079000001_079500000/Compound_079000001_079500000_SELFIES.jsonl.gz",
282
+ "data/Compound_062000001_062500000/Compound_062000001_062500000_SELFIES.jsonl.gz",
283
+ "data/Compound_145000001_145500000/Compound_145000001_145500000_SELFIES.jsonl.gz",
284
+ "data/Compound_163000001_163500000/Compound_163000001_163500000_SELFIES.jsonl.gz",
285
+ "data/Compound_067000001_067500000/Compound_067000001_067500000_SELFIES.jsonl.gz",
286
+ "data/Compound_083000001_083500000/Compound_083000001_083500000_SELFIES.jsonl.gz",
287
+ "data/Compound_068500001_069000000/Compound_068500001_069000000_SELFIES.jsonl.gz",
288
+ "data/Compound_020500001_021000000/Compound_020500001_021000000_SELFIES.jsonl.gz",
289
+ "data/Compound_046000001_046500000/Compound_046000001_046500000_SELFIES.jsonl.gz",
290
+ "data/Compound_096500001_097000000/Compound_096500001_097000000_SELFIES.jsonl.gz",
291
+ "data/Compound_081500001_082000000/Compound_081500001_082000000_SELFIES.jsonl.gz",
292
+ "data/Compound_108500001_109000000/Compound_108500001_109000000_SELFIES.jsonl.gz",
293
+ "data/Compound_085500001_086000000/Compound_085500001_086000000_SELFIES.jsonl.gz",
294
+ "data/Compound_119000001_119500000/Compound_119000001_119500000_SELFIES.jsonl.gz",
295
+ "data/Compound_090500001_091000000/Compound_090500001_091000000_SELFIES.jsonl.gz",
296
+ "data/Compound_036500001_037000000/Compound_036500001_037000000_SELFIES.jsonl.gz",
297
+ "data/Compound_130500001_131000000/Compound_130500001_131000000_SELFIES.jsonl.gz",
298
+ "data/Compound_121500001_122000000/Compound_121500001_122000000_SELFIES.jsonl.gz",
299
+ "data/Compound_113500001_114000000/Compound_113500001_114000000_SELFIES.jsonl.gz",
300
+ "data/Compound_145500001_146000000/Compound_145500001_146000000_SELFIES.jsonl.gz",
301
+ "data/Compound_041500001_042000000/Compound_041500001_042000000_SELFIES.jsonl.gz",
302
+ "data/Compound_083500001_084000000/Compound_083500001_084000000_SELFIES.jsonl.gz",
303
+ "data/Compound_052000001_052500000/Compound_052000001_052500000_SELFIES.jsonl.gz",
304
+ "data/Compound_140500001_141000000/Compound_140500001_141000000_SELFIES.jsonl.gz",
305
+ "data/Compound_154000001_154500000/Compound_154000001_154500000_SELFIES.jsonl.gz",
306
+ "data/Compound_044000001_044500000/Compound_044000001_044500000_SELFIES.jsonl.gz",
307
+ "data/Compound_002000001_002500000/Compound_002000001_002500000_SELFIES.jsonl.gz",
308
+ "data/Compound_010500001_011000000/Compound_010500001_011000000_SELFIES.jsonl.gz",
309
+ "data/Compound_073000001_073500000/Compound_073000001_073500000_SELFIES.jsonl.gz",
310
+ "data/Compound_048500001_049000000/Compound_048500001_049000000_SELFIES.jsonl.gz",
311
+ "data/Compound_032000001_032500000/Compound_032000001_032500000_SELFIES.jsonl.gz",
312
+ "data/Compound_026500001_027000000/Compound_026500001_027000000_SELFIES.jsonl.gz",
313
+ "data/Compound_112500001_113000000/Compound_112500001_113000000_SELFIES.jsonl.gz",
314
+ "data/Compound_069500001_070000000/Compound_069500001_070000000_SELFIES.jsonl.gz",
315
+ "data/Compound_110000001_110500000/Compound_110000001_110500000_SELFIES.jsonl.gz",
316
+ "data/Compound_156000001_156500000/Compound_156000001_156500000_SELFIES.jsonl.gz",
317
+ "data/Compound_037000001_037500000/Compound_037000001_037500000_SELFIES.jsonl.gz",
318
+ "data/Compound_130000001_130500000/Compound_130000001_130500000_SELFIES.jsonl.gz",
319
+ "data/Compound_051000001_051500000/Compound_051000001_051500000_SELFIES.jsonl.gz",
320
+ "data/Compound_093500001_094000000/Compound_093500001_094000000_SELFIES.jsonl.gz",
321
+ "data/Compound_149500001_150000000/Compound_149500001_150000000_SELFIES.jsonl.gz",
322
+ "data/Compound_158500001_159000000/Compound_158500001_159000000_SELFIES.jsonl.gz",
323
+ "data/Compound_074500001_075000000/Compound_074500001_075000000_SELFIES.jsonl.gz",
324
+ "data/Compound_053500001_054000000/Compound_053500001_054000000_SELFIES.jsonl.gz",
325
+ "data/Compound_160500001_161000000/Compound_160500001_161000000_SELFIES.jsonl.gz",
326
+ "data/Compound_022500001_023000000/Compound_022500001_023000000_SELFIES.jsonl.gz",
327
+ "data/Compound_118500001_119000000/Compound_118500001_119000000_SELFIES.jsonl.gz",
328
+ "data/Compound_025000001_025500000/Compound_025000001_025500000_SELFIES.jsonl.gz",
329
+ "data/Compound_128500001_129000000/Compound_128500001_129000000_SELFIES.jsonl.gz",
330
+ "data/Compound_080500001_081000000/Compound_080500001_081000000_SELFIES.jsonl.gz",
331
+ "data/Compound_080000001_080500000/Compound_080000001_080500000_SELFIES.jsonl.gz",
332
+ "data/Compound_101000001_101500000/Compound_101000001_101500000_SELFIES.jsonl.gz",
333
+ "data/Compound_136500001_137000000/Compound_136500001_137000000_SELFIES.jsonl.gz",
334
+ "data/Compound_033500001_034000000/Compound_033500001_034000000_SELFIES.jsonl.gz",
335
+ "data/Compound_048000001_048500000/Compound_048000001_048500000_SELFIES.jsonl.gz",
336
+ "data/Compound_032500001_033000000/Compound_032500001_033000000_SELFIES.jsonl.gz",
337
+ "data/Compound_093000001_093500000/Compound_093000001_093500000_SELFIES.jsonl.gz",
338
+ "data/Compound_123000001_123500000/Compound_123000001_123500000_SELFIES.jsonl.gz",
339
+ "data/Compound_133000001_133500000/Compound_133000001_133500000_SELFIES.jsonl.gz",
340
+ "data/Compound_090000001_090500000/Compound_090000001_090500000_SELFIES.jsonl.gz",
341
+ "data/Compound_042500001_043000000/Compound_042500001_043000000_SELFIES.jsonl.gz",
342
+ "data/Compound_127000001_127500000/Compound_127000001_127500000_SELFIES.jsonl.gz",
343
+ "data/Compound_125000001_125500000/Compound_125000001_125500000_SELFIES.jsonl.gz",
344
+ "data/Compound_138500001_139000000/Compound_138500001_139000000_SELFIES.jsonl.gz",
345
+ "data/Compound_001000001_001500000/Compound_001000001_001500000_SELFIES.jsonl.gz",
346
+ "data/Compound_099000001_099500000/Compound_099000001_099500000_SELFIES.jsonl.gz",
347
+ "data/Compound_002500001_003000000/Compound_002500001_003000000_SELFIES.jsonl.gz",
348
+ "data/Compound_019500001_020000000/Compound_019500001_020000000_SELFIES.jsonl.gz",
349
+ "data/Compound_047500001_048000000/Compound_047500001_048000000_SELFIES.jsonl.gz",
350
+ "data/Compound_097000001_097500000/Compound_097000001_097500000_SELFIES.jsonl.gz",
351
+ "data/Compound_070500001_071000000/Compound_070500001_071000000_SELFIES.jsonl.gz",
352
+ "data/Compound_125500001_126000000/Compound_125500001_126000000_SELFIES.jsonl.gz",
353
+ "data/Compound_064500001_065000000/Compound_064500001_065000000_SELFIES.jsonl.gz",
354
+ "data/Compound_157000001_157500000/Compound_157000001_157500000_SELFIES.jsonl.gz",
355
+ "data/Compound_087000001_087500000/Compound_087000001_087500000_SELFIES.jsonl.gz",
356
+ "data/Compound_071000001_071500000/Compound_071000001_071500000_SELFIES.jsonl.gz",
357
+ "data/Compound_119500001_120000000/Compound_119500001_120000000_SELFIES.jsonl.gz",
358
+ "data/Compound_044500001_045000000/Compound_044500001_045000000_SELFIES.jsonl.gz",
359
+ "data/Compound_016000001_016500000/Compound_016000001_016500000_SELFIES.jsonl.gz",
360
+ "data/Compound_095500001_096000000/Compound_095500001_096000000_SELFIES.jsonl.gz",
361
+ "data/Compound_092500001_093000000/Compound_092500001_093000000_SELFIES.jsonl.gz",
362
+ "data/Compound_000500001_001000000/Compound_000500001_001000000_SELFIES.jsonl.gz",
363
+ "data/Compound_059500001_060000000/Compound_059500001_060000000_SELFIES.jsonl.gz",
364
+ "data/Compound_016500001_017000000/Compound_016500001_017000000_SELFIES.jsonl.gz",
365
+ "data/Compound_061000001_061500000/Compound_061000001_061500000_SELFIES.jsonl.gz",
366
+ "data/Compound_101500001_102000000/Compound_101500001_102000000_SELFIES.jsonl.gz",
367
+ "data/Compound_028500001_029000000/Compound_028500001_029000000_SELFIES.jsonl.gz",
368
+ "data/Compound_042000001_042500000/Compound_042000001_042500000_SELFIES.jsonl.gz",
369
+ "data/Compound_152000001_152500000/Compound_152000001_152500000_SELFIES.jsonl.gz",
370
+ "data/Compound_122500001_123000000/Compound_122500001_123000000_SELFIES.jsonl.gz",
371
+ "data/Compound_150500001_151000000/Compound_150500001_151000000_SELFIES.jsonl.gz",
372
+ "data/Compound_142500001_143000000/Compound_142500001_143000000_SELFIES.jsonl.gz",
373
+ "data/Compound_162000001_162500000/Compound_162000001_162500000_SELFIES.jsonl.gz",
374
+ "data/Compound_053000001_053500000/Compound_053000001_053500000_SELFIES.jsonl.gz",
375
+ "data/Compound_104000001_104500000/Compound_104000001_104500000_SELFIES.jsonl.gz",
376
+ "data/Compound_084500001_085000000/Compound_084500001_085000000_SELFIES.jsonl.gz",
377
+ "data/Compound_140000001_140500000/Compound_140000001_140500000_SELFIES.jsonl.gz",
378
+ "data/Compound_160000001_160500000/Compound_160000001_160500000_SELFIES.jsonl.gz",
379
+ "data/Compound_126000001_126500000/Compound_126000001_126500000_SELFIES.jsonl.gz",
380
+ "data/Compound_153500001_154000000/Compound_153500001_154000000_SELFIES.jsonl.gz",
381
+ "data/Compound_134500001_135000000/Compound_134500001_135000000_SELFIES.jsonl.gz",
382
+ "data/Compound_063500001_064000000/Compound_063500001_064000000_SELFIES.jsonl.gz",
383
+ "data/Compound_109500001_110000000/Compound_109500001_110000000_SELFIES.jsonl.gz",
384
+ "data/Compound_137500001_138000000/Compound_137500001_138000000_SELFIES.jsonl.gz",
385
+ "data/Compound_085000001_085500000/Compound_085000001_085500000_SELFIES.jsonl.gz",
386
+ "data/Compound_024500001_025000000/Compound_024500001_025000000_SELFIES.jsonl.gz",
387
+ "data/Compound_116000001_116500000/Compound_116000001_116500000_SELFIES.jsonl.gz",
388
+ "data/Compound_006000001_006500000/Compound_006000001_006500000_SELFIES.jsonl.gz",
389
+ "data/Compound_128000001_128500000/Compound_128000001_128500000_SELFIES.jsonl.gz",
390
+ "data/Compound_121000001_121500000/Compound_121000001_121500000_SELFIES.jsonl.gz",
391
+ "data/Compound_150000001_150500000/Compound_150000001_150500000_SELFIES.jsonl.gz",
392
+ "data/Compound_124000001_124500000/Compound_124000001_124500000_SELFIES.jsonl.gz",
393
+ "data/Compound_111500001_112000000/Compound_111500001_112000000_SELFIES.jsonl.gz",
394
+ "data/Compound_148000001_148500000/Compound_148000001_148500000_SELFIES.jsonl.gz",
395
+ "data/Compound_006500001_007000000/Compound_006500001_007000000_SELFIES.jsonl.gz",
396
+ "data/Compound_033000001_033500000/Compound_033000001_033500000_SELFIES.jsonl.gz",
397
+ "data/Compound_096000001_096500000/Compound_096000001_096500000_SELFIES.jsonl.gz",
398
+ "data/Compound_038000001_038500000/Compound_038000001_038500000_SELFIES.jsonl.gz",
399
+ "data/Compound_124500001_125000000/Compound_124500001_125000000_SELFIES.jsonl.gz",
400
+ "data/Compound_050500001_051000000/Compound_050500001_051000000_SELFIES.jsonl.gz",
401
+ "data/Compound_003000001_003500000/Compound_003000001_003500000_SELFIES.jsonl.gz",
402
+ "data/Compound_073500001_074000000/Compound_073500001_074000000_SELFIES.jsonl.gz",
403
+ "data/Compound_023000001_023500000/Compound_023000001_023500000_SELFIES.jsonl.gz",
404
+ "data/Compound_060500001_061000000/Compound_060500001_061000000_SELFIES.jsonl.gz",
405
+ "data/Compound_054000001_054500000/Compound_054000001_054500000_SELFIES.jsonl.gz"
406
  ]
407
 
 
408
  class PubchemSelfies(datasets.GeneratorBasedBuilder):
409
+ """A dataset of PubChem molecules represented as SELFIES."""
410
 
411
  VERSION = datasets.Version("1.1.0")
412
 
413
  # You will be able to load one or the other configurations in the following list with
414
  BUILDER_CONFIG = datasets.BuilderConfig(
415
+ version=VERSION, description="A dataset of PubChem molecules represented as SELFIES."
416
+ )
417
 
418
  def _info(self):
419
  return datasets.DatasetInfo(
 
430
  # Homepage of the dataset for documentation
431
  homepage=_HOMEPAGE,
432
  # License for the dataset if available
433
+ license=_LICENSE,
434
  # Citation for the dataset
435
  citation=_CITATION,
436
  )
437
 
438
  def _split_generators(self, dl_manager):
439
+ downloaded_files = dl_manager.download(FILES)
440
+
441
+ train_len = int(len(downloaded_files) * 0.8)
442
+ valid_len = int(len(downloaded_files) * 0.1)
443
 
444
  return [
445
  datasets.SplitGenerator(
446
  name=datasets.Split.TRAIN,
447
  # These kwargs will be passed to _generate_examples
448
  gen_kwargs={
449
+ "subdirs": downloaded_files[:train_len],
450
  "split": "train",
451
  },
452
  ),
 
454
  name=datasets.Split.VALIDATION,
455
  # These kwargs will be passed to _generate_examples
456
  gen_kwargs={
457
+ "subdirs": downloaded_files[train_len : train_len + valid_len],
458
  "split": "valid",
459
  },
460
  ),
 
462
  name=datasets.Split.TEST,
463
  # These kwargs will be passed to _generate_examples
464
  gen_kwargs={
465
+ "subdirs": downloaded_files[-valid_len:],
466
  "split": "test",
467
  },
468
  ),
 
471
  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
472
  def _generate_examples(self, subdirs, split):
473
  # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
474
+ for filepath in subdirs:
 
475
  with gzip.open(filepath, mode="rt") as f:
476
  rows = f.readlines()
477
  for key, row in enumerate(rows):