jglaser commited on
Commit
558c2c3
1 Parent(s): d7c19d0

update to most recent DBs, add split without KRAS

Browse files
.gitattributes CHANGED
@@ -820,3 +820,22 @@ data/dcoid_rf2.parquet filter=lfs diff=lfs merge=lfs -text
820
  data/deepcoy_dekois_predict.parquet filter=lfs diff=lfs merge=lfs -text
821
  data/deepcoy_dude_predict.parquet filter=lfs diff=lfs merge=lfs -text
822
  data/dcoid_predict.parquet filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
820
  data/deepcoy_dekois_predict.parquet filter=lfs diff=lfs merge=lfs -text
821
  data/deepcoy_dude_predict.parquet filter=lfs diff=lfs merge=lfs -text
822
  data/dcoid_predict.parquet filter=lfs diff=lfs merge=lfs -text
823
+ data/all_ic50.parquet filter=lfs diff=lfs merge=lfs -text
824
+ data/biolip_complex.parquet filter=lfs diff=lfs merge=lfs -text
825
+ data/biolip_ic50.parquet filter=lfs diff=lfs merge=lfs -text
826
+ data/biolip.parquet filter=lfs diff=lfs merge=lfs -text
827
+ data/dcoid_rf2_actives.parquet filter=lfs diff=lfs merge=lfs -text
828
+ data/pdbbind.parquet filter=lfs diff=lfs merge=lfs -text
829
+ data/bindingdb.parquet filter=lfs diff=lfs merge=lfs -text
830
+ data/moad_ic50.parquet filter=lfs diff=lfs merge=lfs -text
831
+ data/moad.parquet filter=lfs diff=lfs merge=lfs -text
832
+ data/dcoid_rf2_decoys.parquet filter=lfs diff=lfs merge=lfs -text
833
+ data/all_nokras.parquet filter=lfs diff=lfs merge=lfs -text
834
+ data/pdbbind_ic50.parquet filter=lfs diff=lfs merge=lfs -text
835
+ data/all_maccs_ic50.parquet filter=lfs diff=lfs merge=lfs -text
836
+ data/bindingdb_ic50.parquet filter=lfs diff=lfs merge=lfs -text
837
+ data/dcoid_actives.parquet filter=lfs diff=lfs merge=lfs -text
838
+ data/dcoid_decoys.parquet filter=lfs diff=lfs merge=lfs -text
839
+ data/moad_complex.parquet filter=lfs diff=lfs merge=lfs -text
840
+ data/pdbbind_complex.parquet filter=lfs diff=lfs merge=lfs -text
841
+ data/all_maccs.parquet filter=lfs diff=lfs merge=lfs -text
README.md CHANGED
@@ -50,22 +50,32 @@ Go to <https://bindingmoad.org> and download the files `every.csv`
50
  (`nr_bind.zip`). Place and extract those files into `binding_moad`.
51
 
52
  Run the script `moad.py` in a compute job on an MPI-enabled cluster
53
- (e.g., `mpirun -n 64 moad.py).
54
 
55
  Perform the steps in the notebook `moad.ipynb`
56
 
57
  4. BioLIP
58
 
59
  Download from <https://zhanglab.ccmb.med.umich.edu/BioLiP/> the files
60
- - receptor_nr1.tar.bz2 (Receptor1, Non-redudant set)
61
- - ligand_nr.tar.bz2 (Ligands)
62
- - BioLiP_nr.tar.bz2 (Annotations)
63
  and extract them in `biolip/data`.
64
 
 
 
 
 
 
 
 
 
 
 
65
  Run the script `biolip.py` in a compute job on an MPI-enabled cluster
66
- (e.g., `mpirun -n 64 biolip.py).
67
 
68
- Perform sthe steps in the notebook `biolip.ipynb`
69
 
70
  5. Final concatenation and filtering
71
 
 
50
  (`nr_bind.zip`). Place and extract those files into `binding_moad`.
51
 
52
  Run the script `moad.py` in a compute job on an MPI-enabled cluster
53
+ (e.g., `mpirun -n 64 moad.py`).
54
 
55
  Perform the steps in the notebook `moad.ipynb`
56
 
57
  4. BioLIP
58
 
59
  Download from <https://zhanglab.ccmb.med.umich.edu/BioLiP/> the files
60
+ - receptor1.tar.bz2 (Receptor1, Non-redudant set)
61
+ - ligand_2013-03-6.tar.bz2 (Ligands)
62
+ - BioLiP.tar.bz2 (Annotations)
63
  and extract them in `biolip/data`.
64
 
65
+ The following steps are **optional**, they **do not** result in additional binding affinity data.
66
+
67
+ Download the script
68
+ - download_all_sets.pl
69
+ from the Weekly update subpage.
70
+
71
+ Update the 2013 database to its current state
72
+
73
+ `perl download_all-sets.pl`
74
+
75
  Run the script `biolip.py` in a compute job on an MPI-enabled cluster
76
+ (e.g., `mpirun -n 64 biolip.py`).
77
 
78
+ Perform the steps in the notebook `biolip.ipynb`
79
 
80
  5. Final concatenation and filtering
81
 
binding_affinity.py CHANGED
@@ -47,8 +47,10 @@ _LICENSE = "BSD two-clause"
47
  # TODO: Add link to the official dataset URLs here
48
  # The HuggingFace dataset library don't host the datasets but only point to the original files
49
  # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
 
50
  _URLs = {
51
- 'default': ["https://huggingface.co/datasets/jglaser/binding_affinity/resolve/main/data/all_ic50.parquet"],
 
52
  }
53
 
54
 
@@ -56,7 +58,7 @@ _URLs = {
56
  class BindingAffinity(datasets.ArrowBasedBuilder):
57
  """List of protein sequences, ligand SMILES and binding affinities."""
58
 
59
- VERSION = datasets.Version("1.0.0")
60
 
61
  # If you don't want/need to define several sub-sets in your dataset,
62
  # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
@@ -121,33 +123,23 @@ class BindingAffinity(datasets.ArrowBasedBuilder):
121
  # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLs
122
  # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
123
  # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
124
- my_urls = _URLs[self.config.name]
125
- files = dl_manager.download_and_extract(my_urls)
126
  return [
127
  datasets.SplitGenerator(
128
  name=datasets.Split.TRAIN,
129
  # These kwargs will be passed to _generate_examples
130
  gen_kwargs={
131
- "filepath": files[0],
132
- "split": "train",
133
  },
134
  ),
135
- # datasets.SplitGenerator(
136
- # name=datasets.Split.TEST,
137
- # # These kwargs will be passed to _generate_examples
138
- # gen_kwargs={
139
- # "filepath": os.path.join(data_dir, "test.parquet"),
140
- # "split": "test"
141
- # },
142
- # ),
143
- # datasets.SplitGenerator(
144
- # name=datasets.Split.VALIDATION,
145
- # # These kwargs will be passed to _generate_examples
146
- # gen_kwargs={
147
- # "filepath": os.path.join(data_dir, "dev.parquet"),
148
- # "split": "dev",
149
- # },
150
- # ),
151
  ]
152
 
153
  def _generate_examples(
 
47
  # TODO: Add link to the official dataset URLs here
48
  # The HuggingFace dataset library don't host the datasets but only point to the original files
49
  # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
50
+ _URL = "https://huggingface.co/datasets/jglaser/binding_affinity/resolve/main/data/"
51
  _URLs = {
52
+ "default": [_URL + "all.parquet"],
53
+ "no_kras": [_URL + "all_nokras.parquet"],
54
  }
55
 
56
 
 
58
  class BindingAffinity(datasets.ArrowBasedBuilder):
59
  """List of protein sequences, ligand SMILES and binding affinities."""
60
 
61
+ VERSION = datasets.Version("1.1.0")
62
 
63
  # If you don't want/need to define several sub-sets in your dataset,
64
  # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
 
123
  # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLs
124
  # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
125
  # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
126
+ files = dl_manager.download_and_extract(_URLs)
 
127
  return [
128
  datasets.SplitGenerator(
129
  name=datasets.Split.TRAIN,
130
  # These kwargs will be passed to _generate_examples
131
  gen_kwargs={
132
+ "filepath": files["default"],
 
133
  },
134
  ),
135
+ datasets.SplitGenerator(
136
+ name=datasets.Split.TRAIN+"_no_kras",
137
+ # These kwargs will be passed to _generate_examples
138
+ gen_kwargs={
139
+ "filepath": files["no_kras"],
140
+ },
141
+ ),
142
+
 
 
 
 
 
 
 
 
143
  ]
144
 
145
  def _generate_examples(
bindingdb.ipynb CHANGED
@@ -2,7 +2,7 @@
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
- "execution_count": 6,
6
  "id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
7
  "metadata": {},
8
  "outputs": [],
@@ -12,7 +12,7 @@
12
  },
13
  {
14
  "cell_type": "code",
15
- "execution_count": 7,
16
  "id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
17
  "metadata": {},
18
  "outputs": [],
@@ -22,7 +22,7 @@
22
  },
23
  {
24
  "cell_type": "code",
25
- "execution_count": 8,
26
  "id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
27
  "metadata": {},
28
  "outputs": [],
@@ -32,10 +32,25 @@
32
  },
33
  {
34
  "cell_type": "code",
35
- "execution_count": null,
36
  "id": "e9f76b32-e8f0-47ee-b592-a91a88f4f93e",
37
  "metadata": {},
38
- "outputs": [],
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
39
  "source": [
40
  "for i in tqdm.notebook.tqdm(range(0,13)):\n",
41
  " mycol = 'BindingDB Target Chain Sequence.{}'.format(i)\n",
@@ -60,7 +75,7 @@
60
  },
61
  {
62
  "cell_type": "code",
63
- "execution_count": 68,
64
  "id": "be79bbcf-0622-4d1e-8f08-a723a4167d8b",
65
  "metadata": {},
66
  "outputs": [],
@@ -74,7 +89,7 @@
74
  },
75
  {
76
  "cell_type": "code",
77
- "execution_count": 69,
78
  "id": "35ca09cb-6264-4526-b504-0d29236a03c1",
79
  "metadata": {},
80
  "outputs": [],
@@ -84,7 +99,7 @@
84
  },
85
  {
86
  "cell_type": "code",
87
- "execution_count": 70,
88
  "id": "ba518a9a-0d15-47be-977b-e2dfe2511529",
89
  "metadata": {},
90
  "outputs": [
@@ -196,7 +211,7 @@
196
  "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... "
197
  ]
198
  },
199
- "execution_count": 70,
200
  "metadata": {},
201
  "output_type": "execute_result"
202
  }
@@ -207,7 +222,7 @@
207
  },
208
  {
209
  "cell_type": "code",
210
- "execution_count": 71,
211
  "id": "f504d7aa-dfc1-4346-a136-8814c4b5d979",
212
  "metadata": {},
213
  "outputs": [],
@@ -217,17 +232,17 @@
217
  },
218
  {
219
  "cell_type": "code",
220
- "execution_count": 10,
221
  "id": "d7eafa69-4606-4b34-ae8f-8c6462dcb004",
222
  "metadata": {},
223
  "outputs": [],
224
  "source": [
225
- "ddf = dd.read_parquet('../binding_datasets/bindingdb/parquet_data/all_targets')"
226
  ]
227
  },
228
  {
229
  "cell_type": "code",
230
- "execution_count": 11,
231
  "id": "b151868a-0cd6-405e-8401-f79918fb0b07",
232
  "metadata": {},
233
  "outputs": [
@@ -262,7 +277,7 @@
262
  " <th>seq</th>\n",
263
  " </tr>\n",
264
  " <tr>\n",
265
- " <th>npartitions=459</th>\n",
266
  " <th></th>\n",
267
  " <th></th>\n",
268
  " <th></th>\n",
@@ -326,21 +341,21 @@
326
  " </tbody>\n",
327
  "</table>\n",
328
  "</div>\n",
329
- "<div>Dask Name: read-parquet, 459 tasks</div>"
330
  ],
331
  "text/plain": [
332
  "Dask DataFrame Structure:\n",
333
  " Ligand SMILES IC50 (nM) KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) seq\n",
334
- "npartitions=459 \n",
335
  " object object object object object object object\n",
336
  " ... ... ... ... ... ... ...\n",
337
  "... ... ... ... ... ... ... ...\n",
338
  " ... ... ... ... ... ... ...\n",
339
  " ... ... ... ... ... ... ...\n",
340
- "Dask Name: read-parquet, 459 tasks"
341
  ]
342
  },
343
- "execution_count": 11,
344
  "metadata": {},
345
  "output_type": "execute_result"
346
  }
@@ -351,7 +366,7 @@
351
  },
352
  {
353
  "cell_type": "code",
354
- "execution_count": 12,
355
  "id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
356
  "metadata": {},
357
  "outputs": [],
@@ -361,7 +376,7 @@
361
  },
362
  {
363
  "cell_type": "code",
364
- "execution_count": 13,
365
  "id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
366
  "metadata": {},
367
  "outputs": [
@@ -397,94 +412,115 @@
397
  " </thead>\n",
398
  " <tbody>\n",
399
  " <tr>\n",
400
- " <th>4453</th>\n",
401
- " <td>CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c...</td>\n",
402
- " <td>9.4</td>\n",
403
  " <td>None</td>\n",
404
  " <td>None</td>\n",
 
405
  " <td>None</td>\n",
406
  " <td>None</td>\n",
407
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
408
  " </tr>\n",
409
  " <tr>\n",
410
- " <th>4454</th>\n",
411
- " <td>CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc...</td>\n",
412
- " <td>11</td>\n",
413
  " <td>None</td>\n",
414
  " <td>None</td>\n",
 
415
  " <td>None</td>\n",
416
  " <td>None</td>\n",
417
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
418
  " </tr>\n",
419
  " <tr>\n",
420
- " <th>4455</th>\n",
421
- " <td>CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=...</td>\n",
422
- " <td>355</td>\n",
423
  " <td>None</td>\n",
424
  " <td>None</td>\n",
 
425
  " <td>None</td>\n",
426
  " <td>None</td>\n",
427
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
428
  " </tr>\n",
429
  " <tr>\n",
430
- " <th>4456</th>\n",
431
- " <td>COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(...</td>\n",
432
- " <td>17</td>\n",
433
  " <td>None</td>\n",
434
  " <td>None</td>\n",
 
435
  " <td>None</td>\n",
436
  " <td>None</td>\n",
437
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
438
  " </tr>\n",
439
  " <tr>\n",
440
- " <th>4457</th>\n",
441
- " <td>CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=...</td>\n",
442
- " <td>76</td>\n",
443
  " <td>None</td>\n",
444
  " <td>None</td>\n",
 
445
  " <td>None</td>\n",
446
  " <td>None</td>\n",
447
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
448
  " </tr>\n",
449
  " </tbody>\n",
450
  "</table>\n",
451
  "</div>"
452
  ],
453
  "text/plain": [
454
- " Ligand SMILES IC50 (nM) \\\n",
455
- "4453 CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c... 9.4 \n",
456
- "4454 CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc... 11 \n",
457
- "4455 CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=... 355 \n",
458
- "4456 COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(... 17 \n",
459
- "4457 CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=... 76 \n",
460
  "\n",
461
- " KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) \\\n",
462
- "4453 None None None None \n",
463
- "4454 None None None None \n",
464
- "4455 None None None None \n",
465
- "4456 None None None None \n",
466
- "4457 None None None None \n",
467
  "\n",
468
- " seq \n",
469
- "4453 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
470
- "4454 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
471
- "4455 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
472
- "4456 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
473
- "4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... "
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
474
  ]
475
  },
476
- "execution_count": 13,
477
  "metadata": {},
478
  "output_type": "execute_result"
479
  }
480
  ],
481
  "source": [
482
- "ddf_nonnull.tail()"
483
  ]
484
  },
485
  {
486
  "cell_type": "code",
487
- "execution_count": 21,
488
  "id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
489
  "metadata": {},
490
  "outputs": [],
@@ -499,11 +535,11 @@
499
  "\n",
500
  " vals = []\n",
501
  " \n",
502
- "# try:\n",
503
- "# ic50 = ureg(str(ic50)+'nM').m_as(ureg.uM)\n",
504
- "# vals.append(ic50)\n",
505
- "# except:\n",
506
- "# pass\n",
507
  "\n",
508
  " try:\n",
509
  " Ki = ureg(str(Ki)+'nM').m_as(ureg.uM)\n",
@@ -517,11 +553,11 @@
517
  " except:\n",
518
  " pass\n",
519
  "\n",
520
- "# try:\n",
521
- "# ec50 = ureg(str(ec50)+'nM').m_as(ureg.uM)\n",
522
- "# vals.append(ec50)\n",
523
- "# except:\n",
524
- "# pass\n",
525
  "\n",
526
  " if len(vals) > 0:\n",
527
  " vals = np.array(vals)\n",
@@ -532,7 +568,7 @@
532
  },
533
  {
534
  "cell_type": "code",
535
- "execution_count": 15,
536
  "id": "b3cff13c-19b2-4413-a84b-d99062f516a7",
537
  "metadata": {},
538
  "outputs": [],
@@ -542,35 +578,7 @@
542
  },
543
  {
544
  "cell_type": "code",
545
- "execution_count": 10,
546
- "id": "f11834ef-2b8f-4123-816c-5e54ca92a07a",
547
- "metadata": {},
548
- "outputs": [
549
- {
550
- "name": "stdout",
551
- "output_type": "stream",
552
- "text": [
553
- "Collecting pandarallel\n",
554
- " Using cached pandarallel-1.5.2.tar.gz (16 kB)\n",
555
- "Collecting dill\n",
556
- " Using cached dill-0.3.3-py2.py3-none-any.whl (81 kB)\n",
557
- "Building wheels for collected packages: pandarallel\n",
558
- " Building wheel for pandarallel (setup.py) ... \u001b[?25ldone\n",
559
- "\u001b[?25h Created wheel for pandarallel: filename=pandarallel-1.5.2-py3-none-any.whl size=18384 sha256=d611c0def59d5c3b807ccd787aeba685a821000f283d6082fce6b37d77b4d542\n",
560
- " Stored in directory: /autofs/nccs-svm1_home1/glaser/.cache/pip/wheels/6e/10/a9/c46b278fe836832830eb22a6a781a8379262d9a82ae87009c1\n",
561
- "Successfully built pandarallel\n",
562
- "Installing collected packages: dill, pandarallel\n",
563
- "Successfully installed dill-0.3.3 pandarallel-1.5.2\n"
564
- ]
565
- }
566
- ],
567
- "source": [
568
- "!pip install pandarallel"
569
- ]
570
- },
571
- {
572
- "cell_type": "code",
573
- "execution_count": 16,
574
  "id": "ca9795de-e821-4dc3-a7bf-70ade9e4c7f0",
575
  "metadata": {},
576
  "outputs": [
@@ -590,7 +598,7 @@
590
  },
591
  {
592
  "cell_type": "code",
593
- "execution_count": 22,
594
  "id": "4356a3e2-fede-48e7-a486-343661fe0a0a",
595
  "metadata": {},
596
  "outputs": [],
@@ -601,7 +609,7 @@
601
  },
602
  {
603
  "cell_type": "code",
604
- "execution_count": 23,
605
  "id": "e91c3af8-84a5-42a2-9e25-49cb2f320b0b",
606
  "metadata": {},
607
  "outputs": [],
@@ -611,7 +619,28 @@
611
  },
612
  {
613
  "cell_type": "code",
614
- "execution_count": 26,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
615
  "id": "27194288-cf3e-4c30-ad55-3b0998fdf939",
616
  "metadata": {},
617
  "outputs": [
@@ -729,7 +758,7 @@
729
  "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 "
730
  ]
731
  },
732
- "execution_count": 26,
733
  "metadata": {},
734
  "output_type": "execute_result"
735
  }
@@ -740,17 +769,17 @@
740
  },
741
  {
742
  "cell_type": "code",
743
- "execution_count": 27,
744
  "id": "603fd298-0aa6-4097-b298-c55db013548c",
745
  "metadata": {},
746
  "outputs": [
747
  {
748
  "data": {
749
  "text/plain": [
750
- "2391969"
751
  ]
752
  },
753
- "execution_count": 27,
754
  "metadata": {},
755
  "output_type": "execute_result"
756
  }
@@ -761,17 +790,17 @@
761
  },
762
  {
763
  "cell_type": "code",
764
- "execution_count": 28,
765
  "id": "d95ad9a9-d4ca-4679-8a33-235fe6e7047f",
766
  "metadata": {},
767
  "outputs": [
768
  {
769
  "data": {
770
  "text/plain": [
771
- "632297"
772
  ]
773
  },
774
- "execution_count": 28,
775
  "metadata": {},
776
  "output_type": "execute_result"
777
  }
@@ -780,242 +809,6 @@
780
  "len(df_affinity[~df_affinity['affinity_uM'].isnull()])"
781
  ]
782
  },
783
- {
784
- "cell_type": "code",
785
- "execution_count": 29,
786
- "id": "c3f357f6-e9bc-4a9c-ad11-8f90d609c02b",
787
- "metadata": {},
788
- "outputs": [],
789
- "source": [
790
- "import pandas as pd"
791
- ]
792
- },
793
- {
794
- "cell_type": "code",
795
- "execution_count": 4,
796
- "id": "c6ea5a79-facf-4a50-9d7c-2e1864ebad3d",
797
- "metadata": {},
798
- "outputs": [],
799
- "source": [
800
- "df_affinity = pd.read_parquet('../binding_datasets/data/bindingdb.parquet')"
801
- ]
802
- },
803
- {
804
- "cell_type": "code",
805
- "execution_count": 5,
806
- "id": "587da244-1913-4883-9b22-254fd94e53b6",
807
- "metadata": {},
808
- "outputs": [
809
- {
810
- "data": {
811
- "text/html": [
812
- "<div>\n",
813
- "<style scoped>\n",
814
- " .dataframe tbody tr th:only-of-type {\n",
815
- " vertical-align: middle;\n",
816
- " }\n",
817
- "\n",
818
- " .dataframe tbody tr th {\n",
819
- " vertical-align: top;\n",
820
- " }\n",
821
- "\n",
822
- " .dataframe thead th {\n",
823
- " text-align: right;\n",
824
- " }\n",
825
- "</style>\n",
826
- "<table border=\"1\" class=\"dataframe\">\n",
827
- " <thead>\n",
828
- " <tr style=\"text-align: right;\">\n",
829
- " <th></th>\n",
830
- " <th>Ligand SMILES</th>\n",
831
- " <th>IC50 (nM)</th>\n",
832
- " <th>KEGG ID of Ligand</th>\n",
833
- " <th>Ki (nM)</th>\n",
834
- " <th>Kd (nM)</th>\n",
835
- " <th>EC50 (nM)</th>\n",
836
- " <th>seq</th>\n",
837
- " <th>affinity_uM</th>\n",
838
- " </tr>\n",
839
- " </thead>\n",
840
- " <tbody>\n",
841
- " <tr>\n",
842
- " <th>0</th>\n",
843
- " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
844
- " <td>None</td>\n",
845
- " <td>None</td>\n",
846
- " <td>0.24</td>\n",
847
- " <td>None</td>\n",
848
- " <td>None</td>\n",
849
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
850
- " <td>0.00024</td>\n",
851
- " </tr>\n",
852
- " <tr>\n",
853
- " <th>1</th>\n",
854
- " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
855
- " <td>None</td>\n",
856
- " <td>None</td>\n",
857
- " <td>0.25</td>\n",
858
- " <td>None</td>\n",
859
- " <td>None</td>\n",
860
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
861
- " <td>0.00025</td>\n",
862
- " </tr>\n",
863
- " <tr>\n",
864
- " <th>2</th>\n",
865
- " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
866
- " <td>None</td>\n",
867
- " <td>None</td>\n",
868
- " <td>0.41</td>\n",
869
- " <td>None</td>\n",
870
- " <td>None</td>\n",
871
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
872
- " <td>0.00041</td>\n",
873
- " </tr>\n",
874
- " <tr>\n",
875
- " <th>3</th>\n",
876
- " <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
877
- " <td>None</td>\n",
878
- " <td>None</td>\n",
879
- " <td>0.8</td>\n",
880
- " <td>None</td>\n",
881
- " <td>None</td>\n",
882
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
883
- " <td>0.00080</td>\n",
884
- " </tr>\n",
885
- " <tr>\n",
886
- " <th>4</th>\n",
887
- " <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
888
- " <td>None</td>\n",
889
- " <td>None</td>\n",
890
- " <td>0.99</td>\n",
891
- " <td>None</td>\n",
892
- " <td>None</td>\n",
893
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
894
- " <td>0.00099</td>\n",
895
- " </tr>\n",
896
- " <tr>\n",
897
- " <th>...</th>\n",
898
- " <td>...</td>\n",
899
- " <td>...</td>\n",
900
- " <td>...</td>\n",
901
- " <td>...</td>\n",
902
- " <td>...</td>\n",
903
- " <td>...</td>\n",
904
- " <td>...</td>\n",
905
- " <td>...</td>\n",
906
- " </tr>\n",
907
- " <tr>\n",
908
- " <th>4453</th>\n",
909
- " <td>CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c...</td>\n",
910
- " <td>9.4</td>\n",
911
- " <td>None</td>\n",
912
- " <td>None</td>\n",
913
- " <td>None</td>\n",
914
- " <td>None</td>\n",
915
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
916
- " <td>0.00940</td>\n",
917
- " </tr>\n",
918
- " <tr>\n",
919
- " <th>4454</th>\n",
920
- " <td>CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc...</td>\n",
921
- " <td>11</td>\n",
922
- " <td>None</td>\n",
923
- " <td>None</td>\n",
924
- " <td>None</td>\n",
925
- " <td>None</td>\n",
926
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
927
- " <td>0.01100</td>\n",
928
- " </tr>\n",
929
- " <tr>\n",
930
- " <th>4455</th>\n",
931
- " <td>CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=...</td>\n",
932
- " <td>355</td>\n",
933
- " <td>None</td>\n",
934
- " <td>None</td>\n",
935
- " <td>None</td>\n",
936
- " <td>None</td>\n",
937
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
938
- " <td>0.35500</td>\n",
939
- " </tr>\n",
940
- " <tr>\n",
941
- " <th>4456</th>\n",
942
- " <td>COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(...</td>\n",
943
- " <td>17</td>\n",
944
- " <td>None</td>\n",
945
- " <td>None</td>\n",
946
- " <td>None</td>\n",
947
- " <td>None</td>\n",
948
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
949
- " <td>0.01700</td>\n",
950
- " </tr>\n",
951
- " <tr>\n",
952
- " <th>4457</th>\n",
953
- " <td>CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=...</td>\n",
954
- " <td>76</td>\n",
955
- " <td>None</td>\n",
956
- " <td>None</td>\n",
957
- " <td>None</td>\n",
958
- " <td>None</td>\n",
959
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
960
- " <td>0.07600</td>\n",
961
- " </tr>\n",
962
- " </tbody>\n",
963
- "</table>\n",
964
- "<p>2389700 rows × 8 columns</p>\n",
965
- "</div>"
966
- ],
967
- "text/plain": [
968
- " Ligand SMILES IC50 (nM) \\\n",
969
- "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 None \n",
970
- "1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... None \n",
971
- "2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... None \n",
972
- "3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... None \n",
973
- "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... None \n",
974
- "... ... ... \n",
975
- "4453 CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c... 9.4 \n",
976
- "4454 CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc... 11 \n",
977
- "4455 CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=... 355 \n",
978
- "4456 COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(... 17 \n",
979
- "4457 CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=... 76 \n",
980
- "\n",
981
- " KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) \\\n",
982
- "0 None 0.24 None None \n",
983
- "1 None 0.25 None None \n",
984
- "2 None 0.41 None None \n",
985
- "3 None 0.8 None None \n",
986
- "4 None 0.99 None None \n",
987
- "... ... ... ... ... \n",
988
- "4453 None None None None \n",
989
- "4454 None None None None \n",
990
- "4455 None None None None \n",
991
- "4456 None None None None \n",
992
- "4457 None None None None \n",
993
- "\n",
994
- " seq affinity_uM \n",
995
- "0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00024 \n",
996
- "1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00025 \n",
997
- "2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00041 \n",
998
- "3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00080 \n",
999
- "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 \n",
1000
- "... ... ... \n",
1001
- "4453 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.00940 \n",
1002
- "4454 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.01100 \n",
1003
- "4455 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.35500 \n",
1004
- "4456 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.01700 \n",
1005
- "4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.07600 \n",
1006
- "\n",
1007
- "[2389700 rows x 8 columns]"
1008
- ]
1009
- },
1010
- "execution_count": 5,
1011
- "metadata": {},
1012
- "output_type": "execute_result"
1013
- }
1014
- ],
1015
- "source": [
1016
- "df_affinity"
1017
- ]
1018
- },
1019
  {
1020
  "cell_type": "code",
1021
  "execution_count": null,
 
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
+ "execution_count": 2,
6
  "id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
7
  "metadata": {},
8
  "outputs": [],
 
12
  },
13
  {
14
  "cell_type": "code",
15
+ "execution_count": 2,
16
  "id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
17
  "metadata": {},
18
  "outputs": [],
 
22
  },
23
  {
24
  "cell_type": "code",
25
+ "execution_count": 3,
26
  "id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
27
  "metadata": {},
28
  "outputs": [],
 
32
  },
33
  {
34
  "cell_type": "code",
35
+ "execution_count": 5,
36
  "id": "e9f76b32-e8f0-47ee-b592-a91a88f4f93e",
37
  "metadata": {},
38
+ "outputs": [
39
+ {
40
+ "data": {
41
+ "application/vnd.jupyter.widget-view+json": {
42
+ "model_id": "c988bc89781242ec8c8b7f8fd0b1c233",
43
+ "version_major": 2,
44
+ "version_minor": 0
45
+ },
46
+ "text/plain": [
47
+ " 0%| | 0/13 [00:00<?, ?it/s]"
48
+ ]
49
+ },
50
+ "metadata": {},
51
+ "output_type": "display_data"
52
+ }
53
+ ],
54
  "source": [
55
  "for i in tqdm.notebook.tqdm(range(0,13)):\n",
56
  " mycol = 'BindingDB Target Chain Sequence.{}'.format(i)\n",
 
75
  },
76
  {
77
  "cell_type": "code",
78
+ "execution_count": 15,
79
  "id": "be79bbcf-0622-4d1e-8f08-a723a4167d8b",
80
  "metadata": {},
81
  "outputs": [],
 
89
  },
90
  {
91
  "cell_type": "code",
92
+ "execution_count": 16,
93
  "id": "35ca09cb-6264-4526-b504-0d29236a03c1",
94
  "metadata": {},
95
  "outputs": [],
 
99
  },
100
  {
101
  "cell_type": "code",
102
+ "execution_count": 17,
103
  "id": "ba518a9a-0d15-47be-977b-e2dfe2511529",
104
  "metadata": {},
105
  "outputs": [
 
211
  "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... "
212
  ]
213
  },
214
+ "execution_count": 17,
215
  "metadata": {},
216
  "output_type": "execute_result"
217
  }
 
222
  },
223
  {
224
  "cell_type": "code",
225
+ "execution_count": 9,
226
  "id": "f504d7aa-dfc1-4346-a136-8814c4b5d979",
227
  "metadata": {},
228
  "outputs": [],
 
232
  },
233
  {
234
  "cell_type": "code",
235
+ "execution_count": 4,
236
  "id": "d7eafa69-4606-4b34-ae8f-8c6462dcb004",
237
  "metadata": {},
238
  "outputs": [],
239
  "source": [
240
+ "ddf = dd.read_parquet('../binding_affinity/bindingdb/parquet_data/all_targets')"
241
  ]
242
  },
243
  {
244
  "cell_type": "code",
245
+ "execution_count": 5,
246
  "id": "b151868a-0cd6-405e-8401-f79918fb0b07",
247
  "metadata": {},
248
  "outputs": [
 
277
  " <th>seq</th>\n",
278
  " </tr>\n",
279
  " <tr>\n",
280
+ " <th>npartitions=483</th>\n",
281
  " <th></th>\n",
282
  " <th></th>\n",
283
  " <th></th>\n",
 
341
  " </tbody>\n",
342
  "</table>\n",
343
  "</div>\n",
344
+ "<div>Dask Name: read-parquet, 483 tasks</div>"
345
  ],
346
  "text/plain": [
347
  "Dask DataFrame Structure:\n",
348
  " Ligand SMILES IC50 (nM) KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) seq\n",
349
+ "npartitions=483 \n",
350
  " object object object object object object object\n",
351
  " ... ... ... ... ... ... ...\n",
352
  "... ... ... ... ... ... ... ...\n",
353
  " ... ... ... ... ... ... ...\n",
354
  " ... ... ... ... ... ... ...\n",
355
+ "Dask Name: read-parquet, 483 tasks"
356
  ]
357
  },
358
+ "execution_count": 5,
359
  "metadata": {},
360
  "output_type": "execute_result"
361
  }
 
366
  },
367
  {
368
  "cell_type": "code",
369
+ "execution_count": 6,
370
  "id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
371
  "metadata": {},
372
  "outputs": [],
 
376
  },
377
  {
378
  "cell_type": "code",
379
+ "execution_count": 8,
380
  "id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
381
  "metadata": {},
382
  "outputs": [
 
412
  " </thead>\n",
413
  " <tbody>\n",
414
  " <tr>\n",
415
+ " <th>0</th>\n",
416
+ " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
 
417
  " <td>None</td>\n",
418
  " <td>None</td>\n",
419
+ " <td>0.24</td>\n",
420
  " <td>None</td>\n",
421
  " <td>None</td>\n",
422
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
423
  " </tr>\n",
424
  " <tr>\n",
425
+ " <th>1</th>\n",
426
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
 
427
  " <td>None</td>\n",
428
  " <td>None</td>\n",
429
+ " <td>0.25</td>\n",
430
  " <td>None</td>\n",
431
  " <td>None</td>\n",
432
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
433
  " </tr>\n",
434
  " <tr>\n",
435
+ " <th>2</th>\n",
436
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
 
437
  " <td>None</td>\n",
438
  " <td>None</td>\n",
439
+ " <td>0.41</td>\n",
440
  " <td>None</td>\n",
441
  " <td>None</td>\n",
442
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
443
  " </tr>\n",
444
  " <tr>\n",
445
+ " <th>3</th>\n",
446
+ " <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
 
447
  " <td>None</td>\n",
448
  " <td>None</td>\n",
449
+ " <td>0.8</td>\n",
450
  " <td>None</td>\n",
451
  " <td>None</td>\n",
452
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
453
  " </tr>\n",
454
  " <tr>\n",
455
+ " <th>4</th>\n",
456
+ " <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
 
457
  " <td>None</td>\n",
458
  " <td>None</td>\n",
459
+ " <td>0.99</td>\n",
460
  " <td>None</td>\n",
461
  " <td>None</td>\n",
462
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
463
  " </tr>\n",
464
  " </tbody>\n",
465
  "</table>\n",
466
  "</div>"
467
  ],
468
  "text/plain": [
469
+ " Ligand SMILES IC50 (nM) \\\n",
470
+ "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 None \n",
471
+ "1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... None \n",
472
+ "2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... None \n",
473
+ "3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... None \n",
474
+ "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... None \n",
475
  "\n",
476
+ " KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) \\\n",
477
+ "0 None 0.24 None None \n",
478
+ "1 None 0.25 None None \n",
479
+ "2 None 0.41 None None \n",
480
+ "3 None 0.8 None None \n",
481
+ "4 None 0.99 None None \n",
482
  "\n",
483
+ " seq \n",
484
+ "0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
485
+ "1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
486
+ "2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
487
+ "3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
488
+ "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... "
489
+ ]
490
+ },
491
+ "execution_count": 8,
492
+ "metadata": {},
493
+ "output_type": "execute_result"
494
+ }
495
+ ],
496
+ "source": [
497
+ "ddf_nonnull.head()"
498
+ ]
499
+ },
500
+ {
501
+ "cell_type": "code",
502
+ "execution_count": 17,
503
+ "id": "7b423365-4989-4325-a5a5-845d852d52e9",
504
+ "metadata": {},
505
+ "outputs": [
506
+ {
507
+ "data": {
508
+ "text/plain": [
509
+ "2512985"
510
  ]
511
  },
512
+ "execution_count": 17,
513
  "metadata": {},
514
  "output_type": "execute_result"
515
  }
516
  ],
517
  "source": [
518
+ "len(ddf_nonnull)"
519
  ]
520
  },
521
  {
522
  "cell_type": "code",
523
+ "execution_count": 11,
524
  "id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
525
  "metadata": {},
526
  "outputs": [],
 
535
  "\n",
536
  " vals = []\n",
537
  " \n",
538
+ " try:\n",
539
+ " ic50 = ureg(str(ic50)+'nM').m_as(ureg.uM)\n",
540
+ " vals.append(ic50)\n",
541
+ " except:\n",
542
+ " pass\n",
543
  "\n",
544
  " try:\n",
545
  " Ki = ureg(str(Ki)+'nM').m_as(ureg.uM)\n",
 
553
  " except:\n",
554
  " pass\n",
555
  "\n",
556
+ " try:\n",
557
+ " ec50 = ureg(str(ec50)+'nM').m_as(ureg.uM)\n",
558
+ " vals.append(ec50)\n",
559
+ " except:\n",
560
+ " pass\n",
561
  "\n",
562
  " if len(vals) > 0:\n",
563
  " vals = np.array(vals)\n",
 
568
  },
569
  {
570
  "cell_type": "code",
571
+ "execution_count": 12,
572
  "id": "b3cff13c-19b2-4413-a84b-d99062f516a7",
573
  "metadata": {},
574
  "outputs": [],
 
578
  },
579
  {
580
  "cell_type": "code",
581
+ "execution_count": 13,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
582
  "id": "ca9795de-e821-4dc3-a7bf-70ade9e4c7f0",
583
  "metadata": {},
584
  "outputs": [
 
598
  },
599
  {
600
  "cell_type": "code",
601
+ "execution_count": 14,
602
  "id": "4356a3e2-fede-48e7-a486-343661fe0a0a",
603
  "metadata": {},
604
  "outputs": [],
 
609
  },
610
  {
611
  "cell_type": "code",
612
+ "execution_count": 15,
613
  "id": "e91c3af8-84a5-42a2-9e25-49cb2f320b0b",
614
  "metadata": {},
615
  "outputs": [],
 
619
  },
620
  {
621
  "cell_type": "code",
622
+ "execution_count": 16,
623
+ "id": "f602fdbe-7083-436c-9eac-9d97fbc8be67",
624
+ "metadata": {},
625
+ "outputs": [
626
+ {
627
+ "data": {
628
+ "text/plain": [
629
+ "2512985"
630
+ ]
631
+ },
632
+ "execution_count": 16,
633
+ "metadata": {},
634
+ "output_type": "execute_result"
635
+ }
636
+ ],
637
+ "source": [
638
+ "len(df_affinity)"
639
+ ]
640
+ },
641
+ {
642
+ "cell_type": "code",
643
+ "execution_count": 18,
644
  "id": "27194288-cf3e-4c30-ad55-3b0998fdf939",
645
  "metadata": {},
646
  "outputs": [
 
758
  "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 "
759
  ]
760
  },
761
+ "execution_count": 18,
762
  "metadata": {},
763
  "output_type": "execute_result"
764
  }
 
769
  },
770
  {
771
  "cell_type": "code",
772
+ "execution_count": 19,
773
  "id": "603fd298-0aa6-4097-b298-c55db013548c",
774
  "metadata": {},
775
  "outputs": [
776
  {
777
  "data": {
778
  "text/plain": [
779
+ "2512985"
780
  ]
781
  },
782
+ "execution_count": 19,
783
  "metadata": {},
784
  "output_type": "execute_result"
785
  }
 
790
  },
791
  {
792
  "cell_type": "code",
793
+ "execution_count": 20,
794
  "id": "d95ad9a9-d4ca-4679-8a33-235fe6e7047f",
795
  "metadata": {},
796
  "outputs": [
797
  {
798
  "data": {
799
  "text/plain": [
800
+ "2510716"
801
  ]
802
  },
803
+ "execution_count": 20,
804
  "metadata": {},
805
  "output_type": "execute_result"
806
  }
 
809
  "len(df_affinity[~df_affinity['affinity_uM'].isnull()])"
810
  ]
811
  },
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
812
  {
813
  "cell_type": "code",
814
  "execution_count": null,
biolip.ipynb CHANGED
@@ -2,28 +2,25 @@
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
- "execution_count": 1,
6
- "id": "ee43bf48-5491-4dc4-aa09-cb4a0f460f97",
7
  "metadata": {},
8
  "outputs": [],
9
  "source": [
10
- "from openbabel import pybel\n",
11
- "from Bio.PDB import * \n"
12
  ]
13
  },
14
  {
15
- "cell_type": "code",
16
- "execution_count": 2,
17
- "id": "26bc18a2-a6eb-49d3-be80-876ddc7dd8e1",
18
  "metadata": {},
19
- "outputs": [],
20
  "source": [
21
- "import pandas as pd"
22
  ]
23
  },
24
  {
25
  "cell_type": "code",
26
- "execution_count": 4,
27
  "id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
28
  "metadata": {},
29
  "outputs": [],
@@ -36,18 +33,18 @@
36
  },
37
  {
38
  "cell_type": "code",
39
- "execution_count": 5,
40
  "id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
41
  "metadata": {},
42
  "outputs": [],
43
  "source": [
44
- "base = 'biolip/data/ligand_nr/'\n",
45
  "df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'"
46
  ]
47
  },
48
  {
49
  "cell_type": "code",
50
- "execution_count": 8,
51
  "id": "bd8671da-66ad-40ad-b221-e33228be65f4",
52
  "metadata": {},
53
  "outputs": [],
@@ -57,7 +54,7 @@
57
  },
58
  {
59
  "cell_type": "code",
60
- "execution_count": 14,
61
  "id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
62
  "metadata": {},
63
  "outputs": [],
@@ -68,7 +65,7 @@
68
  },
69
  {
70
  "cell_type": "code",
71
- "execution_count": 62,
72
  "id": "97af5533-10fe-4419-a998-ed80b7d26690",
73
  "metadata": {},
74
  "outputs": [],
@@ -78,7 +75,7 @@
78
  "import re\n",
79
  "ureg = UnitRegistry()\n",
80
  "\n",
81
- "quantities = ['ki','kd','ka','k1/2','kb']\n",
82
  "\n",
83
  "others = set()\n",
84
  "def to_uM(affinities):\n",
@@ -182,7 +179,31 @@
182
  },
183
  {
184
  "cell_type": "code",
185
- "execution_count": 63,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
186
  "id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
187
  "metadata": {},
188
  "outputs": [],
@@ -192,17 +213,17 @@
192
  },
193
  {
194
  "cell_type": "code",
195
- "execution_count": 64,
196
  "id": "6b9526ec-b134-4ecb-8fea-b493c3fdac22",
197
  "metadata": {},
198
  "outputs": [
199
  {
200
  "data": {
201
  "text/plain": [
202
- "{'deltag', 'deltah', 'ec50', 'ic50', 'km', 'none'}"
203
  ]
204
  },
205
- "execution_count": 64,
206
  "metadata": {},
207
  "output_type": "execute_result"
208
  }
@@ -213,7 +234,7 @@
213
  },
214
  {
215
  "cell_type": "code",
216
- "execution_count": 65,
217
  "id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
218
  "metadata": {},
219
  "outputs": [
@@ -264,7 +285,7 @@
264
  " <td>Ki=1.5uM (GTT-EAA)</td>\n",
265
  " <td>None</td>\n",
266
  " <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
267
- " <td>biolip/data/ligand_nr/11gs_EAA_A_1.pdb</td>\n",
268
  " <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
269
  " <td>1.5000</td>\n",
270
  " </tr>\n",
@@ -279,7 +300,7 @@
279
  " <td>Ki=24uM (SAS)</td>\n",
280
  " <td>None</td>\n",
281
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
282
- " <td>biolip/data/ligand_nr/13gs_SAS_A_1.pdb</td>\n",
283
  " <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
284
  " <td>24.0000</td>\n",
285
  " </tr>\n",
@@ -294,7 +315,7 @@
294
  " <td>Ki=6uM (BIS)</td>\n",
295
  " <td>None</td>\n",
296
  " <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
297
- " <td>biolip/data/ligand_nr/16pk_BIS_A_1.pdb</td>\n",
298
  " <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
299
  " <td>6.0000</td>\n",
300
  " </tr>\n",
@@ -309,7 +330,7 @@
309
  " <td>None</td>\n",
310
  " <td>Kd=10000nM</td>\n",
311
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
312
- " <td>biolip/data/ligand_nr/17gs_GTX_A_1.pdb</td>\n",
313
  " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
314
  " <td>10.0000</td>\n",
315
  " </tr>\n",
@@ -324,7 +345,7 @@
324
  " <td>None</td>\n",
325
  " <td>Kd=175000nM</td>\n",
326
  " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
327
- " <td>biolip/data/ligand_nr/181l_BNZ_A_1.pdb</td>\n",
328
  " <td>c1ccccc1</td>\n",
329
  " <td>175.0000</td>\n",
330
  " </tr>\n",
@@ -354,7 +375,7 @@
354
  " <td>Ki=4.5nM (5-mer)</td>\n",
355
  " <td>None</td>\n",
356
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
357
- " <td>biolip/data/ligand_nr/9hvp_0E9_A_1.pdb</td>\n",
358
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
359
  " <td>0.0045</td>\n",
360
  " </tr>\n",
@@ -369,7 +390,7 @@
369
  " <td>Ki=4.5nM (5-mer)</td>\n",
370
  " <td>None</td>\n",
371
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
372
- " <td>biolip/data/ligand_nr/9hvp_0E9_A_1.pdb</td>\n",
373
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
374
  " <td>0.0045</td>\n",
375
  " </tr>\n",
@@ -384,7 +405,7 @@
384
  " <td>Kd=125uM (NAP)</td>\n",
385
  " <td>None</td>\n",
386
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
387
- " <td>biolip/data/ligand_nr/9icd_NAP_A_1.pdb</td>\n",
388
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
389
  " <td>125.0000</td>\n",
390
  " </tr>\n",
@@ -399,7 +420,7 @@
399
  " <td>Ki=2000nM (4-mer)</td>\n",
400
  " <td>None</td>\n",
401
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
402
- " <td>biolip/data/ligand_nr/9lpr_III_P_1.pdb</td>\n",
403
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
404
  " <td>2.0000</td>\n",
405
  " </tr>\n",
@@ -414,13 +435,13 @@
414
  " <td>None</td>\n",
415
  " <td>None</td>\n",
416
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
417
- " <td>biolip/data/ligand_nr/9nse_ISU_B_2.pdb</td>\n",
418
  " <td>CC[Se]C(=N)N</td>\n",
419
  " <td>0.0390</td>\n",
420
  " </tr>\n",
421
  " </tbody>\n",
422
  "</table>\n",
423
- "<p>9341 rows × 12 columns</p>\n",
424
  "</div>"
425
  ],
426
  "text/plain": [
@@ -463,18 +484,18 @@
463
  "105133 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
464
  "105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
465
  "\n",
466
- " ligand_fn \\\n",
467
- "38 biolip/data/ligand_nr/11gs_EAA_A_1.pdb \n",
468
- "43 biolip/data/ligand_nr/13gs_SAS_A_1.pdb \n",
469
- "53 biolip/data/ligand_nr/16pk_BIS_A_1.pdb \n",
470
- "54 biolip/data/ligand_nr/17gs_GTX_A_1.pdb \n",
471
- "55 biolip/data/ligand_nr/181l_BNZ_A_1.pdb \n",
472
- "... ... \n",
473
- "105118 biolip/data/ligand_nr/9hvp_0E9_A_1.pdb \n",
474
- "105119 biolip/data/ligand_nr/9hvp_0E9_A_1.pdb \n",
475
- "105124 biolip/data/ligand_nr/9icd_NAP_A_1.pdb \n",
476
- "105133 biolip/data/ligand_nr/9lpr_III_P_1.pdb \n",
477
- "105138 biolip/data/ligand_nr/9nse_ISU_B_2.pdb \n",
478
  "\n",
479
  " smiles affinity_uM \n",
480
  "38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.5000 \n",
@@ -489,10 +510,10 @@
489
  "105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
490
  "105138 CC[Se]C(=N)N 0.0390 \n",
491
  "\n",
492
- "[9341 rows x 12 columns]"
493
  ]
494
  },
495
- "execution_count": 65,
496
  "metadata": {},
497
  "output_type": "execute_result"
498
  }
@@ -503,7 +524,7 @@
503
  },
504
  {
505
  "cell_type": "code",
506
- "execution_count": 66,
507
  "id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
508
  "metadata": {},
509
  "outputs": [],
@@ -513,9 +534,30 @@
513
  },
514
  {
515
  "cell_type": "code",
516
- "execution_count": null,
517
  "id": "68dd5e45-b31d-492d-a47e-39072b67fa72",
518
  "metadata": {},
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
519
  "outputs": [],
520
  "source": []
521
  }
 
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
+ "execution_count": 3,
6
+ "id": "26bc18a2-a6eb-49d3-be80-876ddc7dd8e1",
7
  "metadata": {},
8
  "outputs": [],
9
  "source": [
10
+ "import pandas as pd"
 
11
  ]
12
  },
13
  {
14
+ "cell_type": "markdown",
15
+ "id": "dbef8a5d-8603-4f40-aa98-fe50aa1160f6",
 
16
  "metadata": {},
 
17
  "source": [
18
+ "the binding affinities are **only** present in the 2013 snapshot, not in the updated ones"
19
  ]
20
  },
21
  {
22
  "cell_type": "code",
23
+ "execution_count": 48,
24
  "id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
25
  "metadata": {},
26
  "outputs": [],
 
33
  },
34
  {
35
  "cell_type": "code",
36
+ "execution_count": 49,
37
  "id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
38
  "metadata": {},
39
  "outputs": [],
40
  "source": [
41
+ "base = 'biolip/data/ligand/'\n",
42
  "df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'"
43
  ]
44
  },
45
  {
46
  "cell_type": "code",
47
+ "execution_count": 50,
48
  "id": "bd8671da-66ad-40ad-b221-e33228be65f4",
49
  "metadata": {},
50
  "outputs": [],
 
54
  },
55
  {
56
  "cell_type": "code",
57
+ "execution_count": 51,
58
  "id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
59
  "metadata": {},
60
  "outputs": [],
 
65
  },
66
  {
67
  "cell_type": "code",
68
+ "execution_count": 57,
69
  "id": "97af5533-10fe-4419-a998-ed80b7d26690",
70
  "metadata": {},
71
  "outputs": [],
 
75
  "import re\n",
76
  "ureg = UnitRegistry()\n",
77
  "\n",
78
+ "quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50','km']\n",
79
  "\n",
80
  "others = set()\n",
81
  "def to_uM(affinities):\n",
 
179
  },
180
  {
181
  "cell_type": "code",
182
+ "execution_count": 58,
183
+ "id": "d2fab1e6-ec5b-46f9-a4a2-f3744128c777",
184
+ "metadata": {},
185
+ "outputs": [
186
+ {
187
+ "data": {
188
+ "text/plain": [
189
+ "Index(['pdb', 'chain', 'l_id', 'l_chain', 'affinity_lit', 'affinity_moad',\n",
190
+ " 'affinity_pdbbind-cn', 'affinity_bindingdb', 'seq', 'ligand_fn',\n",
191
+ " 'smiles', 'affinity_uM'],\n",
192
+ " dtype='object')"
193
+ ]
194
+ },
195
+ "execution_count": 58,
196
+ "metadata": {},
197
+ "output_type": "execute_result"
198
+ }
199
+ ],
200
+ "source": [
201
+ "df_affinity.columns"
202
+ ]
203
+ },
204
+ {
205
+ "cell_type": "code",
206
+ "execution_count": 59,
207
  "id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
208
  "metadata": {},
209
  "outputs": [],
 
213
  },
214
  {
215
  "cell_type": "code",
216
+ "execution_count": 60,
217
  "id": "6b9526ec-b134-4ecb-8fea-b493c3fdac22",
218
  "metadata": {},
219
  "outputs": [
220
  {
221
  "data": {
222
  "text/plain": [
223
+ "{'deltag', 'deltah', 'none'}"
224
  ]
225
  },
226
+ "execution_count": 60,
227
  "metadata": {},
228
  "output_type": "execute_result"
229
  }
 
234
  },
235
  {
236
  "cell_type": "code",
237
+ "execution_count": 61,
238
  "id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
239
  "metadata": {},
240
  "outputs": [
 
285
  " <td>Ki=1.5uM (GTT-EAA)</td>\n",
286
  " <td>None</td>\n",
287
  " <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
288
+ " <td>biolip/data/ligand/11gs_EAA_A_1.pdb</td>\n",
289
  " <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
290
  " <td>1.5000</td>\n",
291
  " </tr>\n",
 
300
  " <td>Ki=24uM (SAS)</td>\n",
301
  " <td>None</td>\n",
302
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
303
+ " <td>biolip/data/ligand/13gs_SAS_A_1.pdb</td>\n",
304
  " <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
305
  " <td>24.0000</td>\n",
306
  " </tr>\n",
 
315
  " <td>Ki=6uM (BIS)</td>\n",
316
  " <td>None</td>\n",
317
  " <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
318
+ " <td>biolip/data/ligand/16pk_BIS_A_1.pdb</td>\n",
319
  " <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
320
  " <td>6.0000</td>\n",
321
  " </tr>\n",
 
330
  " <td>None</td>\n",
331
  " <td>Kd=10000nM</td>\n",
332
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
333
+ " <td>biolip/data/ligand/17gs_GTX_A_1.pdb</td>\n",
334
  " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
335
  " <td>10.0000</td>\n",
336
  " </tr>\n",
 
345
  " <td>None</td>\n",
346
  " <td>Kd=175000nM</td>\n",
347
  " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
348
+ " <td>biolip/data/ligand/181l_BNZ_A_1.pdb</td>\n",
349
  " <td>c1ccccc1</td>\n",
350
  " <td>175.0000</td>\n",
351
  " </tr>\n",
 
375
  " <td>Ki=4.5nM (5-mer)</td>\n",
376
  " <td>None</td>\n",
377
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
378
+ " <td>biolip/data/ligand/9hvp_0E9_A_1.pdb</td>\n",
379
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
380
  " <td>0.0045</td>\n",
381
  " </tr>\n",
 
390
  " <td>Ki=4.5nM (5-mer)</td>\n",
391
  " <td>None</td>\n",
392
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
393
+ " <td>biolip/data/ligand/9hvp_0E9_A_1.pdb</td>\n",
394
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
395
  " <td>0.0045</td>\n",
396
  " </tr>\n",
 
405
  " <td>Kd=125uM (NAP)</td>\n",
406
  " <td>None</td>\n",
407
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
408
+ " <td>biolip/data/ligand/9icd_NAP_A_1.pdb</td>\n",
409
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
410
  " <td>125.0000</td>\n",
411
  " </tr>\n",
 
420
  " <td>Ki=2000nM (4-mer)</td>\n",
421
  " <td>None</td>\n",
422
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
423
+ " <td>biolip/data/ligand/9lpr_III_P_1.pdb</td>\n",
424
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
425
  " <td>2.0000</td>\n",
426
  " </tr>\n",
 
435
  " <td>None</td>\n",
436
  " <td>None</td>\n",
437
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
438
+ " <td>biolip/data/ligand/9nse_ISU_B_2.pdb</td>\n",
439
  " <td>CC[Se]C(=N)N</td>\n",
440
  " <td>0.0390</td>\n",
441
  " </tr>\n",
442
  " </tbody>\n",
443
  "</table>\n",
444
+ "<p>12851 rows × 12 columns</p>\n",
445
  "</div>"
446
  ],
447
  "text/plain": [
 
484
  "105133 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
485
  "105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
486
  "\n",
487
+ " ligand_fn \\\n",
488
+ "38 biolip/data/ligand/11gs_EAA_A_1.pdb \n",
489
+ "43 biolip/data/ligand/13gs_SAS_A_1.pdb \n",
490
+ "53 biolip/data/ligand/16pk_BIS_A_1.pdb \n",
491
+ "54 biolip/data/ligand/17gs_GTX_A_1.pdb \n",
492
+ "55 biolip/data/ligand/181l_BNZ_A_1.pdb \n",
493
+ "... ... \n",
494
+ "105118 biolip/data/ligand/9hvp_0E9_A_1.pdb \n",
495
+ "105119 biolip/data/ligand/9hvp_0E9_A_1.pdb \n",
496
+ "105124 biolip/data/ligand/9icd_NAP_A_1.pdb \n",
497
+ "105133 biolip/data/ligand/9lpr_III_P_1.pdb \n",
498
+ "105138 biolip/data/ligand/9nse_ISU_B_2.pdb \n",
499
  "\n",
500
  " smiles affinity_uM \n",
501
  "38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.5000 \n",
 
510
  "105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
511
  "105138 CC[Se]C(=N)N 0.0390 \n",
512
  "\n",
513
+ "[12851 rows x 12 columns]"
514
  ]
515
  },
516
+ "execution_count": 61,
517
  "metadata": {},
518
  "output_type": "execute_result"
519
  }
 
524
  },
525
  {
526
  "cell_type": "code",
527
+ "execution_count": 63,
528
  "id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
529
  "metadata": {},
530
  "outputs": [],
 
534
  },
535
  {
536
  "cell_type": "code",
537
+ "execution_count": 64,
538
  "id": "68dd5e45-b31d-492d-a47e-39072b67fa72",
539
  "metadata": {},
540
+ "outputs": [
541
+ {
542
+ "data": {
543
+ "text/plain": [
544
+ "13645"
545
+ ]
546
+ },
547
+ "execution_count": 64,
548
+ "metadata": {},
549
+ "output_type": "execute_result"
550
+ }
551
+ ],
552
+ "source": [
553
+ "len(df_affinity)"
554
+ ]
555
+ },
556
+ {
557
+ "cell_type": "code",
558
+ "execution_count": null,
559
+ "id": "cf11317d-bbab-40f1-a8a2-b6fd6126e998",
560
+ "metadata": {},
561
  "outputs": [],
562
  "source": []
563
  }
biolip.py CHANGED
@@ -34,7 +34,7 @@ if __name__ == '__main__':
34
  df = df.rename(columns={0:'pdb',4:'chain',5:'l_id',6:'l_chain',
35
  13: 'affinity_lit',14: 'affinity_moad',15: 'affinity_pdbbind-cn',16:'affinity_bindingdb',
36
  19: 'seq'})
37
- base = 'biolip/data/ligand_nr/'
38
  df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'
39
  smiles = list(executor.map(parse_ligand, df['ligand_fn']))
40
  df['smiles'] = smiles
 
34
  df = df.rename(columns={0:'pdb',4:'chain',5:'l_id',6:'l_chain',
35
  13: 'affinity_lit',14: 'affinity_moad',15: 'affinity_pdbbind-cn',16:'affinity_bindingdb',
36
  19: 'seq'})
37
+ base = 'biolip/data/ligand/'
38
  df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'
39
  smiles = list(executor.map(parse_ligand, df['ligand_fn']))
40
  df['smiles'] = smiles
biolip.slurm CHANGED
@@ -1,9 +1,9 @@
1
  #!/bin/bash
2
- #SBATCH -J preprocess_pdbbind
3
  #SBATCH -p batch
4
  #SBATCH -A BIP214
5
  #SBATCH -t 3:00:00
6
- #SBATCH -N 16
7
  #SBATCH --ntasks-per-node=32
8
 
9
  export PYTHONUNBUFFERED=1
 
1
  #!/bin/bash
2
+ #SBATCH -J preprocess_biolip
3
  #SBATCH -p batch
4
  #SBATCH -A BIP214
5
  #SBATCH -t 3:00:00
6
+ #SBATCH -N 11
7
  #SBATCH --ntasks-per-node=32
8
 
9
  export PYTHONUNBUFFERED=1
combine_dbs.ipynb CHANGED
@@ -2,7 +2,7 @@
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
- "execution_count": 1,
6
  "id": "95bd761a-fe51-4a8e-bc70-1365260ba5f8",
7
  "metadata": {},
8
  "outputs": [],
@@ -12,7 +12,7 @@
12
  },
13
  {
14
  "cell_type": "code",
15
- "execution_count": 2,
16
  "id": "b0859483-5e19-4280-9f53-0d00a6f22d34",
17
  "metadata": {},
18
  "outputs": [],
@@ -23,7 +23,7 @@
23
  },
24
  {
25
  "cell_type": "code",
26
- "execution_count": 3,
27
  "id": "f30732b7-7444-47ad-84e7-566e7a6f2f8e",
28
  "metadata": {},
29
  "outputs": [
@@ -57,32 +57,32 @@
57
  " <tr>\n",
58
  " <th>0</th>\n",
59
  " <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
60
- " <td>CCCCCCCCCCCCCCCCCCC[C-](=O)=O</td>\n",
61
  " <td>0.026</td>\n",
62
  " </tr>\n",
63
  " <tr>\n",
64
  " <th>1</th>\n",
65
- " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
66
- " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)[C-](=O)=O)NC...</td>\n",
67
- " <td>6.430</td>\n",
68
  " </tr>\n",
69
  " <tr>\n",
70
  " <th>2</th>\n",
71
- " <td>PFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNL...</td>\n",
72
- " <td>CC[C@@H]([C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H]...</td>\n",
73
- " <td>190.000</td>\n",
74
  " </tr>\n",
75
  " <tr>\n",
76
  " <th>3</th>\n",
77
- " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
78
- " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
79
- " <td>0.210</td>\n",
80
  " </tr>\n",
81
  " <tr>\n",
82
  " <th>4</th>\n",
83
- " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
84
- " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
85
- " <td>0.050</td>\n",
86
  " </tr>\n",
87
  " </tbody>\n",
88
  "</table>\n",
@@ -91,20 +91,20 @@
91
  "text/plain": [
92
  " seq \\\n",
93
  "0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
94
- "1 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
95
- "2 PFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNL... \n",
96
- "3 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
97
- "4 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
98
  "\n",
99
  " smiles affinity_uM \n",
100
- "0 CCCCCCCCCCCCCCCCCCC[C-](=O)=O 0.026 \n",
101
- "1 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)[C-](=O)=O)NC... 6.430 \n",
102
- "2 CC[C@@H]([C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H]... 190.000 \n",
103
- "3 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.210 \n",
104
- "4 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.050 "
105
  ]
106
  },
107
- "execution_count": 3,
108
  "metadata": {},
109
  "output_type": "execute_result"
110
  }
@@ -115,7 +115,7 @@
115
  },
116
  {
117
  "cell_type": "code",
118
- "execution_count": 4,
119
  "id": "2787b9fd-3d6f-4ae3-a3ad-d3539b72782b",
120
  "metadata": {},
121
  "outputs": [],
@@ -135,7 +135,7 @@
135
  },
136
  {
137
  "cell_type": "code",
138
- "execution_count": 6,
139
  "id": "d1abe1c8-ac66-4289-8964-367a5b18528d",
140
  "metadata": {},
141
  "outputs": [],
@@ -146,7 +146,7 @@
146
  },
147
  {
148
  "cell_type": "code",
149
- "execution_count": 7,
150
  "id": "988bab9c-5147-44e2-92ef-902eaf3c5a90",
151
  "metadata": {},
152
  "outputs": [
@@ -227,7 +227,7 @@
227
  "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 "
228
  ]
229
  },
230
- "execution_count": 7,
231
  "metadata": {},
232
  "output_type": "execute_result"
233
  }
@@ -238,7 +238,7 @@
238
  },
239
  {
240
  "cell_type": "code",
241
- "execution_count": 8,
242
  "id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
243
  "metadata": {},
244
  "outputs": [],
@@ -249,7 +249,7 @@
249
  },
250
  {
251
  "cell_type": "code",
252
- "execution_count": 9,
253
  "id": "25553199-1715-40fb-9260-427bdd6c3706",
254
  "metadata": {},
255
  "outputs": [
@@ -294,15 +294,15 @@
294
  " </tr>\n",
295
  " <tr>\n",
296
  " <th>2</th>\n",
297
- " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
298
- " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
299
- " <td>15.000000</td>\n",
300
  " </tr>\n",
301
  " <tr>\n",
302
  " <th>3</th>\n",
303
- " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
304
- " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
305
- " <td>15.000000</td>\n",
306
  " </tr>\n",
307
  " <tr>\n",
308
  " <th>4</th>\n",
@@ -317,71 +317,71 @@
317
  " <td>...</td>\n",
318
  " </tr>\n",
319
  " <tr>\n",
320
- " <th>17682</th>\n",
321
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
322
  " <td>None</td>\n",
323
  " <td>127.226463</td>\n",
324
  " </tr>\n",
325
  " <tr>\n",
326
- " <th>17683</th>\n",
327
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
328
  " <td>None</td>\n",
329
  " <td>127.226463</td>\n",
330
  " </tr>\n",
331
  " <tr>\n",
332
- " <th>17684</th>\n",
333
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
334
  " <td>None</td>\n",
335
  " <td>169.204738</td>\n",
336
  " </tr>\n",
337
  " <tr>\n",
338
- " <th>17685</th>\n",
339
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
340
  " <td>None</td>\n",
341
  " <td>169.204738</td>\n",
342
  " </tr>\n",
343
  " <tr>\n",
344
- " <th>17686</th>\n",
345
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
346
  " <td>None</td>\n",
347
  " <td>169.204738</td>\n",
348
  " </tr>\n",
349
  " </tbody>\n",
350
  "</table>\n",
351
- "<p>17687 rows × 3 columns</p>\n",
352
  "</div>"
353
  ],
354
  "text/plain": [
355
  " seq \\\n",
356
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
357
  "1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
358
- "2 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
359
- "3 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
360
  "4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
361
  "... ... \n",
362
- "17682 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
363
- "17683 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
364
- "17684 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
365
- "17685 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
366
- "17686 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
367
  "\n",
368
  " smiles affinity_uM \n",
369
  "0 NP(=O)(N)O 0.000620 \n",
370
  "1 CC(=O)NO 2.600000 \n",
371
- "2 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
372
- "3 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
373
  "4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
374
  "... ... ... \n",
375
- "17682 None 127.226463 \n",
376
- "17683 None 127.226463 \n",
377
- "17684 None 169.204738 \n",
378
- "17685 None 169.204738 \n",
379
- "17686 None 169.204738 \n",
380
  "\n",
381
- "[17687 rows x 3 columns]"
382
  ]
383
  },
384
- "execution_count": 9,
385
  "metadata": {},
386
  "output_type": "execute_result"
387
  }
@@ -392,7 +392,7 @@
392
  },
393
  {
394
  "cell_type": "code",
395
- "execution_count": 10,
396
  "id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
397
  "metadata": {},
398
  "outputs": [],
@@ -403,7 +403,7 @@
403
  },
404
  {
405
  "cell_type": "code",
406
- "execution_count": 11,
407
  "id": "cee93018-601d-458b-af44-bd978da7a2bc",
408
  "metadata": {},
409
  "outputs": [
@@ -535,7 +535,7 @@
535
  "[13645 rows x 3 columns]"
536
  ]
537
  },
538
- "execution_count": 11,
539
  "metadata": {},
540
  "output_type": "execute_result"
541
  }
@@ -546,7 +546,7 @@
546
  },
547
  {
548
  "cell_type": "code",
549
- "execution_count": 12,
550
  "id": "195f92db-fe06-4d03-8500-8d6c310a3347",
551
  "metadata": {},
552
  "outputs": [],
@@ -556,17 +556,17 @@
556
  },
557
  {
558
  "cell_type": "code",
559
- "execution_count": 13,
560
  "id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
561
  "metadata": {},
562
  "outputs": [
563
  {
564
  "data": {
565
  "text/plain": [
566
- "674728"
567
  ]
568
  },
569
- "execution_count": 13,
570
  "metadata": {},
571
  "output_type": "execute_result"
572
  }
@@ -577,7 +577,7 @@
577
  },
578
  {
579
  "cell_type": "code",
580
- "execution_count": 14,
581
  "id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
582
  "metadata": {},
583
  "outputs": [
@@ -607,7 +607,7 @@
607
  },
608
  {
609
  "cell_type": "code",
610
- "execution_count": 16,
611
  "id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
612
  "metadata": {},
613
  "outputs": [],
@@ -617,7 +617,7 @@
617
  },
618
  {
619
  "cell_type": "code",
620
- "execution_count": 17,
621
  "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
622
  "metadata": {},
623
  "outputs": [],
@@ -627,7 +627,7 @@
627
  },
628
  {
629
  "cell_type": "code",
630
- "execution_count": 18,
631
  "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
632
  "metadata": {},
633
  "outputs": [],
@@ -638,17 +638,17 @@
638
  },
639
  {
640
  "cell_type": "code",
641
- "execution_count": 19,
642
  "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
643
  "metadata": {},
644
  "outputs": [
645
  {
646
  "data": {
647
  "text/plain": [
648
- "662484"
649
  ]
650
  },
651
- "execution_count": 19,
652
  "metadata": {},
653
  "output_type": "execute_result"
654
  }
@@ -659,7 +659,7 @@
659
  },
660
  {
661
  "cell_type": "code",
662
- "execution_count": 20,
663
  "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
664
  "metadata": {},
665
  "outputs": [],
@@ -670,7 +670,7 @@
670
  },
671
  {
672
  "cell_type": "code",
673
- "execution_count": 21,
674
  "id": "80c15210-1af3-436e-970b-f81fc596fb41",
675
  "metadata": {},
676
  "outputs": [],
@@ -680,7 +680,7 @@
680
  },
681
  {
682
  "cell_type": "code",
683
- "execution_count": 22,
684
  "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
685
  "metadata": {},
686
  "outputs": [
@@ -696,7 +696,7 @@
696
  "dtype: object"
697
  ]
698
  },
699
- "execution_count": 22,
700
  "metadata": {},
701
  "output_type": "execute_result"
702
  }
@@ -707,7 +707,7 @@
707
  },
708
  {
709
  "cell_type": "code",
710
- "execution_count": 23,
711
  "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
712
  "metadata": {},
713
  "outputs": [],
@@ -717,7 +717,7 @@
717
  },
718
  {
719
  "cell_type": "code",
720
- "execution_count": 24,
721
  "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
722
  "metadata": {},
723
  "outputs": [
@@ -756,62 +756,62 @@
756
  " <tbody>\n",
757
  " <tr>\n",
758
  " <th>0</th>\n",
759
- " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
760
- " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
761
- " <td>0.2100</td>\n",
762
- " <td>2147484672</td>\n",
763
- " <td>36176898</td>\n",
764
- " <td>850664773</td>\n",
765
- " <td>3978479102</td>\n",
766
- " <td>1599828989</td>\n",
767
- " <td>252</td>\n",
768
  " </tr>\n",
769
  " <tr>\n",
770
  " <th>1</th>\n",
771
- " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
772
- " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
773
- " <td>0.0500</td>\n",
774
- " <td>0</td>\n",
775
- " <td>1858306115</td>\n",
776
- " <td>4223456596</td>\n",
777
- " <td>4018595822</td>\n",
778
- " <td>4282121085</td>\n",
779
  " <td>124</td>\n",
780
  " </tr>\n",
781
  " <tr>\n",
782
  " <th>2</th>\n",
783
- " <td>RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL...</td>\n",
784
- " <td>CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C</td>\n",
785
- " <td>2.0000</td>\n",
786
- " <td>0</td>\n",
787
- " <td>33947650</td>\n",
788
- " <td>2041877824</td>\n",
789
- " <td>3782085608</td>\n",
790
- " <td>4290771792</td>\n",
791
  " <td>252</td>\n",
792
  " </tr>\n",
793
  " <tr>\n",
794
  " <th>3</th>\n",
795
- " <td>QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH...</td>\n",
796
- " <td>OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N...</td>\n",
797
- " <td>6550.0000</td>\n",
798
  " <td>0</td>\n",
799
- " <td>1107566598</td>\n",
800
- " <td>1755681856</td>\n",
801
- " <td>3846453088</td>\n",
802
- " <td>4293647263</td>\n",
803
- " <td>124</td>\n",
804
  " </tr>\n",
805
  " <tr>\n",
806
  " <th>4</th>\n",
807
- " <td>YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV...</td>\n",
808
- " <td>C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O...</td>\n",
809
- " <td>0.0077</td>\n",
810
- " <td>4194304</td>\n",
811
- " <td>4857858</td>\n",
812
- " <td>515249472</td>\n",
813
- " <td>3969840044</td>\n",
814
- " <td>2061460183</td>\n",
815
  " <td>252</td>\n",
816
  " </tr>\n",
817
  " <tr>\n",
@@ -827,7 +827,7 @@
827
  " <td>...</td>\n",
828
  " </tr>\n",
829
  " <tr>\n",
830
- " <th>662479</th>\n",
831
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
832
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
833
  " <td>0.0045</td>\n",
@@ -839,7 +839,7 @@
839
  " <td>252</td>\n",
840
  " </tr>\n",
841
  " <tr>\n",
842
- " <th>662480</th>\n",
843
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
844
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
845
  " <td>0.0045</td>\n",
@@ -851,7 +851,7 @@
851
  " <td>252</td>\n",
852
  " </tr>\n",
853
  " <tr>\n",
854
- " <th>662481</th>\n",
855
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
856
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
857
  " <td>125.0000</td>\n",
@@ -863,7 +863,7 @@
863
  " <td>124</td>\n",
864
  " </tr>\n",
865
  " <tr>\n",
866
- " <th>662482</th>\n",
867
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
868
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
869
  " <td>2.0000</td>\n",
@@ -875,7 +875,7 @@
875
  " <td>204</td>\n",
876
  " </tr>\n",
877
  " <tr>\n",
878
- " <th>662483</th>\n",
879
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
880
  " <td>CC[Se]C(=N)N</td>\n",
881
  " <td>0.0390</td>\n",
@@ -888,53 +888,53 @@
888
  " </tr>\n",
889
  " </tbody>\n",
890
  "</table>\n",
891
- "<p>662484 rows × 9 columns</p>\n",
892
  "</div>"
893
  ],
894
  "text/plain": [
895
- " seq \\\n",
896
- "0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
897
- "1 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
898
- "2 RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL... \n",
899
- "3 QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH... \n",
900
- "4 YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV... \n",
901
- "... ... \n",
902
- "662479 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
903
- "662480 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
904
- "662481 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
905
- "662482 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
906
- "662483 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
907
  "\n",
908
- " smiles affinity_uM \\\n",
909
- "0 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.2100 \n",
910
- "1 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.0500 \n",
911
- "2 CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C 2.0000 \n",
912
- "3 OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N... 6550.0000 \n",
913
- "4 C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O... 0.0077 \n",
914
- "... ... ... \n",
915
- "662479 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
916
- "662480 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
917
- "662481 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
918
- "662482 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
919
- "662483 CC[Se]C(=N)N 0.0390 \n",
920
  "\n",
921
- " 0 1 2 3 4 5 \n",
922
- "0 2147484672 36176898 850664773 3978479102 1599828989 252 \n",
923
- "1 0 1858306115 4223456596 4018595822 4282121085 124 \n",
924
- "2 0 33947650 2041877824 3782085608 4290771792 252 \n",
925
- "3 0 1107566598 1755681856 3846453088 4293647263 124 \n",
926
- "4 4194304 4857858 515249472 3969840044 2061460183 252 \n",
927
- "... ... ... ... ... ... ... \n",
928
- "662479 65536 393216 964698368 369403648 4284858000 252 \n",
929
- "662480 65536 393216 964698368 369403648 4284858000 252 \n",
930
- "662481 67108864 1115688962 1771869508 4018431718 3744193341 124 \n",
931
- "662482 2097152 137216 958148868 1746307978 2067783280 204 \n",
932
- "662483 16 6144 537396736 2170880 1510015504 192 \n",
933
  "\n",
934
- "[662484 rows x 9 columns]"
935
  ]
936
  },
937
- "execution_count": 24,
938
  "metadata": {},
939
  "output_type": "execute_result"
940
  }
@@ -945,7 +945,7 @@
945
  },
946
  {
947
  "cell_type": "code",
948
- "execution_count": 25,
949
  "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
950
  "metadata": {},
951
  "outputs": [
@@ -955,7 +955,7 @@
955
  "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
956
  ]
957
  },
958
- "execution_count": 25,
959
  "metadata": {},
960
  "output_type": "execute_result"
961
  }
@@ -966,7 +966,7 @@
966
  },
967
  {
968
  "cell_type": "code",
969
- "execution_count": 26,
970
  "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
971
  "metadata": {},
972
  "outputs": [],
@@ -976,7 +976,7 @@
976
  },
977
  {
978
  "cell_type": "code",
979
- "execution_count": 27,
980
  "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
981
  "metadata": {},
982
  "outputs": [
@@ -986,7 +986,7 @@
986
  "Index(['smiles', 'affinity_uM'], dtype='object')"
987
  ]
988
  },
989
- "execution_count": 27,
990
  "metadata": {},
991
  "output_type": "execute_result"
992
  }
@@ -997,7 +997,7 @@
997
  },
998
  {
999
  "cell_type": "code",
1000
- "execution_count": 28,
1001
  "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
1002
  "metadata": {},
1003
  "outputs": [],
@@ -1008,7 +1008,7 @@
1008
  },
1009
  {
1010
  "cell_type": "code",
1011
- "execution_count": 68,
1012
  "id": "6a704c5e-68a6-418f-bcad-8688a13ca1d6",
1013
  "metadata": {},
1014
  "outputs": [],
@@ -1018,7 +1018,7 @@
1018
  },
1019
  {
1020
  "cell_type": "code",
1021
- "execution_count": 30,
1022
  "id": "0cad3882-975d-4693-aad1-63ec26646bd0",
1023
  "metadata": {},
1024
  "outputs": [
@@ -1026,7 +1026,7 @@
1026
  "name": "stderr",
1027
  "output_type": "stream",
1028
  "text": [
1029
- "/ccs/proj/stf006/glaser/conda-envs/bio/lib/python3.9/site-packages/pandas/core/arraylike.py:358: RuntimeWarning: divide by zero encountered in log\n",
1030
  " result = getattr(ufunc, method)(*inputs, **kwargs)\n"
1031
  ]
1032
  }
@@ -1037,7 +1037,7 @@
1037
  },
1038
  {
1039
  "cell_type": "code",
1040
- "execution_count": 31,
1041
  "id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
1042
  "metadata": {},
1043
  "outputs": [
@@ -1071,38 +1071,38 @@
1071
  " <tbody>\n",
1072
  " <tr>\n",
1073
  " <th>0</th>\n",
1074
- " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
1075
- " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
1076
- " <td>0.2100</td>\n",
1077
- " <td>6.677781</td>\n",
1078
  " </tr>\n",
1079
  " <tr>\n",
1080
  " <th>1</th>\n",
1081
- " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
1082
- " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
1083
- " <td>0.0500</td>\n",
1084
- " <td>7.301030</td>\n",
1085
  " </tr>\n",
1086
  " <tr>\n",
1087
  " <th>2</th>\n",
1088
- " <td>RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL...</td>\n",
1089
- " <td>CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C</td>\n",
1090
- " <td>2.0000</td>\n",
1091
- " <td>5.698970</td>\n",
1092
  " </tr>\n",
1093
  " <tr>\n",
1094
  " <th>3</th>\n",
1095
- " <td>QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH...</td>\n",
1096
- " <td>OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N...</td>\n",
1097
- " <td>6550.0000</td>\n",
1098
- " <td>2.183759</td>\n",
1099
  " </tr>\n",
1100
  " <tr>\n",
1101
  " <th>4</th>\n",
1102
- " <td>YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV...</td>\n",
1103
- " <td>C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O...</td>\n",
1104
- " <td>0.0077</td>\n",
1105
- " <td>8.113509</td>\n",
1106
  " </tr>\n",
1107
  " <tr>\n",
1108
  " <th>...</th>\n",
@@ -1112,35 +1112,35 @@
1112
  " <td>...</td>\n",
1113
  " </tr>\n",
1114
  " <tr>\n",
1115
- " <th>488472</th>\n",
 
 
 
 
 
 
 
1116
  " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1117
  " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
1118
  " <td>8.0000</td>\n",
1119
  " <td>5.096910</td>\n",
1120
  " </tr>\n",
1121
  " <tr>\n",
1122
- " <th>488473</th>\n",
1123
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
1124
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
1125
  " <td>0.0045</td>\n",
1126
  " <td>8.346787</td>\n",
1127
  " </tr>\n",
1128
  " <tr>\n",
1129
- " <th>488474</th>\n",
1130
- " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
1131
- " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
1132
- " <td>125.0000</td>\n",
1133
- " <td>3.903090</td>\n",
1134
- " </tr>\n",
1135
- " <tr>\n",
1136
- " <th>488475</th>\n",
1137
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
1138
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
1139
  " <td>2.0000</td>\n",
1140
  " <td>5.698970</td>\n",
1141
  " </tr>\n",
1142
  " <tr>\n",
1143
- " <th>488476</th>\n",
1144
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
1145
  " <td>CC[Se]C(=N)N</td>\n",
1146
  " <td>0.0390</td>\n",
@@ -1148,53 +1148,53 @@
1148
  " </tr>\n",
1149
  " </tbody>\n",
1150
  "</table>\n",
1151
- "<p>488477 rows × 4 columns</p>\n",
1152
  "</div>"
1153
  ],
1154
  "text/plain": [
1155
- " seq \\\n",
1156
- "0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
1157
- "1 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
1158
- "2 RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL... \n",
1159
- "3 QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH... \n",
1160
- "4 YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV... \n",
1161
- "... ... \n",
1162
- "488472 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1163
- "488473 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
1164
- "488474 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
1165
- "488475 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
1166
- "488476 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
1167
  "\n",
1168
- " smiles affinity_uM \\\n",
1169
- "0 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.2100 \n",
1170
- "1 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.0500 \n",
1171
- "2 CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C 2.0000 \n",
1172
- "3 OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N... 6550.0000 \n",
1173
- "4 C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O... 0.0077 \n",
1174
- "... ... ... \n",
1175
- "488472 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.0000 \n",
1176
- "488473 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
1177
- "488474 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
1178
- "488475 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
1179
- "488476 CC[Se]C(=N)N 0.0390 \n",
1180
  "\n",
1181
- " neg_log10_affinity_M \n",
1182
- "0 6.677781 \n",
1183
- "1 7.301030 \n",
1184
- "2 5.698970 \n",
1185
- "3 2.183759 \n",
1186
- "4 8.113509 \n",
1187
- "... ... \n",
1188
- "488472 5.096910 \n",
1189
- "488473 8.346787 \n",
1190
- "488474 3.903090 \n",
1191
- "488475 5.698970 \n",
1192
- "488476 7.408935 \n",
1193
  "\n",
1194
- "[488477 rows x 4 columns]"
1195
  ]
1196
  },
1197
- "execution_count": 31,
1198
  "metadata": {},
1199
  "output_type": "execute_result"
1200
  }
@@ -1205,37 +1205,17 @@
1205
  },
1206
  {
1207
  "cell_type": "code",
1208
- "execution_count": 32,
1209
  "id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
1210
  "metadata": {},
1211
  "outputs": [],
1212
  "source": [
1213
- "df = df_nr[np.isfinite(df_nr['neg_log10_affinity_M'])]"
1214
- ]
1215
- },
1216
- {
1217
- "cell_type": "code",
1218
- "execution_count": 33,
1219
- "id": "b4b9acd7-7784-492b-9fa3-b7fad9d18a9d",
1220
- "metadata": {},
1221
- "outputs": [
1222
- {
1223
- "name": "stdout",
1224
- "output_type": "stream",
1225
- "text": [
1226
- "INFO: Pandarallel will run on 32 workers.\n",
1227
- "INFO: Pandarallel will use Memory file system to transfer data between the main process and workers.\n"
1228
- ]
1229
- }
1230
- ],
1231
- "source": [
1232
- "from pandarallel import pandarallel\n",
1233
- "pandarallel.initialize()\n"
1234
  ]
1235
  },
1236
  {
1237
  "cell_type": "code",
1238
- "execution_count": 34,
1239
  "id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
1240
  "metadata": {},
1241
  "outputs": [],
@@ -1250,30 +1230,17 @@
1250
  },
1251
  {
1252
  "cell_type": "code",
1253
- "execution_count": 35,
1254
  "id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
1255
  "metadata": {},
1256
- "outputs": [
1257
- {
1258
- "name": "stderr",
1259
- "output_type": "stream",
1260
- "text": [
1261
- "<ipython-input-35-c2fe70ccb2b7>:1: SettingWithCopyWarning: \n",
1262
- "A value is trying to be set on a copy of a slice from a DataFrame.\n",
1263
- "Try using .loc[row_indexer,col_indexer] = value instead\n",
1264
- "\n",
1265
- "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
1266
- " df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)\n"
1267
- ]
1268
- }
1269
- ],
1270
  "source": [
1271
  "df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)"
1272
  ]
1273
  },
1274
  {
1275
  "cell_type": "code",
1276
- "execution_count": 36,
1277
  "id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
1278
  "metadata": {},
1279
  "outputs": [],
@@ -1283,7 +1250,7 @@
1283
  },
1284
  {
1285
  "cell_type": "code",
1286
- "execution_count": 37,
1287
  "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
1288
  "metadata": {},
1289
  "outputs": [],
@@ -1293,7 +1260,7 @@
1293
  },
1294
  {
1295
  "cell_type": "code",
1296
- "execution_count": 38,
1297
  "id": "0c027988-0b44-4010-ad61-7d70eead1654",
1298
  "metadata": {},
1299
  "outputs": [],
@@ -1303,7 +1270,7 @@
1303
  },
1304
  {
1305
  "cell_type": "code",
1306
- "execution_count": 39,
1307
  "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
1308
  "metadata": {},
1309
  "outputs": [],
@@ -1313,17 +1280,17 @@
1313
  },
1314
  {
1315
  "cell_type": "code",
1316
- "execution_count": 40,
1317
  "id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
1318
  "metadata": {},
1319
  "outputs": [
1320
  {
1321
  "data": {
1322
  "text/plain": [
1323
- "(array([6.86202031]), array([2.57502859]))"
1324
  ]
1325
  },
1326
- "execution_count": 40,
1327
  "metadata": {},
1328
  "output_type": "execute_result"
1329
  }
@@ -1334,7 +1301,7 @@
1334
  },
1335
  {
1336
  "cell_type": "code",
1337
- "execution_count": 43,
1338
  "id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
1339
  "metadata": {},
1340
  "outputs": [],
@@ -1344,7 +1311,7 @@
1344
  },
1345
  {
1346
  "cell_type": "code",
1347
- "execution_count": 45,
1348
  "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
1349
  "metadata": {},
1350
  "outputs": [],
@@ -1354,7 +1321,7 @@
1354
  },
1355
  {
1356
  "cell_type": "code",
1357
- "execution_count": 46,
1358
  "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
1359
  "metadata": {},
1360
  "outputs": [
@@ -1366,7 +1333,7 @@
1366
  " dtype='object')"
1367
  ]
1368
  },
1369
- "execution_count": 46,
1370
  "metadata": {},
1371
  "output_type": "execute_result"
1372
  }
@@ -1377,13 +1344,13 @@
1377
  },
1378
  {
1379
  "cell_type": "code",
1380
- "execution_count": 47,
1381
  "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
1382
  "metadata": {},
1383
  "outputs": [
1384
  {
1385
  "data": {
1386
- "image/png": "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\n",
1387
  "text/plain": [
1388
  "<Figure size 432x288 with 1 Axes>"
1389
  ]
@@ -1395,7 +1362,7 @@
1395
  }
1396
  ],
1397
  "source": [
1398
- "ax = df['neg_log10_affinity_M'].hist(bins=50,density=True)\n",
1399
  "ax.set_xlabel('-$\\log_{10}$ affinity[M]',fontsize=16)\n",
1400
  "ax.set_ylabel('probability',fontsize=16)\n",
1401
  "ax.figure.savefig('affinity_neglog10_M.pdf')"
@@ -1403,17 +1370,17 @@
1403
  },
1404
  {
1405
  "cell_type": "code",
1406
- "execution_count": 48,
1407
  "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
1408
  "metadata": {},
1409
  "outputs": [
1410
  {
1411
  "data": {
1412
  "text/plain": [
1413
- "487412"
1414
  ]
1415
  },
1416
- "execution_count": 48,
1417
  "metadata": {},
1418
  "output_type": "execute_result"
1419
  }
@@ -1422,10 +1389,148 @@
1422
  "len(df)"
1423
  ]
1424
  },
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1425
  {
1426
  "cell_type": "code",
1427
  "execution_count": null,
1428
- "id": "462ddcda-33ae-42d5-9ff4-1f3b057618a4",
1429
  "metadata": {},
1430
  "outputs": [],
1431
  "source": []
 
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
+ "execution_count": 3,
6
  "id": "95bd761a-fe51-4a8e-bc70-1365260ba5f8",
7
  "metadata": {},
8
  "outputs": [],
 
12
  },
13
  {
14
  "cell_type": "code",
15
+ "execution_count": 5,
16
  "id": "b0859483-5e19-4280-9f53-0d00a6f22d34",
17
  "metadata": {},
18
  "outputs": [],
 
23
  },
24
  {
25
  "cell_type": "code",
26
+ "execution_count": 6,
27
  "id": "f30732b7-7444-47ad-84e7-566e7a6f2f8e",
28
  "metadata": {},
29
  "outputs": [
 
57
  " <tr>\n",
58
  " <th>0</th>\n",
59
  " <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
60
+ " <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
61
  " <td>0.026</td>\n",
62
  " </tr>\n",
63
  " <tr>\n",
64
  " <th>1</th>\n",
65
+ " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
66
+ " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
67
+ " <td>500.000</td>\n",
68
  " </tr>\n",
69
  " <tr>\n",
70
  " <th>2</th>\n",
71
+ " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
72
+ " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
73
+ " <td>0.023</td>\n",
74
  " </tr>\n",
75
  " <tr>\n",
76
  " <th>3</th>\n",
77
+ " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
78
+ " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",
79
+ " <td>6.430</td>\n",
80
  " </tr>\n",
81
  " <tr>\n",
82
  " <th>4</th>\n",
83
+ " <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",
84
+ " <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",
85
+ " <td>0.185</td>\n",
86
  " </tr>\n",
87
  " </tbody>\n",
88
  "</table>\n",
 
91
  "text/plain": [
92
  " seq \\\n",
93
  "0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
94
+ "1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
95
+ "2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
96
+ "3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
97
+ "4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
98
  "\n",
99
  " smiles affinity_uM \n",
100
+ "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.026 \n",
101
+ "1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.000 \n",
102
+ "2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.023 \n",
103
+ "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.430 \n",
104
+ "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.185 "
105
  ]
106
  },
107
+ "execution_count": 6,
108
  "metadata": {},
109
  "output_type": "execute_result"
110
  }
 
115
  },
116
  {
117
  "cell_type": "code",
118
+ "execution_count": 7,
119
  "id": "2787b9fd-3d6f-4ae3-a3ad-d3539b72782b",
120
  "metadata": {},
121
  "outputs": [],
 
135
  },
136
  {
137
  "cell_type": "code",
138
+ "execution_count": 8,
139
  "id": "d1abe1c8-ac66-4289-8964-367a5b18528d",
140
  "metadata": {},
141
  "outputs": [],
 
146
  },
147
  {
148
  "cell_type": "code",
149
+ "execution_count": 9,
150
  "id": "988bab9c-5147-44e2-92ef-902eaf3c5a90",
151
  "metadata": {},
152
  "outputs": [
 
227
  "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 "
228
  ]
229
  },
230
+ "execution_count": 9,
231
  "metadata": {},
232
  "output_type": "execute_result"
233
  }
 
238
  },
239
  {
240
  "cell_type": "code",
241
+ "execution_count": 10,
242
  "id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
243
  "metadata": {},
244
  "outputs": [],
 
249
  },
250
  {
251
  "cell_type": "code",
252
+ "execution_count": 11,
253
  "id": "25553199-1715-40fb-9260-427bdd6c3706",
254
  "metadata": {},
255
  "outputs": [
 
294
  " </tr>\n",
295
  " <tr>\n",
296
  " <th>2</th>\n",
297
+ " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
298
+ " <td>C#CCCOP(=O)(O)OP(=O)(O)O</td>\n",
299
+ " <td>0.580000</td>\n",
300
  " </tr>\n",
301
  " <tr>\n",
302
  " <th>3</th>\n",
303
+ " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
304
+ " <td>C#CCOP(=O)(O)OP(=O)(O)O</td>\n",
305
+ " <td>0.770000</td>\n",
306
  " </tr>\n",
307
  " <tr>\n",
308
  " <th>4</th>\n",
 
317
  " <td>...</td>\n",
318
  " </tr>\n",
319
  " <tr>\n",
320
+ " <th>25420</th>\n",
321
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
322
  " <td>None</td>\n",
323
  " <td>127.226463</td>\n",
324
  " </tr>\n",
325
  " <tr>\n",
326
+ " <th>25421</th>\n",
327
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
328
  " <td>None</td>\n",
329
  " <td>127.226463</td>\n",
330
  " </tr>\n",
331
  " <tr>\n",
332
+ " <th>25422</th>\n",
333
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
334
  " <td>None</td>\n",
335
  " <td>169.204738</td>\n",
336
  " </tr>\n",
337
  " <tr>\n",
338
+ " <th>25423</th>\n",
339
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
340
  " <td>None</td>\n",
341
  " <td>169.204738</td>\n",
342
  " </tr>\n",
343
  " <tr>\n",
344
+ " <th>25424</th>\n",
345
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
346
  " <td>None</td>\n",
347
  " <td>169.204738</td>\n",
348
  " </tr>\n",
349
  " </tbody>\n",
350
  "</table>\n",
351
+ "<p>25425 rows × 3 columns</p>\n",
352
  "</div>"
353
  ],
354
  "text/plain": [
355
  " seq \\\n",
356
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
357
  "1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
358
+ "2 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
359
+ "3 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
360
  "4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
361
  "... ... \n",
362
+ "25420 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
363
+ "25421 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
364
+ "25422 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
365
+ "25423 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
366
+ "25424 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
367
  "\n",
368
  " smiles affinity_uM \n",
369
  "0 NP(=O)(N)O 0.000620 \n",
370
  "1 CC(=O)NO 2.600000 \n",
371
+ "2 C#CCCOP(=O)(O)OP(=O)(O)O 0.580000 \n",
372
+ "3 C#CCOP(=O)(O)OP(=O)(O)O 0.770000 \n",
373
  "4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
374
  "... ... ... \n",
375
+ "25420 None 127.226463 \n",
376
+ "25421 None 127.226463 \n",
377
+ "25422 None 169.204738 \n",
378
+ "25423 None 169.204738 \n",
379
+ "25424 None 169.204738 \n",
380
  "\n",
381
+ "[25425 rows x 3 columns]"
382
  ]
383
  },
384
+ "execution_count": 11,
385
  "metadata": {},
386
  "output_type": "execute_result"
387
  }
 
392
  },
393
  {
394
  "cell_type": "code",
395
+ "execution_count": 12,
396
  "id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
397
  "metadata": {},
398
  "outputs": [],
 
403
  },
404
  {
405
  "cell_type": "code",
406
+ "execution_count": 13,
407
  "id": "cee93018-601d-458b-af44-bd978da7a2bc",
408
  "metadata": {},
409
  "outputs": [
 
535
  "[13645 rows x 3 columns]"
536
  ]
537
  },
538
+ "execution_count": 13,
539
  "metadata": {},
540
  "output_type": "execute_result"
541
  }
 
546
  },
547
  {
548
  "cell_type": "code",
549
+ "execution_count": 14,
550
  "id": "195f92db-fe06-4d03-8500-8d6c310a3347",
551
  "metadata": {},
552
  "outputs": [],
 
556
  },
557
  {
558
  "cell_type": "code",
559
+ "execution_count": 15,
560
  "id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
561
  "metadata": {},
562
  "outputs": [
563
  {
564
  "data": {
565
  "text/plain": [
566
+ "2574545"
567
  ]
568
  },
569
+ "execution_count": 15,
570
  "metadata": {},
571
  "output_type": "execute_result"
572
  }
 
577
  },
578
  {
579
  "cell_type": "code",
580
+ "execution_count": 16,
581
  "id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
582
  "metadata": {},
583
  "outputs": [
 
607
  },
608
  {
609
  "cell_type": "code",
610
+ "execution_count": 18,
611
  "id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
612
  "metadata": {},
613
  "outputs": [],
 
617
  },
618
  {
619
  "cell_type": "code",
620
+ "execution_count": 19,
621
  "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
622
  "metadata": {},
623
  "outputs": [],
 
627
  },
628
  {
629
  "cell_type": "code",
630
+ "execution_count": 20,
631
  "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
632
  "metadata": {},
633
  "outputs": [],
 
638
  },
639
  {
640
  "cell_type": "code",
641
+ "execution_count": 21,
642
  "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
643
  "metadata": {},
644
  "outputs": [
645
  {
646
  "data": {
647
  "text/plain": [
648
+ "2568079"
649
  ]
650
  },
651
+ "execution_count": 21,
652
  "metadata": {},
653
  "output_type": "execute_result"
654
  }
 
659
  },
660
  {
661
  "cell_type": "code",
662
+ "execution_count": 22,
663
  "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
664
  "metadata": {},
665
  "outputs": [],
 
670
  },
671
  {
672
  "cell_type": "code",
673
+ "execution_count": 23,
674
  "id": "80c15210-1af3-436e-970b-f81fc596fb41",
675
  "metadata": {},
676
  "outputs": [],
 
680
  },
681
  {
682
  "cell_type": "code",
683
+ "execution_count": 24,
684
  "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
685
  "metadata": {},
686
  "outputs": [
 
696
  "dtype: object"
697
  ]
698
  },
699
+ "execution_count": 24,
700
  "metadata": {},
701
  "output_type": "execute_result"
702
  }
 
707
  },
708
  {
709
  "cell_type": "code",
710
+ "execution_count": 25,
711
  "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
712
  "metadata": {},
713
  "outputs": [],
 
717
  },
718
  {
719
  "cell_type": "code",
720
+ "execution_count": 26,
721
  "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
722
  "metadata": {},
723
  "outputs": [
 
756
  " <tbody>\n",
757
  " <tr>\n",
758
  " <th>0</th>\n",
759
+ " <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
760
+ " <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
761
+ " <td>0.0260</td>\n",
762
+ " <td>0</td>\n",
763
+ " <td>0</td>\n",
764
+ " <td>805306368</td>\n",
765
+ " <td>272271360</td>\n",
766
+ " <td>890245320</td>\n",
767
+ " <td>136</td>\n",
768
  " </tr>\n",
769
  " <tr>\n",
770
  " <th>1</th>\n",
771
+ " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
772
+ " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
773
+ " <td>500.0000</td>\n",
774
+ " <td>2147483648</td>\n",
775
+ " <td>3242590208</td>\n",
776
+ " <td>1914732547</td>\n",
777
+ " <td>994116706</td>\n",
778
+ " <td>3748288829</td>\n",
779
  " <td>124</td>\n",
780
  " </tr>\n",
781
  " <tr>\n",
782
  " <th>2</th>\n",
783
+ " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
784
+ " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
785
+ " <td>0.0230</td>\n",
786
+ " <td>131072</td>\n",
787
+ " <td>1109655552</td>\n",
788
+ " <td>2123376961</td>\n",
789
+ " <td>3477340882</td>\n",
790
+ " <td>2951175957</td>\n",
791
  " <td>252</td>\n",
792
  " </tr>\n",
793
  " <tr>\n",
794
  " <th>3</th>\n",
795
+ " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
796
+ " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",
797
+ " <td>6.4300</td>\n",
798
  " <td>0</td>\n",
799
+ " <td>6685696</td>\n",
800
+ " <td>2033191680</td>\n",
801
+ " <td>1345701844</td>\n",
802
+ " <td>2133187096</td>\n",
803
+ " <td>220</td>\n",
804
  " </tr>\n",
805
  " <tr>\n",
806
  " <th>4</th>\n",
807
+ " <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",
808
+ " <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",
809
+ " <td>0.1850</td>\n",
810
+ " <td>1048576</td>\n",
811
+ " <td>1107427332</td>\n",
812
+ " <td>2109513024</td>\n",
813
+ " <td>4081492984</td>\n",
814
+ " <td>4026260436</td>\n",
815
  " <td>252</td>\n",
816
  " </tr>\n",
817
  " <tr>\n",
 
827
  " <td>...</td>\n",
828
  " </tr>\n",
829
  " <tr>\n",
830
+ " <th>2568074</th>\n",
831
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
832
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
833
  " <td>0.0045</td>\n",
 
839
  " <td>252</td>\n",
840
  " </tr>\n",
841
  " <tr>\n",
842
+ " <th>2568075</th>\n",
843
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
844
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
845
  " <td>0.0045</td>\n",
 
851
  " <td>252</td>\n",
852
  " </tr>\n",
853
  " <tr>\n",
854
+ " <th>2568076</th>\n",
855
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
856
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
857
  " <td>125.0000</td>\n",
 
863
  " <td>124</td>\n",
864
  " </tr>\n",
865
  " <tr>\n",
866
+ " <th>2568077</th>\n",
867
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
868
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
869
  " <td>2.0000</td>\n",
 
875
  " <td>204</td>\n",
876
  " </tr>\n",
877
  " <tr>\n",
878
+ " <th>2568078</th>\n",
879
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
880
  " <td>CC[Se]C(=N)N</td>\n",
881
  " <td>0.0390</td>\n",
 
888
  " </tr>\n",
889
  " </tbody>\n",
890
  "</table>\n",
891
+ "<p>2568079 rows × 9 columns</p>\n",
892
  "</div>"
893
  ],
894
  "text/plain": [
895
+ " seq \\\n",
896
+ "0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
897
+ "1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
898
+ "2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
899
+ "3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
900
+ "4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
901
+ "... ... \n",
902
+ "2568074 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
903
+ "2568075 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
904
+ "2568076 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
905
+ "2568077 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
906
+ "2568078 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
907
  "\n",
908
+ " smiles affinity_uM \\\n",
909
+ "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
910
+ "1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.0000 \n",
911
+ "2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.0230 \n",
912
+ "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
913
+ "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
914
+ "... ... ... \n",
915
+ "2568074 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
916
+ "2568075 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
917
+ "2568076 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
918
+ "2568077 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
919
+ "2568078 CC[Se]C(=N)N 0.0390 \n",
920
  "\n",
921
+ " 0 1 2 3 4 5 \n",
922
+ "0 0 0 805306368 272271360 890245320 136 \n",
923
+ "1 2147483648 3242590208 1914732547 994116706 3748288829 124 \n",
924
+ "2 131072 1109655552 2123376961 3477340882 2951175957 252 \n",
925
+ "3 0 6685696 2033191680 1345701844 2133187096 220 \n",
926
+ "4 1048576 1107427332 2109513024 4081492984 4026260436 252 \n",
927
+ "... ... ... ... ... ... ... \n",
928
+ "2568074 65536 393216 964698368 369403648 4284858000 252 \n",
929
+ "2568075 65536 393216 964698368 369403648 4284858000 252 \n",
930
+ "2568076 67108864 1115688962 1771869508 4018431718 3744193341 124 \n",
931
+ "2568077 2097152 137216 958148868 1746307978 2067783280 204 \n",
932
+ "2568078 16 6144 537396736 2170880 1510015504 192 \n",
933
  "\n",
934
+ "[2568079 rows x 9 columns]"
935
  ]
936
  },
937
+ "execution_count": 26,
938
  "metadata": {},
939
  "output_type": "execute_result"
940
  }
 
945
  },
946
  {
947
  "cell_type": "code",
948
+ "execution_count": 27,
949
  "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
950
  "metadata": {},
951
  "outputs": [
 
955
  "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
956
  ]
957
  },
958
+ "execution_count": 27,
959
  "metadata": {},
960
  "output_type": "execute_result"
961
  }
 
966
  },
967
  {
968
  "cell_type": "code",
969
+ "execution_count": 28,
970
  "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
971
  "metadata": {},
972
  "outputs": [],
 
976
  },
977
  {
978
  "cell_type": "code",
979
+ "execution_count": 29,
980
  "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
981
  "metadata": {},
982
  "outputs": [
 
986
  "Index(['smiles', 'affinity_uM'], dtype='object')"
987
  ]
988
  },
989
+ "execution_count": 29,
990
  "metadata": {},
991
  "output_type": "execute_result"
992
  }
 
997
  },
998
  {
999
  "cell_type": "code",
1000
+ "execution_count": 30,
1001
  "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
1002
  "metadata": {},
1003
  "outputs": [],
 
1008
  },
1009
  {
1010
  "cell_type": "code",
1011
+ "execution_count": 31,
1012
  "id": "6a704c5e-68a6-418f-bcad-8688a13ca1d6",
1013
  "metadata": {},
1014
  "outputs": [],
 
1018
  },
1019
  {
1020
  "cell_type": "code",
1021
+ "execution_count": 32,
1022
  "id": "0cad3882-975d-4693-aad1-63ec26646bd0",
1023
  "metadata": {},
1024
  "outputs": [
 
1026
  "name": "stderr",
1027
  "output_type": "stream",
1028
  "text": [
1029
+ "/ccs/proj/stf006/glaser/conda-envs/dask/lib/python3.9/site-packages/pandas/core/arraylike.py:358: RuntimeWarning: divide by zero encountered in log\n",
1030
  " result = getattr(ufunc, method)(*inputs, **kwargs)\n"
1031
  ]
1032
  }
 
1037
  },
1038
  {
1039
  "cell_type": "code",
1040
+ "execution_count": 33,
1041
  "id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
1042
  "metadata": {},
1043
  "outputs": [
 
1071
  " <tbody>\n",
1072
  " <tr>\n",
1073
  " <th>0</th>\n",
1074
+ " <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
1075
+ " <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
1076
+ " <td>0.0260</td>\n",
1077
+ " <td>7.585027</td>\n",
1078
  " </tr>\n",
1079
  " <tr>\n",
1080
  " <th>1</th>\n",
1081
+ " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
1082
+ " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
1083
+ " <td>500.0000</td>\n",
1084
+ " <td>3.301030</td>\n",
1085
  " </tr>\n",
1086
  " <tr>\n",
1087
  " <th>2</th>\n",
1088
+ " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
1089
+ " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
1090
+ " <td>0.0230</td>\n",
1091
+ " <td>7.638272</td>\n",
1092
  " </tr>\n",
1093
  " <tr>\n",
1094
  " <th>3</th>\n",
1095
+ " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
1096
+ " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",
1097
+ " <td>6.4300</td>\n",
1098
+ " <td>5.191789</td>\n",
1099
  " </tr>\n",
1100
  " <tr>\n",
1101
  " <th>4</th>\n",
1102
+ " <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",
1103
+ " <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",
1104
+ " <td>0.1850</td>\n",
1105
+ " <td>6.732828</td>\n",
1106
  " </tr>\n",
1107
  " <tr>\n",
1108
  " <th>...</th>\n",
 
1112
  " <td>...</td>\n",
1113
  " </tr>\n",
1114
  " <tr>\n",
1115
+ " <th>1929143</th>\n",
1116
+ " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1117
+ " <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
1118
+ " <td>8.0000</td>\n",
1119
+ " <td>5.096910</td>\n",
1120
+ " </tr>\n",
1121
+ " <tr>\n",
1122
+ " <th>1929144</th>\n",
1123
  " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1124
  " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
1125
  " <td>8.0000</td>\n",
1126
  " <td>5.096910</td>\n",
1127
  " </tr>\n",
1128
  " <tr>\n",
1129
+ " <th>1929145</th>\n",
1130
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
1131
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
1132
  " <td>0.0045</td>\n",
1133
  " <td>8.346787</td>\n",
1134
  " </tr>\n",
1135
  " <tr>\n",
1136
+ " <th>1929146</th>\n",
 
 
 
 
 
 
 
1137
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
1138
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
1139
  " <td>2.0000</td>\n",
1140
  " <td>5.698970</td>\n",
1141
  " </tr>\n",
1142
  " <tr>\n",
1143
+ " <th>1929147</th>\n",
1144
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
1145
  " <td>CC[Se]C(=N)N</td>\n",
1146
  " <td>0.0390</td>\n",
 
1148
  " </tr>\n",
1149
  " </tbody>\n",
1150
  "</table>\n",
1151
+ "<p>1929148 rows × 4 columns</p>\n",
1152
  "</div>"
1153
  ],
1154
  "text/plain": [
1155
+ " seq \\\n",
1156
+ "0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
1157
+ "1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
1158
+ "2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
1159
+ "3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
1160
+ "4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
1161
+ "... ... \n",
1162
+ "1929143 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1163
+ "1929144 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1164
+ "1929145 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
1165
+ "1929146 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
1166
+ "1929147 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
1167
  "\n",
1168
+ " smiles affinity_uM \\\n",
1169
+ "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
1170
+ "1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.0000 \n",
1171
+ "2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.0230 \n",
1172
+ "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
1173
+ "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
1174
+ "... ... ... \n",
1175
+ "1929143 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.0000 \n",
1176
+ "1929144 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.0000 \n",
1177
+ "1929145 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
1178
+ "1929146 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
1179
+ "1929147 CC[Se]C(=N)N 0.0390 \n",
1180
  "\n",
1181
+ " neg_log10_affinity_M \n",
1182
+ "0 7.585027 \n",
1183
+ "1 3.301030 \n",
1184
+ "2 7.638272 \n",
1185
+ "3 5.191789 \n",
1186
+ "4 6.732828 \n",
1187
+ "... ... \n",
1188
+ "1929143 5.096910 \n",
1189
+ "1929144 5.096910 \n",
1190
+ "1929145 8.346787 \n",
1191
+ "1929146 5.698970 \n",
1192
+ "1929147 7.408935 \n",
1193
  "\n",
1194
+ "[1929148 rows x 4 columns]"
1195
  ]
1196
  },
1197
+ "execution_count": 33,
1198
  "metadata": {},
1199
  "output_type": "execute_result"
1200
  }
 
1205
  },
1206
  {
1207
  "cell_type": "code",
1208
+ "execution_count": 34,
1209
  "id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
1210
  "metadata": {},
1211
  "outputs": [],
1212
  "source": [
1213
+ "df = df_nr[np.isfinite(df_nr['neg_log10_affinity_M'])].copy()"
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1214
  ]
1215
  },
1216
  {
1217
  "cell_type": "code",
1218
+ "execution_count": 35,
1219
  "id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
1220
  "metadata": {},
1221
  "outputs": [],
 
1230
  },
1231
  {
1232
  "cell_type": "code",
1233
+ "execution_count": 36,
1234
  "id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
1235
  "metadata": {},
1236
+ "outputs": [],
 
 
 
 
 
 
 
 
 
 
 
 
 
1237
  "source": [
1238
  "df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)"
1239
  ]
1240
  },
1241
  {
1242
  "cell_type": "code",
1243
+ "execution_count": 37,
1244
  "id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
1245
  "metadata": {},
1246
  "outputs": [],
 
1250
  },
1251
  {
1252
  "cell_type": "code",
1253
+ "execution_count": 38,
1254
  "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
1255
  "metadata": {},
1256
  "outputs": [],
 
1260
  },
1261
  {
1262
  "cell_type": "code",
1263
+ "execution_count": 39,
1264
  "id": "0c027988-0b44-4010-ad61-7d70eead1654",
1265
  "metadata": {},
1266
  "outputs": [],
 
1270
  },
1271
  {
1272
  "cell_type": "code",
1273
+ "execution_count": 40,
1274
  "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
1275
  "metadata": {},
1276
  "outputs": [],
 
1280
  },
1281
  {
1282
  "cell_type": "code",
1283
+ "execution_count": 41,
1284
  "id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
1285
  "metadata": {},
1286
  "outputs": [
1287
  {
1288
  "data": {
1289
  "text/plain": [
1290
+ "(array([6.51286529]), array([2.4379995]))"
1291
  ]
1292
  },
1293
+ "execution_count": 41,
1294
  "metadata": {},
1295
  "output_type": "execute_result"
1296
  }
 
1301
  },
1302
  {
1303
  "cell_type": "code",
1304
+ "execution_count": 42,
1305
  "id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
1306
  "metadata": {},
1307
  "outputs": [],
 
1311
  },
1312
  {
1313
  "cell_type": "code",
1314
+ "execution_count": 43,
1315
  "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
1316
  "metadata": {},
1317
  "outputs": [],
 
1321
  },
1322
  {
1323
  "cell_type": "code",
1324
+ "execution_count": 44,
1325
  "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
1326
  "metadata": {},
1327
  "outputs": [
 
1333
  " dtype='object')"
1334
  ]
1335
  },
1336
+ "execution_count": 44,
1337
  "metadata": {},
1338
  "output_type": "execute_result"
1339
  }
 
1344
  },
1345
  {
1346
  "cell_type": "code",
1347
+ "execution_count": 48,
1348
  "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
1349
  "metadata": {},
1350
  "outputs": [
1351
  {
1352
  "data": {
1353
+ "image/png": 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/AM4hOdcxKf16DvD29KuZmY1RRYen3gmcHxEXZPb9DrggnYzwFJLEYmZmY1DRnsY+wC0Nym7Gy72amY1pRZPGJuCwBmWvpcCUIGZmNvoUHZ66Ajhb0pPp8/uAvUmmAzkb+HRrwzMzsyopmjTOJVkj/Lz0+QAB3073m5nZGFV0jfDtwDskXQC8nuQ+jYeAn9SsvmdmbeA77m2k5U4a6ay095Pci7EcWDtiUZmZWSXlThoR8YSk7cCfRzAeMyvIy8BamYpePXUNyTToZmY2DhU9Ef5D4IuSvkeSQO6jZrnWiLixNaGZmVnVFE0aV6Zf/z59DAiSK6iCZHElMzMbg4omje4RicKsAY/Xm1VL0UtufwIg6TnAy4CpwEbg9oj4U+vDMzOzKim8noakc4AzgCk8PSTVL+kzEfHJFsdnZmYVUnQ9jfOAj5GsG94DbAY6SNbXOE/SxIg4t9VBmplZNRTtafwjcFFEfCizby1wo6StwAKeOb2ImZmNIUXv09gNuL5B2XVpuZmZjVFFk8Z/A69uUPbqtNzMzMaooknjNOBUSR+SNF3SpPTrPwOnAosk7TTwqHcASbMl3SVpnaTFdcpfKukWSY9LOrNIWzMzG1lFz2ncln69MH1kCejLbEft8dMlYS8GjgQ2AKskLa+ZIfchkuR0XBNtzWwIngnXhqNo0vgENdOGFHQwsC4i7gGQ1APMAZ5644+ILcAWSbV/zUO2NTOzkaWI4eSAgi8mHQ/Mjoj56fZJwCERsahO3XOB/oj4bBNtF5BcyUVHR8esnp6epuLt7+9nypQpTbUtQ5Xj69u4FYCOSbDXHrvtsB9g5tT6+8vWMQk2b2vbyw+p2fiyP9+sRr+D4ajy3yJUPz6oVozd3d1rIqKzXlnhm/uGSXX25c1audtGxFJgKUBnZ2d0dXXlfIln6u3tpdm2ZahyfPPSIZAzZm7nHzIxzstOC9L3aKZF2X+KTztj5nYu6mvf6w+l2fjWz+2quz/7O2hUp6gq/y1C9eOD0REjFD8RPlwbgH0z29OATSW0NTOzFig7aawCZkjaP10J8ARgeQltzcysBUrtk0fEdkmLSG4QnABcFhFrJS1My5dI2htYDTwHeFLS6cCBEfGnem3LjN/MbLwrfSA3IlYAK2r2Lck8v59k6ClXWzMzK0/Zw1NmZjaKOWmYmVluThpmZpabk4aZmeXmpGFmZrk5aZiZWW5OGmZmlpuThpmZ5VbdWdpszMiu32Bmo5t7GmZmlpuThpmZ5eakYWZmufmchtkY5bXAbSS4p2FmZrk5aZiZWW4enjIbB3zZs7WKexpmZpabk4aZmeXmpGFmZrk5aZiZWW5OGmZmlpuThpmZ5eZLbs3GMd81bkWV3tOQNFvSXZLWSVpcp1ySvpiW3ybpVZmy9ZL6JP1S0upyIzczs1J7GpImABcDRwIbgFWSlkfEHZlqRwEz0schwJfTrwO6I+KBkkI2M7OMsoenDgbWRcQ9AJJ6gDlANmnMAS6PiABulbS7pBdExH0lx2o2rtTeNe7hKqtHyXtzSS8mHQ/Mjoj56fZJwCERsShT5wfAhRHxs3T7BuDDEbFa0r3Aw0AAX4mIpQ1eZwGwAKCjo2NWT09PU/H29/czZcqUptqWocrx9W3cCkDHJNi8rc3BDKHqMbYrvplTd8tdt8p/i1D9+KBaMXZ3d6+JiM56ZWX3NFRnX23WGqzOYRGxSdJewEpJd0bETTtUTpLJUoDOzs7o6upqKtje3l6abVuGKsc3L/3UesbM7VzUV+3rLaoeY7viWz+3K3fdKv8tQvXjg9ERI5R/InwDsG9mexqwKW+diBj4ugW4mmS4y8zMSlJ20lgFzJC0v6SdgROA5TV1lgMnp1dRHQpsjYj7JE2WtCuApMnAm4DbywzezGy8K7XPGxHbJS0CrgcmAJdFxFpJC9PyJcAK4GhgHfAYcEravAO4WtJA3N+KiOvKjN/MbLwrfaA0IlaQJIbsviWZ5wG8v067e4CDRjxAK8Q3h5mNL55GxMzMcqvuJSNWWV4Fzmz8ctKwlnEyMRv7nDTMrC6fr7J6nDTMbEhOIDbAJ8LNzCw3Jw0zM8vNScPMzHJz0jAzs9x8Itxy8eW0ZgZOGlbDV8mY2WA8PGVmZrm5p2FmTZueWWyrq72hWEnc0zAzs9zc0zCzQnxRxPjmnoaZmeXmpGFmZrk5aZiZWW4+p2FmLeF7fMYHJw1ryCc8rVlOIGOXh6fMzCw3Jw0zM8vNw1Oj1PTF13LGzO3MW3xt7u5/oyEDD0PZSMrz9+UhrNGj9KQhaTbwBWACcGlEXFhTrrT8aOAxYF5E/DxPW8s/luxEYVXl8yHVVmrSkDQBuBg4EtgArJK0PCLuyFQ7CpiRPg4BvgwckrPtuNQoATgxmFmrld3TOBhYFxH3AEjqAeYA2Tf+OcDlERHArZJ2l/QCYHqOti3Vt3Er89I33jyfeDz8Y9acVn3wafR/WvR/2RorO2lMBf4ns72BpDcxVJ2pOdsCIGkBsCDd7Jd0V5Px7gk8AKBPF2tYtH4zTsvEV1WOcfiqHh9UJ8ZB/u+a/l8uUSV+hqn9GhWUnTRUZ1/krJOnbbIzYimwtFhoO5K0OiI6h3uckVL1+MAxtkLV44Pqx1j1+GB0xAjlJ40NwL6Z7WnAppx1ds7R1szMRlDZ92msAmZI2l/SzsAJwPKaOsuBk5U4FNgaEfflbGtmZiOo1J5GRGyXtAi4nuSy2csiYq2khWn5EmAFyeW260guuT1lsLYjHPKwh7hGWNXjA8fYClWPD6ofY9Xjg9ERI0ouUjIzMxuapxExM7PcnDTMzCw3J406JM2WdJekdZIWtzueWpL2lfRjSb+WtFbSB9odUz2SJkj6haQftDuWetIbR78n6c70Z/madsdUS9IH09/x7ZK+LWmXNsdzmaQtkm7P7NtD0kpJv0m/PreCMX4m/T3fJulqSbu3McS6MWbKzpQUkvZsR2xDcdKokZmu5CjgQOBESQe2N6odbAfOiIi/BQ4F3l/BGAE+APy63UEM4gvAdRHxUuAgKharpKnAaUBnRLyM5AKQE9obFcuA2TX7FgM3RMQM4IZ0u52WsWOMK4GXRcTLgbuBj5QdVI1l7BgjkvYlmSrp92UHlJeTxo6emuokIp4ABqYrqYyIuG9gEseIeITkzW5qe6N6JknTgGOAS9sdSz2SngO8HvgqQEQ8ERF/bGtQ9U0EJkmaCDybNt+bFBE3AQ/V7J4DfD19/nXguDJjqlUvxoj4UURsTzdvJbnPq20a/BwB/gX4ZxrcuFwFTho7ajSNSSVJmg68EvjvNodS6/Mkf/xPtjmORl4E/AH4WjqEdqmkye0OKisiNgKfJfnUeR/JPUs/am9UdXWk91KRft2rzfEM5VTgh+0OopakY4GNEfGrdscyGCeNHeWerqTdJE0BrgROj4g/tTueAZLeDGyJiDXtjmUQE4FXAV+OiFcCj9L+YZVnSM8NzAH2B/YBJkt6Z3ujGt0knU0yvHtFu2PJkvRs4GzgnHbHMhQnjR3lmeqk7SQ9iyRhXBERV7U7nhqHAcdKWk8yvHeEpG+2N6QdbAA2RMRAD+17JEmkSt4I3BsRf4iIvwBXAa9tc0z1bE5noib9uqXN8dQl6V3Am4G5Ub0b1F5M8uHgV+n/zTTg55L2bmtUdThp7Kjy05WkC1V9Ffh1RHyu3fHUioiPRMS0iJhO8vO7MSIq9Qk5Iu4H/kfS36S73sAITrPfpN8Dh0p6dvo7fwMVO1mfWg68K33+LuD7bYylrnQBtw8Dx0bEY+2Op1ZE9EXEXhExPf2/2QC8Kv07rRQnjRrpybKB6Up+Dfx7CdOVFHUYcBLJJ/hfpo+j2x3UKPRPwBWSbgNeAfzf9obzTGkv6HvAz4E+kv/Xtk41IenbwC3A30jaIOndwIXAkZJ+Q3LlT1tX1GwQ478CuwIr0/+XJRWMcVTwNCJmZpabexpmZpabk4aZmeXmpGFmZrk5aZiZWW5OGmZmlpuThpmZ5eakYWZmuTlpWKVIOlfSmLx5SNKp6ZoTT0j642D7m/051Gsn6ThJ/6fJmJelazuEpN6asnmZsgPqtO3KlL8x3ffRzL4NzcRk7eWkYVYCSfuQ3M19M3AEybxSDfeTTCnfzKJQ9dodBzSVNFL3p8d8X4PyR0hmKKh1clqW9bX0WCuGEY+10cR2B2A2TswgWUTp6xHxs6H2R8QGkvmHCmm23RAej4hbBym/CninpHMGJgKUNAl4K8mkmvMy8W0ENkr6Q4tjtJK4p2GjgpIleG+RtE3SVknXZCYbzNY7MV3W88+S+iQdK6m3dmilxbG9RNI3JN2bxnePpC8PLHsqaRkw8Po3pEMzyxrtT9s8Y5hpYFvSDEnXSuqX9DtJ50jaqbZeZnsZySSCUzPDQuslHZ8+P6jO99Mr6ZYCP4JvAPsBr8vsewtJMryywHFsFHBPwyovnaH0WuBG4O3AFOATwM8kvSL99IqkI0nWSVgOnAHsSbIY1C4kS3yOlH1IPt2fDjxMssDTWSRDMK8BzgfWAF8E3k8yAeHAJ+1G+xu5mmSI51+A/w2cR7Jo2Nca1D8feD7wauDYdN/jJBMgbgLeQ2bYKU3EhwOnDBFH1u+Am0iGqH6a7js5jbW/wHFsFHDSsNHgk8A9wFEDS3amn4TvJkkOA+P155FMb/6WzDBJH8kb84gljXTpzpsGtiXdDKwDfirplRHxC0kDU5rfkR3qabR/EBdFxECC+E9JRwAn0iBpRMRv06GgJ2qPL+nfgA9K+lBEPJrufg/wR+A7OWLJuhy4SNJpwHNJzs0cVfAYNgp4eMraQomJ2UeDepNJFkf6TmaNZyLiXuC/SD4VI2kC0AlcmV1gJ11L/d6aY54l6S5JT0o6rqbsxZJ+JuluJcvAdub4XnZOj3mnpG3AX3j6E/cOQ2jDdG3N9u3AC5s81lKSdcdPBJC0C8lQ1uURsa3gsb4L/C+S3s9ckpPnNzQZl1WYk4a1y+Ekb67ZRz3PJVmC9746ZfcDe6TP9wSeRf1V4zbXbN8AHE2md5CxBFgWEQeQrHF+haR6SwBnfQo4F/gmcAxwMPD3adkuQ7Qt6qGa7cebfY2I2ESyYNLCdNfbSH6eX2niWI8A15AMUZ1MsqJkVdeHt2Hw8JS1yxqScfahPEyyRnu9ZS/3Bh5Mnz9Aknj2qlOvg2QVPOCpxY2ozQWSng8cSpJQiIiVaZ1ZwOpBYjyB5NP5JzPHmjJI/Sq5hOQk/CySoamfRkSzKxheTtIT2om092Jjj3sa1hYR8UhErM4+GtR7lCTBvC0dggJA0n4k62X/JK33V5I39rdmewbpm+H+OcN6IbApXY97wO8Yevjn2ezYUypyInmkPQ5MqlcQETeSrFD5OZIVIYezot1K4N+BJRVc7dJaxD0NGw0+RvIJ9geSLiG5euo8YCtwUabex4EfAVdLWkoyZHUuyTBWs0MlQw1NAVwHvCs96b6OZGjqtU2+3ki4A9hD0ntJEuufI6IvU74E+AJJb63pS2TTxO0exhjnnoZVXkRcR3KuYHfST7Ikn45fl47LD9RbSXIS9m9JLvf8MMnVVfeTJJih/B7YR9KzMvv2IzO01cA/kVzmewHJVUe7Uq03z0uBHpI10P8f8B815d9Nvy6LiMfLDMxGH68RbmOapGkkn/4viIjza8p6gc9HxDWZfTcAPRHxb+l9H5cAB8QY/keR9I8kJ78PiIh1NWXLgC7gJUCkvYnhvJZIbvr7KvCGiJg2nONZ+dzTsDFD0qT0Tuy3Sjpc0ikk4+yPkXzaHqj30XSyvNcAl0raIGngRPtC4BRJdwOfAeaO1YQh6UBJAzcIXlObMDL2Izln04pLaM9Oj3VyC45lbeCeho0ZknYmGR46FHge8CjJ/RJnRcTt7YytitKe1mtJJkt8R3aoL1NnOsm5IYBHIuKuYb7mC4Cp6eYTEXHbcI5n5XPSMDOz3Dw8ZWZmuTlpmJlZbk4aZmaWm5OGmZnl5qRhZma5OWmYmVluThpmZpbb/wcMNwymqdNzCAAAAABJRU5ErkJggg==\n",
1354
  "text/plain": [
1355
  "<Figure size 432x288 with 1 Axes>"
1356
  ]
 
1362
  }
1363
  ],
1364
  "source": [
1365
+ "ax = df['neg_log10_affinity_M'].hist(bins=100,density=True)\n",
1366
  "ax.set_xlabel('-$\\log_{10}$ affinity[M]',fontsize=16)\n",
1367
  "ax.set_ylabel('probability',fontsize=16)\n",
1368
  "ax.figure.savefig('affinity_neglog10_M.pdf')"
 
1370
  },
1371
  {
1372
  "cell_type": "code",
1373
+ "execution_count": 49,
1374
  "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
1375
  "metadata": {},
1376
  "outputs": [
1377
  {
1378
  "data": {
1379
  "text/plain": [
1380
+ "1927202"
1381
  ]
1382
  },
1383
+ "execution_count": 49,
1384
  "metadata": {},
1385
  "output_type": "execute_result"
1386
  }
 
1389
  "len(df)"
1390
  ]
1391
  },
1392
+ {
1393
+ "cell_type": "code",
1394
+ "execution_count": 54,
1395
+ "id": "b85f8b72-8dfc-4a24-b5b8-51fcbe6dcf63",
1396
+ "metadata": {},
1397
+ "outputs": [
1398
+ {
1399
+ "data": {
1400
+ "text/plain": [
1401
+ "{'with_mean': True,\n",
1402
+ " 'with_std': True,\n",
1403
+ " 'copy': True,\n",
1404
+ " 'n_features_in_': 1,\n",
1405
+ " 'n_samples_seen_': 1927202,\n",
1406
+ " 'mean_': array([6.51286529]),\n",
1407
+ " 'var_': array([2.4379995]),\n",
1408
+ " 'scale_': array([1.56140946])}"
1409
+ ]
1410
+ },
1411
+ "execution_count": 54,
1412
+ "metadata": {},
1413
+ "output_type": "execute_result"
1414
+ }
1415
+ ],
1416
+ "source": [
1417
+ "scaler.__dict__"
1418
+ ]
1419
+ },
1420
+ {
1421
+ "cell_type": "code",
1422
+ "execution_count": 63,
1423
+ "id": "ec0ef8e2-c0e9-4c9b-bf3a-c98cc3889475",
1424
+ "metadata": {},
1425
+ "outputs": [
1426
+ {
1427
+ "data": {
1428
+ "text/plain": [
1429
+ "{'with_mean': True,\n",
1430
+ " 'with_std': True,\n",
1431
+ " 'copy': True,\n",
1432
+ " 'n_features_in_': 1,\n",
1433
+ " 'n_samples_seen_': 1927202,\n",
1434
+ " 'mean_': array([6.51286529]),\n",
1435
+ " 'var_': array([2.4379995]),\n",
1436
+ " 'scale_': array([1.56140946])}"
1437
+ ]
1438
+ },
1439
+ "execution_count": 63,
1440
+ "metadata": {},
1441
+ "output_type": "execute_result"
1442
+ }
1443
+ ],
1444
+ "source": [
1445
+ "scaler.__dict__"
1446
+ ]
1447
+ },
1448
+ {
1449
+ "cell_type": "code",
1450
+ "execution_count": 67,
1451
+ "id": "15f8d5b9-37d5-453e-a6df-df6510cc5c81",
1452
+ "metadata": {},
1453
+ "outputs": [],
1454
+ "source": [
1455
+ "# output the normalization\n",
1456
+ "\n",
1457
+ "import json\n",
1458
+ "\n",
1459
+ "class NumpyEncoder(json.JSONEncoder):\n",
1460
+ " def default(self, obj):\n",
1461
+ " if isinstance(obj, np.ndarray):\n",
1462
+ " return obj.tolist()\n",
1463
+ " if isinstance(obj, np.int64):\n",
1464
+ " return int(obj)\n",
1465
+ " return json.JSONEncoder.default(self, obj)\n",
1466
+ " \n",
1467
+ "json.dump(scaler.__dict__,open('data/scaling.json','w'),cls=NumpyEncoder)"
1468
+ ]
1469
+ },
1470
+ {
1471
+ "cell_type": "markdown",
1472
+ "id": "210b39d3-505b-4a6e-b186-35e660f4d510",
1473
+ "metadata": {},
1474
+ "source": [
1475
+ "**without KRAS**"
1476
+ ]
1477
+ },
1478
+ {
1479
+ "cell_type": "code",
1480
+ "execution_count": 78,
1481
+ "id": "8dec95dc-a014-4d39-ae51-8de981173573",
1482
+ "metadata": {},
1483
+ "outputs": [],
1484
+ "source": [
1485
+ "smiles_sotorasib = 'C=CC(=O)N1CCN(c2nc(=O)n(-c3c(C)ccnc3C(C)C)c3nc(-c4c(O)cccc4F)c(F)cc23)[C@@H](C)C1'\n",
1486
+ "seq_kras_wt = 'MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM'"
1487
+ ]
1488
+ },
1489
+ {
1490
+ "cell_type": "code",
1491
+ "execution_count": 81,
1492
+ "id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
1493
+ "metadata": {},
1494
+ "outputs": [],
1495
+ "source": [
1496
+ "df_nokras = df[df.seq!=seq_kras_wt]"
1497
+ ]
1498
+ },
1499
+ {
1500
+ "cell_type": "code",
1501
+ "execution_count": 83,
1502
+ "id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
1503
+ "metadata": {},
1504
+ "outputs": [
1505
+ {
1506
+ "data": {
1507
+ "text/plain": [
1508
+ "1926945"
1509
+ ]
1510
+ },
1511
+ "execution_count": 83,
1512
+ "metadata": {},
1513
+ "output_type": "execute_result"
1514
+ }
1515
+ ],
1516
+ "source": [
1517
+ "len(df_nokras)"
1518
+ ]
1519
+ },
1520
+ {
1521
+ "cell_type": "code",
1522
+ "execution_count": 84,
1523
+ "id": "47966268-c97c-4bd9-9c90-eb568249f2ef",
1524
+ "metadata": {},
1525
+ "outputs": [],
1526
+ "source": [
1527
+ "df_nokras.to_parquet('data/all_nokras.parquet')"
1528
+ ]
1529
+ },
1530
  {
1531
  "cell_type": "code",
1532
  "execution_count": null,
1533
+ "id": "bfbf0bcd-8cd5-4efa-a9ca-f8d7ee5870e0",
1534
  "metadata": {},
1535
  "outputs": [],
1536
  "source": []
data/all.parquet CHANGED
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data/all_nokras.parquet ADDED
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data/bindingdb.parquet ADDED
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data/moad.parquet ADDED
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  " <td>NaN</td>\n",
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488
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489
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490
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491
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492
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493
  " 0 1 pdb ligand_name ligand_valid affinity_quantity 6 \\\n",
494
  "0 NaN NaN NaN 2PA:C:613 valid Ki = \n",
495
  "1 NaN NaN NaN HAE:C:800 valid Ki = \n",
496
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497
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498
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499
  "... ... ... ... ... ... ... .. \n",
500
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501
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502
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503
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504
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505
  "\n",
506
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507
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508
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509
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510
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511
  "4 15.00 uM \n",
512
  "... ... ... \n",
513
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514
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515
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516
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517
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518
  "\n",
519
  " smiles 10 is_sep cum_sum \\\n",
520
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521
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522
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523
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524
  "4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN False 5 \n",
525
  "... ... .. ... ... \n",
526
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527
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528
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529
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530
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531
  "\n",
532
  " pdb_ref affinity_uM name \\\n",
533
  "0 6H8J 0.000620 6H8J \n",
534
  "1 6H8J 2.600000 6H8J \n",
535
- "2 2GL0 15.000000 2GL0 \n",
536
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537
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538
  "... ... ... ... \n",
539
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540
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541
- "17684 2WDB 169.204738 2WDB \n",
542
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543
- "17686 2WDB 169.204738 2WDB \n",
544
  "\n",
545
  " seq \n",
546
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
547
  "1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
548
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550
  "4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
551
  "... ... \n",
552
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553
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554
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555
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556
- "17686 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
557
  "\n",
558
- "[17687 rows x 17 columns]"
559
  ]
560
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561
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562
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563
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564
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569
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570
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571
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573
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54
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111
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115
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116
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117
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118
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119
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120
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121
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126
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127
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128
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130
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132
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136
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140
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151
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152
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156
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157
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158
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159
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160
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161
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162
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167
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168
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183
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188
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190
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191
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192
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194
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199
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200
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201
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217
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227
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233
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317
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318
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320
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327
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329
+ " <td>2</td>\n",
330
+ " <td>4S3F</td>\n",
331
+ " <td>0.580000</td>\n",
332
+ " <td>4S3F</td>\n",
333
+ " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
334
  " </tr>\n",
335
  " <tr>\n",
336
  " <th>3</th>\n",
337
  " <td>NaN</td>\n",
338
  " <td>NaN</td>\n",
339
  " <td>NaN</td>\n",
340
+ " <td>0CG:A:902</td>\n",
341
  " <td>valid</td>\n",
342
+ " <td>ic50</td>\n",
343
  " <td>=</td>\n",
344
+ " <td>770.00</td>\n",
345
+ " <td>nM</td>\n",
346
+ " <td>C#CCOP(=O)(O)OP(=O)(O)O</td>\n",
347
  " <td>NaN</td>\n",
348
  " <td>False</td>\n",
349
+ " <td>2</td>\n",
350
+ " <td>4S3F</td>\n",
351
+ " <td>0.770000</td>\n",
352
+ " <td>4S3F</td>\n",
353
+ " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
354
  " </tr>\n",
355
  " <tr>\n",
356
  " <th>4</th>\n",
357
  " <td>NaN</td>\n",
358
  " <td>NaN</td>\n",
359
  " <td>NaN</td>\n",
360
+ " <td>ADN:A:901</td>\n",
361
  " <td>valid</td>\n",
362
  " <td>Kd</td>\n",
363
  " <td>=</td>\n",
 
393
  " <td>...</td>\n",
394
  " </tr>\n",
395
  " <tr>\n",
396
+ " <th>25420</th>\n",
397
  " <td>NaN</td>\n",
398
  " <td>NaN</td>\n",
399
  " <td>NaN</td>\n",
 
413
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
414
  " </tr>\n",
415
  " <tr>\n",
416
+ " <th>25421</th>\n",
417
  " <td>NaN</td>\n",
418
  " <td>NaN</td>\n",
419
  " <td>NaN</td>\n",
 
433
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
434
  " </tr>\n",
435
  " <tr>\n",
436
+ " <th>25422</th>\n",
437
  " <td>NaN</td>\n",
438
  " <td>NaN</td>\n",
439
  " <td>NaN</td>\n",
 
453
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
454
  " </tr>\n",
455
  " <tr>\n",
456
+ " <th>25423</th>\n",
457
  " <td>NaN</td>\n",
458
  " <td>NaN</td>\n",
459
  " <td>NaN</td>\n",
 
473
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
474
  " </tr>\n",
475
  " <tr>\n",
476
+ " <th>25424</th>\n",
477
  " <td>NaN</td>\n",
478
  " <td>NaN</td>\n",
479
  " <td>NaN</td>\n",
 
494
  " </tr>\n",
495
  " </tbody>\n",
496
  "</table>\n",
497
+ "<p>25425 rows × 17 columns</p>\n",
498
  "</div>"
499
  ],
500
  "text/plain": [
501
  " 0 1 pdb ligand_name ligand_valid affinity_quantity 6 \\\n",
502
  "0 NaN NaN NaN 2PA:C:613 valid Ki = \n",
503
  "1 NaN NaN NaN HAE:C:800 valid Ki = \n",
504
+ "2 NaN NaN NaN 43W:A:902 valid ic50 = \n",
505
+ "3 NaN NaN NaN 0CG:A:902 valid ic50 = \n",
506
+ "4 NaN NaN NaN ADN:A:901 valid Kd = \n",
507
  "... ... ... ... ... ... ... .. \n",
508
+ "25420 NaN NaN NaN MAN NAG:G:1 valid Ka = \n",
509
+ "25421 NaN NaN NaN MAN NAG:F:1 valid Ka = \n",
510
+ "25422 NaN NaN NaN NGA NAG:F:1 valid Ka = \n",
511
+ "25423 NaN NaN NaN NGA NAG:E:1 valid Ka = \n",
512
+ "25424 NaN NaN NaN NGA NAG:H:1 valid Ka = \n",
513
  "\n",
514
  " affinity_val affinity_unit \\\n",
515
  "0 0.62 nM \n",
516
  "1 2.60 uM \n",
517
+ "2 580.00 nM \n",
518
+ "3 770.00 nM \n",
519
  "4 15.00 uM \n",
520
  "... ... ... \n",
521
+ "25420 7860.00 M^-1 \n",
522
+ "25421 7860.00 M^-1 \n",
523
+ "25422 5910.00 M^-1 \n",
524
+ "25423 5910.00 M^-1 \n",
525
+ "25424 5910.00 M^-1 \n",
526
  "\n",
527
  " smiles 10 is_sep cum_sum \\\n",
528
  "0 NP(=O)(N)O NaN False 1 \n",
529
  "1 CC(=O)NO NaN False 1 \n",
530
+ "2 C#CCCOP(=O)(O)OP(=O)(O)O NaN False 2 \n",
531
+ "3 C#CCOP(=O)(O)OP(=O)(O)O NaN False 2 \n",
532
  "4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN False 5 \n",
533
  "... ... .. ... ... \n",
534
+ "25420 NaN NaN False 10499 \n",
535
+ "25421 NaN NaN False 10499 \n",
536
+ "25422 NaN NaN False 10499 \n",
537
+ "25423 NaN NaN False 10499 \n",
538
+ "25424 NaN NaN False 10499 \n",
539
  "\n",
540
  " pdb_ref affinity_uM name \\\n",
541
  "0 6H8J 0.000620 6H8J \n",
542
  "1 6H8J 2.600000 6H8J \n",
543
+ "2 4S3F 0.580000 4S3F \n",
544
+ "3 4S3F 0.770000 4S3F \n",
545
  "4 2GL0 15.000000 2GL0 \n",
546
  "... ... ... ... \n",
547
+ "25420 2WDB 127.226463 2WDB \n",
548
+ "25421 2WDB 127.226463 2WDB \n",
549
+ "25422 2WDB 169.204738 2WDB \n",
550
+ "25423 2WDB 169.204738 2WDB \n",
551
+ "25424 2WDB 169.204738 2WDB \n",
552
  "\n",
553
  " seq \n",
554
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
555
  "1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
556
+ "2 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
557
+ "3 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
558
  "4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
559
  "... ... \n",
560
+ "25420 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
561
+ "25421 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
562
+ "25422 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
563
+ "25423 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
564
+ "25424 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
565
  "\n",
566
+ "[25425 rows x 17 columns]"
567
  ]
568
  },
569
+ "execution_count": 26,
570
  "metadata": {},
571
  "output_type": "execute_result"
572
  }
 
577
  },
578
  {
579
  "cell_type": "code",
580
+ "execution_count": 27,
581
  "id": "bebc962b-10f7-478c-8e23-e2d3722e875c",
582
  "metadata": {},
583
  "outputs": [],
pdbbind.ipynb CHANGED
@@ -10,7 +10,7 @@
10
  },
11
  {
12
  "cell_type": "code",
13
- "execution_count": 3,
14
  "id": "86476f6e-802a-463b-a1b0-2ae228bb92af",
15
  "metadata": {},
16
  "outputs": [],
@@ -20,38 +20,31 @@
20
  },
21
  {
22
  "cell_type": "code",
23
- "execution_count": 5,
24
  "id": "9b2be11c-f4bb-4107-af49-abd78052afcf",
25
  "metadata": {},
26
  "outputs": [],
27
  "source": [
28
- "df = pd.read_table('../binding_datasets/pdbbind/data/plain-text-index/index/INDEX_general_PL_data.2019',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
29
- "df = df.rename(columns={'#': 'name','release': 'affinity'})"
 
 
 
30
  ]
31
  },
32
  {
33
  "cell_type": "code",
34
- "execution_count": 6,
35
- "id": "16e0fe44-96aa-4d3a-ae42-3609e895418b",
36
- "metadata": {},
37
- "outputs": [],
38
- "source": [
39
- "from numericalunits import mL, nm"
40
- ]
41
- },
42
- {
43
- "cell_type": "code",
44
- "execution_count": 13,
45
  "id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e",
46
  "metadata": {},
47
  "outputs": [],
48
  "source": [
49
- "quantities = ['ki','kd','ka','k1/2','kb']"
50
  ]
51
  },
52
  {
53
  "cell_type": "code",
54
- "execution_count": 14,
55
  "id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",
56
  "metadata": {},
57
  "outputs": [],
@@ -74,7 +67,7 @@
74
  },
75
  {
76
  "cell_type": "code",
77
- "execution_count": 15,
78
  "id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",
79
  "metadata": {},
80
  "outputs": [],
@@ -85,7 +78,7 @@
85
  },
86
  {
87
  "cell_type": "code",
88
- "execution_count": 12,
89
  "id": "d92f0004-68c1-4487-94b9-56b4fd598de4",
90
  "metadata": {},
91
  "outputs": [
@@ -95,13 +88,13 @@
95
  "<AxesSubplot:>"
96
  ]
97
  },
98
- "execution_count": 12,
99
  "metadata": {},
100
  "output_type": "execute_result"
101
  },
102
  {
103
  "data": {
104
- "image/png": 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\n",
105
  "text/plain": [
106
  "<Figure size 432x288 with 1 Axes>"
107
  ]
@@ -118,7 +111,7 @@
118
  },
119
  {
120
  "cell_type": "code",
121
- "execution_count": 24,
122
  "id": "aa358835-55f3-4551-9217-e76a15de4fe8",
123
  "metadata": {},
124
  "outputs": [],
@@ -128,17 +121,17 @@
128
  },
129
  {
130
  "cell_type": "code",
131
- "execution_count": 25,
132
  "id": "d6dda488-f709-4fe7-b372-080042cf7c66",
133
  "metadata": {},
134
  "outputs": [],
135
  "source": [
136
- "df_complex = pd.read_parquet('../binding_datasets/data/pdbbind_complex.parquet')"
137
  ]
138
  },
139
  {
140
  "cell_type": "code",
141
- "execution_count": 26,
142
  "id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",
143
  "metadata": {},
144
  "outputs": [],
@@ -148,7 +141,7 @@
148
  },
149
  {
150
  "cell_type": "code",
151
- "execution_count": 27,
152
  "id": "4d105c42-0d11-49db-9012-52fafc9cd299",
153
  "metadata": {},
154
  "outputs": [],
@@ -158,17 +151,17 @@
158
  },
159
  {
160
  "cell_type": "code",
161
- "execution_count": 28,
162
  "id": "2955b056-26dd-45fa-8d74-f17661253a9a",
163
  "metadata": {},
164
  "outputs": [
165
  {
166
  "data": {
167
  "text/plain": [
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- "11099"
169
  ]
170
  },
171
- "execution_count": 28,
172
  "metadata": {},
173
  "output_type": "execute_result"
174
  }
 
10
  },
11
  {
12
  "cell_type": "code",
13
+ "execution_count": 27,
14
  "id": "86476f6e-802a-463b-a1b0-2ae228bb92af",
15
  "metadata": {},
16
  "outputs": [],
 
20
  },
21
  {
22
  "cell_type": "code",
23
+ "execution_count": 45,
24
  "id": "9b2be11c-f4bb-4107-af49-abd78052afcf",
25
  "metadata": {},
26
  "outputs": [],
27
  "source": [
28
+ "df = pd.read_table('pdbbind/data/index/INDEX_general_PL_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
29
+ "df = df.rename(columns={'#': 'name','release': 'affinity'})\n",
30
+ "df_refined = pd.read_table('pdbbind/data/index/INDEX_refined_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
31
+ "df_refined = df_refined.rename(columns={'#': 'name','release': 'affinity'})\n",
32
+ "df = pd.concat([df,df_refined])"
33
  ]
34
  },
35
  {
36
  "cell_type": "code",
37
+ "execution_count": 46,
 
 
 
 
 
 
 
 
 
 
38
  "id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e",
39
  "metadata": {},
40
  "outputs": [],
41
  "source": [
42
+ "quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50']"
43
  ]
44
  },
45
  {
46
  "cell_type": "code",
47
+ "execution_count": 47,
48
  "id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",
49
  "metadata": {},
50
  "outputs": [],
 
67
  },
68
  {
69
  "cell_type": "code",
70
+ "execution_count": 48,
71
  "id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",
72
  "metadata": {},
73
  "outputs": [],
 
78
  },
79
  {
80
  "cell_type": "code",
81
+ "execution_count": 49,
82
  "id": "d92f0004-68c1-4487-94b9-56b4fd598de4",
83
  "metadata": {},
84
  "outputs": [
 
88
  "<AxesSubplot:>"
89
  ]
90
  },
91
+ "execution_count": 49,
92
  "metadata": {},
93
  "output_type": "execute_result"
94
  },
95
  {
96
  "data": {
97
+ "image/png": "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\n",
98
  "text/plain": [
99
  "<Figure size 432x288 with 1 Axes>"
100
  ]
 
111
  },
112
  {
113
  "cell_type": "code",
114
+ "execution_count": 50,
115
  "id": "aa358835-55f3-4551-9217-e76a15de4fe8",
116
  "metadata": {},
117
  "outputs": [],
 
121
  },
122
  {
123
  "cell_type": "code",
124
+ "execution_count": 51,
125
  "id": "d6dda488-f709-4fe7-b372-080042cf7c66",
126
  "metadata": {},
127
  "outputs": [],
128
  "source": [
129
+ "df_complex = pd.read_parquet('data/pdbbind_complex.parquet')"
130
  ]
131
  },
132
  {
133
  "cell_type": "code",
134
+ "execution_count": 52,
135
  "id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",
136
  "metadata": {},
137
  "outputs": [],
 
141
  },
142
  {
143
  "cell_type": "code",
144
+ "execution_count": 53,
145
  "id": "4d105c42-0d11-49db-9012-52fafc9cd299",
146
  "metadata": {},
147
  "outputs": [],
 
151
  },
152
  {
153
  "cell_type": "code",
154
+ "execution_count": 54,
155
  "id": "2955b056-26dd-45fa-8d74-f17661253a9a",
156
  "metadata": {},
157
  "outputs": [
158
  {
159
  "data": {
160
  "text/plain": [
161
+ "24759"
162
  ]
163
  },
164
+ "execution_count": 54,
165
  "metadata": {},
166
  "output_type": "execute_result"
167
  }
pdbbind.py CHANGED
@@ -19,7 +19,7 @@ def parse_complex(fn):
19
  if __name__ == '__main__':
20
  import glob
21
 
22
- filenames = glob.glob('pdbbind/data/v2019-other-PL/*')
23
  filenames.extend(glob.glob('pdbbind/data/refined-set/*'))
24
  comm = MPI.COMM_WORLD
25
  with MPICommExecutor(comm, root=0) as executor:
 
19
  if __name__ == '__main__':
20
  import glob
21
 
22
+ filenames = glob.glob('pdbbind/data/v2020-other-PL/*')
23
  filenames.extend(glob.glob('pdbbind/data/refined-set/*'))
24
  comm = MPI.COMM_WORLD
25
  with MPICommExecutor(comm, root=0) as executor:
pdbbind.slurm CHANGED
@@ -1,7 +1,7 @@
1
  #!/bin/bash
2
  #SBATCH -J preprocess_pdbbind
3
  #SBATCH -p batch
4
- #SBATCH -A BIP214
5
  #SBATCH -t 3:00:00
6
  #SBATCH -N 12
7
  #SBATCH --ntasks-per-node=8
 
1
  #!/bin/bash
2
  #SBATCH -J preprocess_pdbbind
3
  #SBATCH -p batch
4
+ #SBATCH -A STF006
5
  #SBATCH -t 3:00:00
6
  #SBATCH -N 12
7
  #SBATCH --ntasks-per-node=8