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update notebooks

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Files changed (2) hide show
  1. bindingdb_single.ipynb +1036 -0
  2. combine_dbs.ipynb +148 -125
bindingdb_single.ipynb ADDED
@@ -0,0 +1,1036 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "cells": [
3
+ {
4
+ "cell_type": "code",
5
+ "execution_count": 1,
6
+ "id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
7
+ "metadata": {},
8
+ "outputs": [],
9
+ "source": [
10
+ "import pandas as pd\n",
11
+ "import dask.dataframe as dd"
12
+ ]
13
+ },
14
+ {
15
+ "cell_type": "code",
16
+ "execution_count": 2,
17
+ "id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
18
+ "metadata": {},
19
+ "outputs": [],
20
+ "source": [
21
+ "cols = ['Ligand SMILES', 'IC50 (nM)','KEGG ID of Ligand','Ki (nM)', 'Kd (nM)','EC50 (nM)']"
22
+ ]
23
+ },
24
+ {
25
+ "cell_type": "code",
26
+ "execution_count": 3,
27
+ "id": "1b923f02-e858-4737-ab5e-4c98c2def1b6",
28
+ "metadata": {},
29
+ "outputs": [],
30
+ "source": [
31
+ "allseq = ['BindingDB Target Chain Sequence']+['BindingDB Target Chain Sequence.{}'.format(j) for j in range(1,13)]"
32
+ ]
33
+ },
34
+ {
35
+ "cell_type": "code",
36
+ "execution_count": 4,
37
+ "id": "54f0721e-1e36-48cc-a635-a1617a04f9e5",
38
+ "metadata": {},
39
+ "outputs": [],
40
+ "source": [
41
+ "dtypes = {'BindingDB Target Chain Sequence.{}'.format(i): 'object' for i in range(1,13)}"
42
+ ]
43
+ },
44
+ {
45
+ "cell_type": "code",
46
+ "execution_count": 5,
47
+ "id": "c1843c65-a5ef-4604-adca-40fb18bc2991",
48
+ "metadata": {},
49
+ "outputs": [],
50
+ "source": [
51
+ "dtypes.update({'BindingDB Target Chain Sequence': 'object',\n",
52
+ " 'IC50 (nM)': 'object',\n",
53
+ " 'KEGG ID of Ligand': 'object',\n",
54
+ " 'Ki (nM)': 'object',\n",
55
+ " 'Kd (nM)': 'object',\n",
56
+ " 'EC50 (nM)': 'object',\n",
57
+ " 'koff (s-1)': 'object'})"
58
+ ]
59
+ },
60
+ {
61
+ "cell_type": "code",
62
+ "execution_count": 6,
63
+ "id": "aa337ac3-4ca1-4369-a9c7-ab705221a137",
64
+ "metadata": {},
65
+ "outputs": [],
66
+ "source": [
67
+ "seq_name = 'BindingDB Target Chain Sequence'"
68
+ ]
69
+ },
70
+ {
71
+ "cell_type": "code",
72
+ "execution_count": 7,
73
+ "id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
74
+ "metadata": {},
75
+ "outputs": [],
76
+ "source": [
77
+ "import tqdm.notebook"
78
+ ]
79
+ },
80
+ {
81
+ "cell_type": "code",
82
+ "execution_count": 8,
83
+ "id": "e97d29e6-d153-480e-a1ee-c216c22af8d2",
84
+ "metadata": {},
85
+ "outputs": [],
86
+ "source": [
87
+ "ddf = dd.read_csv('bindingdb/data/BindingDB_All.tsv',sep='\\t',\n",
88
+ " error_bad_lines=False,\n",
89
+ " usecols=cols+allseq,\n",
90
+ " dtype=dtypes)"
91
+ ]
92
+ },
93
+ {
94
+ "cell_type": "code",
95
+ "execution_count": 11,
96
+ "id": "a4b381c0-968b-4248-a24f-9609acb12136",
97
+ "metadata": {},
98
+ "outputs": [
99
+ {
100
+ "data": {
101
+ "text/plain": [
102
+ "0.04789522637942933"
103
+ ]
104
+ },
105
+ "execution_count": 11,
106
+ "metadata": {},
107
+ "output_type": "execute_result"
108
+ }
109
+ ],
110
+ "source": [
111
+ "len(ddf[~ddf['BindingDB Target Chain Sequence.1'].isnull()])/len(ddf[~ddf['BindingDB Target Chain Sequence'].isnull()])"
112
+ ]
113
+ },
114
+ {
115
+ "cell_type": "code",
116
+ "execution_count": 18,
117
+ "id": "7a8efd3f-c9c4-4f6a-83e5-9e9610deb17f",
118
+ "metadata": {},
119
+ "outputs": [],
120
+ "source": [
121
+ "# remove rows with more than one target\n",
122
+ "ddf_prune = ddf[ddf['BindingDB Target Chain Sequence.1'].isnull()]\n",
123
+ "ddf_prune = ddf_prune.rename(columns={'BindingDB Target Chain Sequence': 'seq'})"
124
+ ]
125
+ },
126
+ {
127
+ "cell_type": "code",
128
+ "execution_count": 19,
129
+ "id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
130
+ "metadata": {},
131
+ "outputs": [],
132
+ "source": [
133
+ "ddf_nonnull = ddf_prune[~ddf_prune.seq.isnull()].copy()"
134
+ ]
135
+ },
136
+ {
137
+ "cell_type": "code",
138
+ "execution_count": 20,
139
+ "id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
140
+ "metadata": {},
141
+ "outputs": [
142
+ {
143
+ "data": {
144
+ "text/html": [
145
+ "<div>\n",
146
+ "<style scoped>\n",
147
+ " .dataframe tbody tr th:only-of-type {\n",
148
+ " vertical-align: middle;\n",
149
+ " }\n",
150
+ "\n",
151
+ " .dataframe tbody tr th {\n",
152
+ " vertical-align: top;\n",
153
+ " }\n",
154
+ "\n",
155
+ " .dataframe thead th {\n",
156
+ " text-align: right;\n",
157
+ " }\n",
158
+ "</style>\n",
159
+ "<table border=\"1\" class=\"dataframe\">\n",
160
+ " <thead>\n",
161
+ " <tr style=\"text-align: right;\">\n",
162
+ " <th></th>\n",
163
+ " <th>Ligand SMILES</th>\n",
164
+ " <th>Ki (nM)</th>\n",
165
+ " <th>IC50 (nM)</th>\n",
166
+ " <th>Kd (nM)</th>\n",
167
+ " <th>EC50 (nM)</th>\n",
168
+ " <th>KEGG ID of Ligand</th>\n",
169
+ " <th>seq</th>\n",
170
+ " <th>BindingDB Target Chain Sequence.1</th>\n",
171
+ " <th>BindingDB Target Chain Sequence.2</th>\n",
172
+ " <th>BindingDB Target Chain Sequence.3</th>\n",
173
+ " <th>BindingDB Target Chain Sequence.4</th>\n",
174
+ " <th>BindingDB Target Chain Sequence.5</th>\n",
175
+ " <th>BindingDB Target Chain Sequence.6</th>\n",
176
+ " <th>BindingDB Target Chain Sequence.7</th>\n",
177
+ " <th>BindingDB Target Chain Sequence.8</th>\n",
178
+ " <th>BindingDB Target Chain Sequence.9</th>\n",
179
+ " <th>BindingDB Target Chain Sequence.10</th>\n",
180
+ " <th>BindingDB Target Chain Sequence.11</th>\n",
181
+ " <th>BindingDB Target Chain Sequence.12</th>\n",
182
+ " </tr>\n",
183
+ " </thead>\n",
184
+ " <tbody>\n",
185
+ " <tr>\n",
186
+ " <th>0</th>\n",
187
+ " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
188
+ " <td>0.24</td>\n",
189
+ " <td>NaN</td>\n",
190
+ " <td>NaN</td>\n",
191
+ " <td>NaN</td>\n",
192
+ " <td>NaN</td>\n",
193
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
194
+ " <td>NaN</td>\n",
195
+ " <td>NaN</td>\n",
196
+ " <td>NaN</td>\n",
197
+ " <td>NaN</td>\n",
198
+ " <td>NaN</td>\n",
199
+ " <td>NaN</td>\n",
200
+ " <td>NaN</td>\n",
201
+ " <td>NaN</td>\n",
202
+ " <td>NaN</td>\n",
203
+ " <td>NaN</td>\n",
204
+ " <td>NaN</td>\n",
205
+ " <td>NaN</td>\n",
206
+ " </tr>\n",
207
+ " <tr>\n",
208
+ " <th>1</th>\n",
209
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
210
+ " <td>0.25</td>\n",
211
+ " <td>NaN</td>\n",
212
+ " <td>NaN</td>\n",
213
+ " <td>NaN</td>\n",
214
+ " <td>NaN</td>\n",
215
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
216
+ " <td>NaN</td>\n",
217
+ " <td>NaN</td>\n",
218
+ " <td>NaN</td>\n",
219
+ " <td>NaN</td>\n",
220
+ " <td>NaN</td>\n",
221
+ " <td>NaN</td>\n",
222
+ " <td>NaN</td>\n",
223
+ " <td>NaN</td>\n",
224
+ " <td>NaN</td>\n",
225
+ " <td>NaN</td>\n",
226
+ " <td>NaN</td>\n",
227
+ " <td>NaN</td>\n",
228
+ " </tr>\n",
229
+ " <tr>\n",
230
+ " <th>2</th>\n",
231
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
232
+ " <td>0.41</td>\n",
233
+ " <td>NaN</td>\n",
234
+ " <td>NaN</td>\n",
235
+ " <td>NaN</td>\n",
236
+ " <td>NaN</td>\n",
237
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
238
+ " <td>NaN</td>\n",
239
+ " <td>NaN</td>\n",
240
+ " <td>NaN</td>\n",
241
+ " <td>NaN</td>\n",
242
+ " <td>NaN</td>\n",
243
+ " <td>NaN</td>\n",
244
+ " <td>NaN</td>\n",
245
+ " <td>NaN</td>\n",
246
+ " <td>NaN</td>\n",
247
+ " <td>NaN</td>\n",
248
+ " <td>NaN</td>\n",
249
+ " <td>NaN</td>\n",
250
+ " </tr>\n",
251
+ " <tr>\n",
252
+ " <th>3</th>\n",
253
+ " <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
254
+ " <td>0.8</td>\n",
255
+ " <td>NaN</td>\n",
256
+ " <td>NaN</td>\n",
257
+ " <td>NaN</td>\n",
258
+ " <td>NaN</td>\n",
259
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
260
+ " <td>NaN</td>\n",
261
+ " <td>NaN</td>\n",
262
+ " <td>NaN</td>\n",
263
+ " <td>NaN</td>\n",
264
+ " <td>NaN</td>\n",
265
+ " <td>NaN</td>\n",
266
+ " <td>NaN</td>\n",
267
+ " <td>NaN</td>\n",
268
+ " <td>NaN</td>\n",
269
+ " <td>NaN</td>\n",
270
+ " <td>NaN</td>\n",
271
+ " <td>NaN</td>\n",
272
+ " </tr>\n",
273
+ " <tr>\n",
274
+ " <th>4</th>\n",
275
+ " <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
276
+ " <td>0.99</td>\n",
277
+ " <td>NaN</td>\n",
278
+ " <td>NaN</td>\n",
279
+ " <td>NaN</td>\n",
280
+ " <td>NaN</td>\n",
281
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
282
+ " <td>NaN</td>\n",
283
+ " <td>NaN</td>\n",
284
+ " <td>NaN</td>\n",
285
+ " <td>NaN</td>\n",
286
+ " <td>NaN</td>\n",
287
+ " <td>NaN</td>\n",
288
+ " <td>NaN</td>\n",
289
+ " <td>NaN</td>\n",
290
+ " <td>NaN</td>\n",
291
+ " <td>NaN</td>\n",
292
+ " <td>NaN</td>\n",
293
+ " <td>NaN</td>\n",
294
+ " </tr>\n",
295
+ " </tbody>\n",
296
+ "</table>\n",
297
+ "</div>"
298
+ ],
299
+ "text/plain": [
300
+ " Ligand SMILES Ki (nM) IC50 (nM) \\\n",
301
+ "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 0.24 NaN \n",
302
+ "1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... 0.25 NaN \n",
303
+ "2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... 0.41 NaN \n",
304
+ "3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... 0.8 NaN \n",
305
+ "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.99 NaN \n",
306
+ "\n",
307
+ " Kd (nM) EC50 (nM) KEGG ID of Ligand \\\n",
308
+ "0 NaN NaN NaN \n",
309
+ "1 NaN NaN NaN \n",
310
+ "2 NaN NaN NaN \n",
311
+ "3 NaN NaN NaN \n",
312
+ "4 NaN NaN NaN \n",
313
+ "\n",
314
+ " seq \\\n",
315
+ "0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
316
+ "1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
317
+ "2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
318
+ "3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
319
+ "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
320
+ "\n",
321
+ " BindingDB Target Chain Sequence.1 BindingDB Target Chain Sequence.2 \\\n",
322
+ "0 NaN NaN \n",
323
+ "1 NaN NaN \n",
324
+ "2 NaN NaN \n",
325
+ "3 NaN NaN \n",
326
+ "4 NaN NaN \n",
327
+ "\n",
328
+ " BindingDB Target Chain Sequence.3 BindingDB Target Chain Sequence.4 \\\n",
329
+ "0 NaN NaN \n",
330
+ "1 NaN NaN \n",
331
+ "2 NaN NaN \n",
332
+ "3 NaN NaN \n",
333
+ "4 NaN NaN \n",
334
+ "\n",
335
+ " BindingDB Target Chain Sequence.5 BindingDB Target Chain Sequence.6 \\\n",
336
+ "0 NaN NaN \n",
337
+ "1 NaN NaN \n",
338
+ "2 NaN NaN \n",
339
+ "3 NaN NaN \n",
340
+ "4 NaN NaN \n",
341
+ "\n",
342
+ " BindingDB Target Chain Sequence.7 BindingDB Target Chain Sequence.8 \\\n",
343
+ "0 NaN NaN \n",
344
+ "1 NaN NaN \n",
345
+ "2 NaN NaN \n",
346
+ "3 NaN NaN \n",
347
+ "4 NaN NaN \n",
348
+ "\n",
349
+ " BindingDB Target Chain Sequence.9 BindingDB Target Chain Sequence.10 \\\n",
350
+ "0 NaN NaN \n",
351
+ "1 NaN NaN \n",
352
+ "2 NaN NaN \n",
353
+ "3 NaN NaN \n",
354
+ "4 NaN NaN \n",
355
+ "\n",
356
+ " BindingDB Target Chain Sequence.11 BindingDB Target Chain Sequence.12 \n",
357
+ "0 NaN NaN \n",
358
+ "1 NaN NaN \n",
359
+ "2 NaN NaN \n",
360
+ "3 NaN NaN \n",
361
+ "4 NaN NaN "
362
+ ]
363
+ },
364
+ "execution_count": 20,
365
+ "metadata": {},
366
+ "output_type": "execute_result"
367
+ }
368
+ ],
369
+ "source": [
370
+ "ddf_nonnull.head()"
371
+ ]
372
+ },
373
+ {
374
+ "cell_type": "code",
375
+ "execution_count": 21,
376
+ "id": "7b423365-4989-4325-a5a5-845d852d52e9",
377
+ "metadata": {},
378
+ "outputs": [
379
+ {
380
+ "data": {
381
+ "text/plain": [
382
+ "2221761"
383
+ ]
384
+ },
385
+ "execution_count": 21,
386
+ "metadata": {},
387
+ "output_type": "execute_result"
388
+ }
389
+ ],
390
+ "source": [
391
+ "len(ddf_nonnull)"
392
+ ]
393
+ },
394
+ {
395
+ "cell_type": "code",
396
+ "execution_count": 22,
397
+ "id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
398
+ "metadata": {},
399
+ "outputs": [],
400
+ "source": [
401
+ "from pint import UnitRegistry\n",
402
+ "import numpy as np\n",
403
+ "import re\n",
404
+ "ureg = UnitRegistry()\n",
405
+ "\n",
406
+ "def to_uM(affinities):\n",
407
+ " ic50, Ki, Kd, ec50 = affinities\n",
408
+ "\n",
409
+ " vals = []\n",
410
+ " \n",
411
+ " try:\n",
412
+ " ic50 = ureg(str(ic50)+'nM').m_as(ureg.uM)\n",
413
+ " vals.append(ic50)\n",
414
+ " except:\n",
415
+ " pass\n",
416
+ "\n",
417
+ " try:\n",
418
+ " Ki = ureg(str(Ki)+'nM').m_as(ureg.uM)\n",
419
+ " vals.append(Ki)\n",
420
+ " except:\n",
421
+ " pass\n",
422
+ "\n",
423
+ " try:\n",
424
+ " Kd = ureg(str(Kd)+'nM').m_as(ureg.uM)\n",
425
+ " vals.append(Kd)\n",
426
+ " except:\n",
427
+ " pass\n",
428
+ "\n",
429
+ " try:\n",
430
+ " ec50 = ureg(str(ec50)+'nM').m_as(ureg.uM)\n",
431
+ " vals.append(ec50)\n",
432
+ " except:\n",
433
+ " pass\n",
434
+ "\n",
435
+ " if len(vals) > 0:\n",
436
+ " vals = np.array(vals)\n",
437
+ " return np.mean(vals[~np.isnan(vals)])\n",
438
+ " \n",
439
+ " return None"
440
+ ]
441
+ },
442
+ {
443
+ "cell_type": "code",
444
+ "execution_count": 23,
445
+ "id": "b3cff13c-19b2-4413-a84b-d99062f516a7",
446
+ "metadata": {},
447
+ "outputs": [],
448
+ "source": [
449
+ "df_nonnull = ddf_nonnull.compute()"
450
+ ]
451
+ },
452
+ {
453
+ "cell_type": "code",
454
+ "execution_count": 24,
455
+ "id": "ca9795de-e821-4dc3-a7bf-70ade9e4c7f0",
456
+ "metadata": {},
457
+ "outputs": [
458
+ {
459
+ "name": "stdout",
460
+ "output_type": "stream",
461
+ "text": [
462
+ "INFO: Pandarallel will run on 32 workers.\n",
463
+ "INFO: Pandarallel will use Memory file system to transfer data between the main process and workers.\n"
464
+ ]
465
+ }
466
+ ],
467
+ "source": [
468
+ "from pandarallel import pandarallel\n",
469
+ "pandarallel.initialize()\n"
470
+ ]
471
+ },
472
+ {
473
+ "cell_type": "code",
474
+ "execution_count": 25,
475
+ "id": "4356a3e2-fede-48e7-a486-343661fe0a0a",
476
+ "metadata": {},
477
+ "outputs": [],
478
+ "source": [
479
+ "df_affinity = df_nonnull.copy()\n",
480
+ "df_affinity['affinity_uM'] = df_affinity[['IC50 (nM)', 'Ki (nM)', 'Kd (nM)','EC50 (nM)']].parallel_apply(to_uM,axis=1)"
481
+ ]
482
+ },
483
+ {
484
+ "cell_type": "code",
485
+ "execution_count": 26,
486
+ "id": "e91c3af8-84a5-42a2-9e25-49cb2f320b0b",
487
+ "metadata": {},
488
+ "outputs": [],
489
+ "source": [
490
+ "df_affinity[~df_affinity['affinity_uM'].isnull()].to_parquet('data/bindingdb.parquet')"
491
+ ]
492
+ },
493
+ {
494
+ "cell_type": "code",
495
+ "execution_count": 27,
496
+ "id": "f3a9173e-d574-4314-9cea-f8c0a66766c0",
497
+ "metadata": {},
498
+ "outputs": [],
499
+ "source": [
500
+ "import pandas as pd\n",
501
+ "df_affinity = pd.read_parquet('data/bindingdb.parquet')"
502
+ ]
503
+ },
504
+ {
505
+ "cell_type": "code",
506
+ "execution_count": 28,
507
+ "id": "f602fdbe-7083-436c-9eac-9d97fbc8be67",
508
+ "metadata": {},
509
+ "outputs": [
510
+ {
511
+ "data": {
512
+ "text/plain": [
513
+ "2219812"
514
+ ]
515
+ },
516
+ "execution_count": 28,
517
+ "metadata": {},
518
+ "output_type": "execute_result"
519
+ }
520
+ ],
521
+ "source": [
522
+ "len(df_affinity)"
523
+ ]
524
+ },
525
+ {
526
+ "cell_type": "code",
527
+ "execution_count": 29,
528
+ "id": "27194288-cf3e-4c30-ad55-3b0998fdf939",
529
+ "metadata": {},
530
+ "outputs": [
531
+ {
532
+ "data": {
533
+ "text/html": [
534
+ "<div>\n",
535
+ "<style scoped>\n",
536
+ " .dataframe tbody tr th:only-of-type {\n",
537
+ " vertical-align: middle;\n",
538
+ " }\n",
539
+ "\n",
540
+ " .dataframe tbody tr th {\n",
541
+ " vertical-align: top;\n",
542
+ " }\n",
543
+ "\n",
544
+ " .dataframe thead th {\n",
545
+ " text-align: right;\n",
546
+ " }\n",
547
+ "</style>\n",
548
+ "<table border=\"1\" class=\"dataframe\">\n",
549
+ " <thead>\n",
550
+ " <tr style=\"text-align: right;\">\n",
551
+ " <th></th>\n",
552
+ " <th>Ligand SMILES</th>\n",
553
+ " <th>Ki (nM)</th>\n",
554
+ " <th>IC50 (nM)</th>\n",
555
+ " <th>Kd (nM)</th>\n",
556
+ " <th>EC50 (nM)</th>\n",
557
+ " <th>KEGG ID of Ligand</th>\n",
558
+ " <th>seq</th>\n",
559
+ " <th>BindingDB Target Chain Sequence.1</th>\n",
560
+ " <th>BindingDB Target Chain Sequence.2</th>\n",
561
+ " <th>BindingDB Target Chain Sequence.3</th>\n",
562
+ " <th>BindingDB Target Chain Sequence.4</th>\n",
563
+ " <th>BindingDB Target Chain Sequence.5</th>\n",
564
+ " <th>BindingDB Target Chain Sequence.6</th>\n",
565
+ " <th>BindingDB Target Chain Sequence.7</th>\n",
566
+ " <th>BindingDB Target Chain Sequence.8</th>\n",
567
+ " <th>BindingDB Target Chain Sequence.9</th>\n",
568
+ " <th>BindingDB Target Chain Sequence.10</th>\n",
569
+ " <th>BindingDB Target Chain Sequence.11</th>\n",
570
+ " <th>BindingDB Target Chain Sequence.12</th>\n",
571
+ " <th>affinity_uM</th>\n",
572
+ " </tr>\n",
573
+ " </thead>\n",
574
+ " <tbody>\n",
575
+ " <tr>\n",
576
+ " <th>0</th>\n",
577
+ " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
578
+ " <td>0.24</td>\n",
579
+ " <td>None</td>\n",
580
+ " <td>None</td>\n",
581
+ " <td>None</td>\n",
582
+ " <td>None</td>\n",
583
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
584
+ " <td>None</td>\n",
585
+ " <td>None</td>\n",
586
+ " <td>None</td>\n",
587
+ " <td>None</td>\n",
588
+ " <td>None</td>\n",
589
+ " <td>None</td>\n",
590
+ " <td>None</td>\n",
591
+ " <td>None</td>\n",
592
+ " <td>None</td>\n",
593
+ " <td>None</td>\n",
594
+ " <td>None</td>\n",
595
+ " <td>None</td>\n",
596
+ " <td>0.00024</td>\n",
597
+ " </tr>\n",
598
+ " <tr>\n",
599
+ " <th>1</th>\n",
600
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
601
+ " <td>0.25</td>\n",
602
+ " <td>None</td>\n",
603
+ " <td>None</td>\n",
604
+ " <td>None</td>\n",
605
+ " <td>None</td>\n",
606
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
607
+ " <td>None</td>\n",
608
+ " <td>None</td>\n",
609
+ " <td>None</td>\n",
610
+ " <td>None</td>\n",
611
+ " <td>None</td>\n",
612
+ " <td>None</td>\n",
613
+ " <td>None</td>\n",
614
+ " <td>None</td>\n",
615
+ " <td>None</td>\n",
616
+ " <td>None</td>\n",
617
+ " <td>None</td>\n",
618
+ " <td>None</td>\n",
619
+ " <td>0.00025</td>\n",
620
+ " </tr>\n",
621
+ " <tr>\n",
622
+ " <th>2</th>\n",
623
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
624
+ " <td>0.41</td>\n",
625
+ " <td>None</td>\n",
626
+ " <td>None</td>\n",
627
+ " <td>None</td>\n",
628
+ " <td>None</td>\n",
629
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
630
+ " <td>None</td>\n",
631
+ " <td>None</td>\n",
632
+ " <td>None</td>\n",
633
+ " <td>None</td>\n",
634
+ " <td>None</td>\n",
635
+ " <td>None</td>\n",
636
+ " <td>None</td>\n",
637
+ " <td>None</td>\n",
638
+ " <td>None</td>\n",
639
+ " <td>None</td>\n",
640
+ " <td>None</td>\n",
641
+ " <td>None</td>\n",
642
+ " <td>0.00041</td>\n",
643
+ " </tr>\n",
644
+ " <tr>\n",
645
+ " <th>3</th>\n",
646
+ " <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
647
+ " <td>0.8</td>\n",
648
+ " <td>None</td>\n",
649
+ " <td>None</td>\n",
650
+ " <td>None</td>\n",
651
+ " <td>None</td>\n",
652
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
653
+ " <td>None</td>\n",
654
+ " <td>None</td>\n",
655
+ " <td>None</td>\n",
656
+ " <td>None</td>\n",
657
+ " <td>None</td>\n",
658
+ " <td>None</td>\n",
659
+ " <td>None</td>\n",
660
+ " <td>None</td>\n",
661
+ " <td>None</td>\n",
662
+ " <td>None</td>\n",
663
+ " <td>None</td>\n",
664
+ " <td>None</td>\n",
665
+ " <td>0.00080</td>\n",
666
+ " </tr>\n",
667
+ " <tr>\n",
668
+ " <th>4</th>\n",
669
+ " <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
670
+ " <td>0.99</td>\n",
671
+ " <td>None</td>\n",
672
+ " <td>None</td>\n",
673
+ " <td>None</td>\n",
674
+ " <td>None</td>\n",
675
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
676
+ " <td>None</td>\n",
677
+ " <td>None</td>\n",
678
+ " <td>None</td>\n",
679
+ " <td>None</td>\n",
680
+ " <td>None</td>\n",
681
+ " <td>None</td>\n",
682
+ " <td>None</td>\n",
683
+ " <td>None</td>\n",
684
+ " <td>None</td>\n",
685
+ " <td>None</td>\n",
686
+ " <td>None</td>\n",
687
+ " <td>None</td>\n",
688
+ " <td>0.00099</td>\n",
689
+ " </tr>\n",
690
+ " </tbody>\n",
691
+ "</table>\n",
692
+ "</div>"
693
+ ],
694
+ "text/plain": [
695
+ " Ligand SMILES Ki (nM) IC50 (nM) \\\n",
696
+ "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 0.24 None \n",
697
+ "1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... 0.25 None \n",
698
+ "2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... 0.41 None \n",
699
+ "3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... 0.8 None \n",
700
+ "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.99 None \n",
701
+ "\n",
702
+ " Kd (nM) EC50 (nM) KEGG ID of Ligand \\\n",
703
+ "0 None None None \n",
704
+ "1 None None None \n",
705
+ "2 None None None \n",
706
+ "3 None None None \n",
707
+ "4 None None None \n",
708
+ "\n",
709
+ " seq \\\n",
710
+ "0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
711
+ "1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
712
+ "2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
713
+ "3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
714
+ "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
715
+ "\n",
716
+ " BindingDB Target Chain Sequence.1 BindingDB Target Chain Sequence.2 \\\n",
717
+ "0 None None \n",
718
+ "1 None None \n",
719
+ "2 None None \n",
720
+ "3 None None \n",
721
+ "4 None None \n",
722
+ "\n",
723
+ " BindingDB Target Chain Sequence.3 BindingDB Target Chain Sequence.4 \\\n",
724
+ "0 None None \n",
725
+ "1 None None \n",
726
+ "2 None None \n",
727
+ "3 None None \n",
728
+ "4 None None \n",
729
+ "\n",
730
+ " BindingDB Target Chain Sequence.5 BindingDB Target Chain Sequence.6 \\\n",
731
+ "0 None None \n",
732
+ "1 None None \n",
733
+ "2 None None \n",
734
+ "3 None None \n",
735
+ "4 None None \n",
736
+ "\n",
737
+ " BindingDB Target Chain Sequence.7 BindingDB Target Chain Sequence.8 \\\n",
738
+ "0 None None \n",
739
+ "1 None None \n",
740
+ "2 None None \n",
741
+ "3 None None \n",
742
+ "4 None None \n",
743
+ "\n",
744
+ " BindingDB Target Chain Sequence.9 BindingDB Target Chain Sequence.10 \\\n",
745
+ "0 None None \n",
746
+ "1 None None \n",
747
+ "2 None None \n",
748
+ "3 None None \n",
749
+ "4 None None \n",
750
+ "\n",
751
+ " BindingDB Target Chain Sequence.11 BindingDB Target Chain Sequence.12 \\\n",
752
+ "0 None None \n",
753
+ "1 None None \n",
754
+ "2 None None \n",
755
+ "3 None None \n",
756
+ "4 None None \n",
757
+ "\n",
758
+ " affinity_uM \n",
759
+ "0 0.00024 \n",
760
+ "1 0.00025 \n",
761
+ "2 0.00041 \n",
762
+ "3 0.00080 \n",
763
+ "4 0.00099 "
764
+ ]
765
+ },
766
+ "execution_count": 29,
767
+ "metadata": {},
768
+ "output_type": "execute_result"
769
+ }
770
+ ],
771
+ "source": [
772
+ "df_affinity.head()"
773
+ ]
774
+ },
775
+ {
776
+ "cell_type": "code",
777
+ "execution_count": 30,
778
+ "id": "603fd298-0aa6-4097-b298-c55db013548c",
779
+ "metadata": {},
780
+ "outputs": [
781
+ {
782
+ "data": {
783
+ "text/plain": [
784
+ "2219812"
785
+ ]
786
+ },
787
+ "execution_count": 30,
788
+ "metadata": {},
789
+ "output_type": "execute_result"
790
+ }
791
+ ],
792
+ "source": [
793
+ "len(df_affinity)"
794
+ ]
795
+ },
796
+ {
797
+ "cell_type": "code",
798
+ "execution_count": 31,
799
+ "id": "d95ad9a9-d4ca-4679-8a33-235fe6e7047f",
800
+ "metadata": {},
801
+ "outputs": [
802
+ {
803
+ "data": {
804
+ "text/plain": [
805
+ "2219812"
806
+ ]
807
+ },
808
+ "execution_count": 31,
809
+ "metadata": {},
810
+ "output_type": "execute_result"
811
+ }
812
+ ],
813
+ "source": [
814
+ "len(df_affinity[~df_affinity['affinity_uM'].isnull()])"
815
+ ]
816
+ },
817
+ {
818
+ "cell_type": "code",
819
+ "execution_count": 25,
820
+ "id": "20690729",
821
+ "metadata": {},
822
+ "outputs": [],
823
+ "source": [
824
+ "import rdkit.Chem as Chem"
825
+ ]
826
+ },
827
+ {
828
+ "cell_type": "code",
829
+ "execution_count": 27,
830
+ "id": "48114dcc",
831
+ "metadata": {},
832
+ "outputs": [],
833
+ "source": [
834
+ "df_pdb = df[~df['PDB ID(s) for Ligand-Target Complex'].isnull()][['PDB ID(s) for Ligand-Target Complex','Ligand SMILES']]"
835
+ ]
836
+ },
837
+ {
838
+ "cell_type": "code",
839
+ "execution_count": 28,
840
+ "id": "caa0497c",
841
+ "metadata": {},
842
+ "outputs": [],
843
+ "source": [
844
+ "def make_canonical(smi):\n",
845
+ " return Chem.MolToSmiles(Chem.MolFromSmiles(smi))\n",
846
+ "\n",
847
+ "df_pdb['can_smiles'] = df_pdb['Ligand SMILES'].apply(make_canonical)"
848
+ ]
849
+ },
850
+ {
851
+ "cell_type": "code",
852
+ "execution_count": 29,
853
+ "id": "e82d64f3",
854
+ "metadata": {},
855
+ "outputs": [
856
+ {
857
+ "data": {
858
+ "text/html": [
859
+ "<div>\n",
860
+ "<style scoped>\n",
861
+ " .dataframe tbody tr th:only-of-type {\n",
862
+ " vertical-align: middle;\n",
863
+ " }\n",
864
+ "\n",
865
+ " .dataframe tbody tr th {\n",
866
+ " vertical-align: top;\n",
867
+ " }\n",
868
+ "\n",
869
+ " .dataframe thead th {\n",
870
+ " text-align: right;\n",
871
+ " }\n",
872
+ "</style>\n",
873
+ "<table border=\"1\" class=\"dataframe\">\n",
874
+ " <thead>\n",
875
+ " <tr style=\"text-align: right;\">\n",
876
+ " <th></th>\n",
877
+ " <th>PDB ID(s) for Ligand-Target Complex</th>\n",
878
+ " <th>Ligand SMILES</th>\n",
879
+ " <th>can_smiles</th>\n",
880
+ " </tr>\n",
881
+ " </thead>\n",
882
+ " <tbody>\n",
883
+ " <tr>\n",
884
+ " <th>0</th>\n",
885
+ " <td>2IVU</td>\n",
886
+ " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
887
+ " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
888
+ " </tr>\n",
889
+ " <tr>\n",
890
+ " <th>29</th>\n",
891
+ " <td>1HWR</td>\n",
892
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC=C)C(=O)...</td>\n",
893
+ " <td>C=CCN1C(=O)N(CC=C)[C@H](Cc2ccccc2)[C@H](O)[C@@...</td>\n",
894
+ " </tr>\n",
895
+ " <tr>\n",
896
+ " <th>34</th>\n",
897
+ " <td>6DGY,6DH1,6DH4,6DH7,3O99</td>\n",
898
+ " <td>CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O...</td>\n",
899
+ " <td>CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O...</td>\n",
900
+ " </tr>\n",
901
+ " <tr>\n",
902
+ " <th>129</th>\n",
903
+ " <td>1MES,1MEU,1MET,1BVG,1BVE,3JVW,1QBS</td>\n",
904
+ " <td>OCc1ccc(CN2[C@H](Cc3ccccc3)[C@H](O)[C@@H](O)[C...</td>\n",
905
+ " <td>O=C1N(Cc2ccc(CO)cc2)[C@H](Cc2ccccc2)[C@H](O)[C...</td>\n",
906
+ " </tr>\n",
907
+ " <tr>\n",
908
+ " <th>130</th>\n",
909
+ " <td>1MER,1DMP,1RQ9</td>\n",
910
+ " <td>Nc1cccc(CN2[C@H](Cc3ccccc3)[C@H](O)[C@@H](O)[C...</td>\n",
911
+ " <td>Nc1cccc(CN2C(=O)N(Cc3cccc(N)c3)[C@H](Cc3ccccc3...</td>\n",
912
+ " </tr>\n",
913
+ " <tr>\n",
914
+ " <th>...</th>\n",
915
+ " <td>...</td>\n",
916
+ " <td>...</td>\n",
917
+ " <td>...</td>\n",
918
+ " </tr>\n",
919
+ " <tr>\n",
920
+ " <th>2333375</th>\n",
921
+ " <td>1MUI,2RKG,2RKF,1RV7,2Q5K,2O4S,6DJ1,6DJ2,3OGQ,2...</td>\n",
922
+ " <td>CC(C)[C@H](N1CCCNC1=O)C(=O)N[C@H](C[C@H](O)[C@...</td>\n",
923
+ " <td>Cc1cccc(C)c1OCC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)...</td>\n",
924
+ " </tr>\n",
925
+ " <tr>\n",
926
+ " <th>2333376</th>\n",
927
+ " <td>4NPT,4DQH,4DQE,5E5J,3JW2,6OPU,6OPX,2HS2,2HS1,2...</td>\n",
928
+ " <td>CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]...</td>\n",
929
+ " <td>CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]...</td>\n",
930
+ " </tr>\n",
931
+ " <tr>\n",
932
+ " <th>2333380</th>\n",
933
+ " <td>6EKZ,1DY4,5FUK,6PS5</td>\n",
934
+ " <td>CC(C)NCC(O)COc1cccc2ccccc12</td>\n",
935
+ " <td>CC(C)NCC(O)COc1cccc2ccccc12</td>\n",
936
+ " </tr>\n",
937
+ " <tr>\n",
938
+ " <th>2333384</th>\n",
939
+ " <td>6EKZ,1DY4,5FUK,6PS5</td>\n",
940
+ " <td>CC(C)NCC(O)COc1cccc2ccccc12</td>\n",
941
+ " <td>CC(C)NCC(O)COc1cccc2ccccc12</td>\n",
942
+ " </tr>\n",
943
+ " <tr>\n",
944
+ " <th>2333385</th>\n",
945
+ " <td>6A60,3DCT</td>\n",
946
+ " <td>CC(C)c1onc(c1COc1ccc(\\C=C\\c2cccc(c2)C(O)=O)c(C...</td>\n",
947
+ " <td>CC(C)c1onc(-c2c(Cl)cccc2Cl)c1COc1ccc(/C=C/c2cc...</td>\n",
948
+ " </tr>\n",
949
+ " </tbody>\n",
950
+ "</table>\n",
951
+ "<p>123385 rows × 3 columns</p>\n",
952
+ "</div>"
953
+ ],
954
+ "text/plain": [
955
+ " PDB ID(s) for Ligand-Target Complex \\\n",
956
+ "0 2IVU \n",
957
+ "29 1HWR \n",
958
+ "34 6DGY,6DH1,6DH4,6DH7,3O99 \n",
959
+ "129 1MES,1MEU,1MET,1BVG,1BVE,3JVW,1QBS \n",
960
+ "130 1MER,1DMP,1RQ9 \n",
961
+ "... ... \n",
962
+ "2333375 1MUI,2RKG,2RKF,1RV7,2Q5K,2O4S,6DJ1,6DJ2,3OGQ,2... \n",
963
+ "2333376 4NPT,4DQH,4DQE,5E5J,3JW2,6OPU,6OPX,2HS2,2HS1,2... \n",
964
+ "2333380 6EKZ,1DY4,5FUK,6PS5 \n",
965
+ "2333384 6EKZ,1DY4,5FUK,6PS5 \n",
966
+ "2333385 6A60,3DCT \n",
967
+ "\n",
968
+ " Ligand SMILES \\\n",
969
+ "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 \n",
970
+ "29 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC=C)C(=O)... \n",
971
+ "34 CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O... \n",
972
+ "129 OCc1ccc(CN2[C@H](Cc3ccccc3)[C@H](O)[C@@H](O)[C... \n",
973
+ "130 Nc1cccc(CN2[C@H](Cc3ccccc3)[C@H](O)[C@@H](O)[C... \n",
974
+ "... ... \n",
975
+ "2333375 CC(C)[C@H](N1CCCNC1=O)C(=O)N[C@H](C[C@H](O)[C@... \n",
976
+ "2333376 CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]... \n",
977
+ "2333380 CC(C)NCC(O)COc1cccc2ccccc12 \n",
978
+ "2333384 CC(C)NCC(O)COc1cccc2ccccc12 \n",
979
+ "2333385 CC(C)c1onc(c1COc1ccc(\\C=C\\c2cccc(c2)C(O)=O)c(C... \n",
980
+ "\n",
981
+ " can_smiles \n",
982
+ "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 \n",
983
+ "29 C=CCN1C(=O)N(CC=C)[C@H](Cc2ccccc2)[C@H](O)[C@@... \n",
984
+ "34 CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O... \n",
985
+ "129 O=C1N(Cc2ccc(CO)cc2)[C@H](Cc2ccccc2)[C@H](O)[C... \n",
986
+ "130 Nc1cccc(CN2C(=O)N(Cc3cccc(N)c3)[C@H](Cc3ccccc3... \n",
987
+ "... ... \n",
988
+ "2333375 Cc1cccc(C)c1OCC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)... \n",
989
+ "2333376 CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]... \n",
990
+ "2333380 CC(C)NCC(O)COc1cccc2ccccc12 \n",
991
+ "2333384 CC(C)NCC(O)COc1cccc2ccccc12 \n",
992
+ "2333385 CC(C)c1onc(-c2c(Cl)cccc2Cl)c1COc1ccc(/C=C/c2cc... \n",
993
+ "\n",
994
+ "[123385 rows x 3 columns]"
995
+ ]
996
+ },
997
+ "execution_count": 29,
998
+ "metadata": {},
999
+ "output_type": "execute_result"
1000
+ }
1001
+ ],
1002
+ "source": [
1003
+ "df_pdb"
1004
+ ]
1005
+ },
1006
+ {
1007
+ "cell_type": "code",
1008
+ "execution_count": null,
1009
+ "id": "593c9aec",
1010
+ "metadata": {},
1011
+ "outputs": [],
1012
+ "source": []
1013
+ }
1014
+ ],
1015
+ "metadata": {
1016
+ "kernelspec": {
1017
+ "display_name": "Python 3",
1018
+ "language": "python",
1019
+ "name": "python3"
1020
+ },
1021
+ "language_info": {
1022
+ "codemirror_mode": {
1023
+ "name": "ipython",
1024
+ "version": 3
1025
+ },
1026
+ "file_extension": ".py",
1027
+ "mimetype": "text/x-python",
1028
+ "name": "python",
1029
+ "nbconvert_exporter": "python",
1030
+ "pygments_lexer": "ipython3",
1031
+ "version": "3.9.4"
1032
+ }
1033
+ },
1034
+ "nbformat": 4,
1035
+ "nbformat_minor": 5
1036
+ }
combine_dbs.ipynb CHANGED
@@ -238,7 +238,7 @@
238
  },
239
  {
240
  "cell_type": "code",
241
- "execution_count": 10,
242
  "id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
243
  "metadata": {},
244
  "outputs": [],
@@ -249,7 +249,7 @@
249
  },
250
  {
251
  "cell_type": "code",
252
- "execution_count": 11,
253
  "id": "25553199-1715-40fb-9260-427bdd6c3706",
254
  "metadata": {},
255
  "outputs": [
@@ -381,7 +381,7 @@
381
  "[25425 rows x 3 columns]"
382
  ]
383
  },
384
- "execution_count": 11,
385
  "metadata": {},
386
  "output_type": "execute_result"
387
  }
@@ -392,7 +392,7 @@
392
  },
393
  {
394
  "cell_type": "code",
395
- "execution_count": 12,
396
  "id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
397
  "metadata": {},
398
  "outputs": [],
@@ -403,7 +403,7 @@
403
  },
404
  {
405
  "cell_type": "code",
406
- "execution_count": 13,
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": 13,
539
  "metadata": {},
540
  "output_type": "execute_result"
541
  }
@@ -546,7 +546,7 @@
546
  },
547
  {
548
  "cell_type": "code",
549
- "execution_count": 14,
550
  "id": "195f92db-fe06-4d03-8500-8d6c310a3347",
551
  "metadata": {},
552
  "outputs": [],
@@ -556,17 +556,17 @@
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
  }
@@ -577,7 +577,7 @@
577
  },
578
  {
579
  "cell_type": "code",
580
- "execution_count": 16,
581
  "id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
582
  "metadata": {},
583
  "outputs": [
@@ -607,7 +607,7 @@
607
  },
608
  {
609
  "cell_type": "code",
610
- "execution_count": 18,
611
  "id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
612
  "metadata": {},
613
  "outputs": [],
@@ -617,7 +617,7 @@
617
  },
618
  {
619
  "cell_type": "code",
620
- "execution_count": 7,
621
  "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
622
  "metadata": {},
623
  "outputs": [],
@@ -627,7 +627,28 @@
627
  },
628
  {
629
  "cell_type": "code",
630
- "execution_count": 2,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
631
  "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
632
  "metadata": {},
633
  "outputs": [],
@@ -638,17 +659,17 @@
638
  },
639
  {
640
  "cell_type": "code",
641
- "execution_count": 3,
642
  "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
643
  "metadata": {},
644
  "outputs": [
645
  {
646
  "data": {
647
  "text/plain": [
648
- "2568079"
649
  ]
650
  },
651
- "execution_count": 3,
652
  "metadata": {},
653
  "output_type": "execute_result"
654
  }
@@ -659,7 +680,7 @@
659
  },
660
  {
661
  "cell_type": "code",
662
- "execution_count": 4,
663
  "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
664
  "metadata": {},
665
  "outputs": [],
@@ -670,7 +691,7 @@
670
  },
671
  {
672
  "cell_type": "code",
673
- "execution_count": 8,
674
  "id": "80c15210-1af3-436e-970b-f81fc596fb41",
675
  "metadata": {},
676
  "outputs": [],
@@ -680,7 +701,7 @@
680
  },
681
  {
682
  "cell_type": "code",
683
- "execution_count": 9,
684
  "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
685
  "metadata": {},
686
  "outputs": [
@@ -696,7 +717,7 @@
696
  "dtype: object"
697
  ]
698
  },
699
- "execution_count": 9,
700
  "metadata": {},
701
  "output_type": "execute_result"
702
  }
@@ -707,7 +728,7 @@
707
  },
708
  {
709
  "cell_type": "code",
710
- "execution_count": 10,
711
  "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
712
  "metadata": {},
713
  "outputs": [],
@@ -717,7 +738,7 @@
717
  },
718
  {
719
  "cell_type": "code",
720
- "execution_count": 11,
721
  "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
722
  "metadata": {},
723
  "outputs": [
@@ -827,7 +848,7 @@
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",
@@ -839,7 +860,7 @@
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",
@@ -851,7 +872,7 @@
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",
@@ -863,7 +884,7 @@
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",
@@ -875,7 +896,7 @@
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",
@@ -888,7 +909,7 @@
888
  " </tr>\n",
889
  " </tbody>\n",
890
  "</table>\n",
891
- "<p>2568079 rows × 9 columns</p>\n",
892
  "</div>"
893
  ],
894
  "text/plain": [
@@ -899,11 +920,11 @@
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",
@@ -912,11 +933,11 @@
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",
@@ -925,16 +946,16 @@
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": 11,
938
  "metadata": {},
939
  "output_type": "execute_result"
940
  }
@@ -945,7 +966,7 @@
945
  },
946
  {
947
  "cell_type": "code",
948
- "execution_count": 12,
949
  "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
950
  "metadata": {},
951
  "outputs": [
@@ -955,7 +976,7 @@
955
  "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
956
  ]
957
  },
958
- "execution_count": 12,
959
  "metadata": {},
960
  "output_type": "execute_result"
961
  }
@@ -966,7 +987,7 @@
966
  },
967
  {
968
  "cell_type": "code",
969
- "execution_count": 13,
970
  "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
971
  "metadata": {},
972
  "outputs": [],
@@ -976,7 +997,7 @@
976
  },
977
  {
978
  "cell_type": "code",
979
- "execution_count": 14,
980
  "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
981
  "metadata": {},
982
  "outputs": [
@@ -986,7 +1007,7 @@
986
  "Index(['smiles', 'affinity_uM'], dtype='object')"
987
  ]
988
  },
989
- "execution_count": 14,
990
  "metadata": {},
991
  "output_type": "execute_result"
992
  }
@@ -997,7 +1018,7 @@
997
  },
998
  {
999
  "cell_type": "code",
1000
- "execution_count": 15,
1001
  "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
1002
  "metadata": {},
1003
  "outputs": [],
@@ -1008,7 +1029,7 @@
1008
  },
1009
  {
1010
  "cell_type": "code",
1011
- "execution_count": 31,
1012
  "id": "6a704c5e-68a6-418f-bcad-8688a13ca1d6",
1013
  "metadata": {},
1014
  "outputs": [],
@@ -1018,7 +1039,7 @@
1018
  },
1019
  {
1020
  "cell_type": "code",
1021
- "execution_count": 32,
1022
  "id": "0cad3882-975d-4693-aad1-63ec26646bd0",
1023
  "metadata": {},
1024
  "outputs": [
@@ -1037,7 +1058,7 @@
1037
  },
1038
  {
1039
  "cell_type": "code",
1040
- "execution_count": 33,
1041
  "id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
1042
  "metadata": {},
1043
  "outputs": [
@@ -1112,35 +1133,35 @@
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",
@@ -1148,7 +1169,7 @@
1148
  " </tr>\n",
1149
  " </tbody>\n",
1150
  "</table>\n",
1151
- "<p>1929148 rows × 4 columns</p>\n",
1152
  "</div>"
1153
  ],
1154
  "text/plain": [
@@ -1159,11 +1180,11 @@
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",
@@ -1172,11 +1193,11 @@
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",
@@ -1185,16 +1206,16 @@
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
  }
@@ -1205,7 +1226,7 @@
1205
  },
1206
  {
1207
  "cell_type": "code",
1208
- "execution_count": 34,
1209
  "id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
1210
  "metadata": {},
1211
  "outputs": [],
@@ -1215,7 +1236,7 @@
1215
  },
1216
  {
1217
  "cell_type": "code",
1218
- "execution_count": 35,
1219
  "id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
1220
  "metadata": {},
1221
  "outputs": [],
@@ -1230,7 +1251,7 @@
1230
  },
1231
  {
1232
  "cell_type": "code",
1233
- "execution_count": 36,
1234
  "id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
1235
  "metadata": {},
1236
  "outputs": [],
@@ -1240,7 +1261,7 @@
1240
  },
1241
  {
1242
  "cell_type": "code",
1243
- "execution_count": 37,
1244
  "id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
1245
  "metadata": {},
1246
  "outputs": [],
@@ -1250,7 +1271,7 @@
1250
  },
1251
  {
1252
  "cell_type": "code",
1253
- "execution_count": 23,
1254
  "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
1255
  "metadata": {},
1256
  "outputs": [],
@@ -1260,7 +1281,7 @@
1260
  },
1261
  {
1262
  "cell_type": "code",
1263
- "execution_count": 24,
1264
  "id": "0c027988-0b44-4010-ad61-7d70eead1654",
1265
  "metadata": {},
1266
  "outputs": [],
@@ -1270,7 +1291,7 @@
1270
  },
1271
  {
1272
  "cell_type": "code",
1273
- "execution_count": 25,
1274
  "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
1275
  "metadata": {},
1276
  "outputs": [],
@@ -1280,17 +1301,17 @@
1280
  },
1281
  {
1282
  "cell_type": "code",
1283
- "execution_count": 26,
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": 26,
1294
  "metadata": {},
1295
  "output_type": "execute_result"
1296
  }
@@ -1301,7 +1322,7 @@
1301
  },
1302
  {
1303
  "cell_type": "code",
1304
- "execution_count": 28,
1305
  "id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
1306
  "metadata": {},
1307
  "outputs": [],
@@ -1311,18 +1332,18 @@
1311
  },
1312
  {
1313
  "cell_type": "code",
1314
- "execution_count": 50,
1315
  "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
1316
  "metadata": {},
1317
  "outputs": [],
1318
  "source": [
1319
  "#df.to_parquet('data/all.parquet')\n",
1320
- "df = pd.read_parquet('data/all.parquet')"
1321
  ]
1322
  },
1323
  {
1324
  "cell_type": "code",
1325
- "execution_count": 30,
1326
  "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
1327
  "metadata": {},
1328
  "outputs": [
@@ -1334,7 +1355,7 @@
1334
  " dtype='object')"
1335
  ]
1336
  },
1337
- "execution_count": 30,
1338
  "metadata": {},
1339
  "output_type": "execute_result"
1340
  }
@@ -1345,13 +1366,13 @@
1345
  },
1346
  {
1347
  "cell_type": "code",
1348
- "execution_count": 31,
1349
  "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
1350
  "metadata": {},
1351
  "outputs": [
1352
  {
1353
  "data": {
1354
- "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",
1355
  "text/plain": [
1356
  "<Figure size 432x288 with 1 Axes>"
1357
  ]
@@ -1371,17 +1392,17 @@
1371
  },
1372
  {
1373
  "cell_type": "code",
1374
- "execution_count": 32,
1375
  "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
1376
  "metadata": {},
1377
  "outputs": [
1378
  {
1379
  "data": {
1380
  "text/plain": [
1381
- "1927202"
1382
  ]
1383
  },
1384
- "execution_count": 32,
1385
  "metadata": {},
1386
  "output_type": "execute_result"
1387
  }
@@ -1392,7 +1413,7 @@
1392
  },
1393
  {
1394
  "cell_type": "code",
1395
- "execution_count": 34,
1396
  "id": "3af855d3-a943-4574-985c-540d3f6b6f80",
1397
  "metadata": {},
1398
  "outputs": [
@@ -1403,13 +1424,13 @@
1403
  " 'with_std': True,\n",
1404
  " 'copy': True,\n",
1405
  " 'n_features_in_': 1,\n",
1406
- " 'n_samples_seen_': 1927202,\n",
1407
- " 'mean_': array([6.51286529]),\n",
1408
- " 'var_': array([2.4379995]),\n",
1409
- " 'scale_': array([1.56140946])}"
1410
  ]
1411
  },
1412
- "execution_count": 34,
1413
  "metadata": {},
1414
  "output_type": "execute_result"
1415
  }
@@ -1420,7 +1441,7 @@
1420
  },
1421
  {
1422
  "cell_type": "code",
1423
- "execution_count": 27,
1424
  "id": "15f8d5b9-37d5-453e-a6df-df6510cc5c81",
1425
  "metadata": {},
1426
  "outputs": [],
@@ -1450,7 +1471,7 @@
1450
  },
1451
  {
1452
  "cell_type": "code",
1453
- "execution_count": 35,
1454
  "id": "8dec95dc-a014-4d39-ae51-8de981173573",
1455
  "metadata": {},
1456
  "outputs": [],
@@ -1461,7 +1482,7 @@
1461
  },
1462
  {
1463
  "cell_type": "code",
1464
- "execution_count": 36,
1465
  "id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
1466
  "metadata": {},
1467
  "outputs": [],
@@ -1471,17 +1492,17 @@
1471
  },
1472
  {
1473
  "cell_type": "code",
1474
- "execution_count": 37,
1475
  "id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
1476
  "metadata": {},
1477
  "outputs": [
1478
  {
1479
  "data": {
1480
  "text/plain": [
1481
- "1926799"
1482
  ]
1483
  },
1484
- "execution_count": 37,
1485
  "metadata": {},
1486
  "output_type": "execute_result"
1487
  }
@@ -1492,7 +1513,7 @@
1492
  },
1493
  {
1494
  "cell_type": "code",
1495
- "execution_count": 47,
1496
  "id": "47966268-c97c-4bd9-9c90-eb568249f2ef",
1497
  "metadata": {},
1498
  "outputs": [],
@@ -1510,7 +1531,7 @@
1510
  },
1511
  {
1512
  "cell_type": "code",
1513
- "execution_count": 40,
1514
  "id": "c0d250a3-5680-446c-9c98-7d6623643304",
1515
  "metadata": {},
1516
  "outputs": [],
@@ -1521,7 +1542,7 @@
1521
  },
1522
  {
1523
  "cell_type": "code",
1524
- "execution_count": 44,
1525
  "id": "0c7c0b26-1f2a-4b80-8117-f1e02719aac9",
1526
  "metadata": {},
1527
  "outputs": [
@@ -1529,14 +1550,14 @@
1529
  "name": "stderr",
1530
  "output_type": "stream",
1531
  "text": [
1532
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1533
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1534
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1535
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1536
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1537
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1538
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1539
- "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n"
1540
  ]
1541
  }
1542
  ],
@@ -1547,7 +1568,7 @@
1547
  },
1548
  {
1549
  "cell_type": "code",
1550
- "execution_count": 63,
1551
  "id": "258f593c-1cba-45cb-936e-8c1360075926",
1552
  "metadata": {},
1553
  "outputs": [],
@@ -1557,7 +1578,7 @@
1557
  },
1558
  {
1559
  "cell_type": "code",
1560
- "execution_count": 66,
1561
  "id": "ee3fa0bc-9ad3-4ea7-9393-cbc7504f634c",
1562
  "metadata": {},
1563
  "outputs": [],
@@ -1568,10 +1589,12 @@
1568
  {
1569
  "cell_type": "code",
1570
  "execution_count": null,
1571
- "id": "b068dbaa-6d77-402d-ab9b-fb4f266dc854",
1572
  "metadata": {},
1573
  "outputs": [],
1574
- "source": []
 
 
1575
  }
1576
  ],
1577
  "metadata": {
 
238
  },
239
  {
240
  "cell_type": "code",
241
+ "execution_count": 7,
242
  "id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
243
  "metadata": {},
244
  "outputs": [],
 
249
  },
250
  {
251
  "cell_type": "code",
252
+ "execution_count": 8,
253
  "id": "25553199-1715-40fb-9260-427bdd6c3706",
254
  "metadata": {},
255
  "outputs": [
 
381
  "[25425 rows x 3 columns]"
382
  ]
383
  },
384
+ "execution_count": 8,
385
  "metadata": {},
386
  "output_type": "execute_result"
387
  }
 
392
  },
393
  {
394
  "cell_type": "code",
395
+ "execution_count": 9,
396
  "id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
397
  "metadata": {},
398
  "outputs": [],
 
403
  },
404
  {
405
  "cell_type": "code",
406
+ "execution_count": 10,
407
  "id": "cee93018-601d-458b-af44-bd978da7a2bc",
408
  "metadata": {},
409
  "outputs": [
 
535
  "[13645 rows x 3 columns]"
536
  ]
537
  },
538
+ "execution_count": 10,
539
  "metadata": {},
540
  "output_type": "execute_result"
541
  }
 
546
  },
547
  {
548
  "cell_type": "code",
549
+ "execution_count": 11,
550
  "id": "195f92db-fe06-4d03-8500-8d6c310a3347",
551
  "metadata": {},
552
  "outputs": [],
 
556
  },
557
  {
558
  "cell_type": "code",
559
+ "execution_count": 12,
560
  "id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
561
  "metadata": {},
562
  "outputs": [
563
  {
564
  "data": {
565
  "text/plain": [
566
+ "2283641"
567
  ]
568
  },
569
+ "execution_count": 12,
570
  "metadata": {},
571
  "output_type": "execute_result"
572
  }
 
577
  },
578
  {
579
  "cell_type": "code",
580
+ "execution_count": 13,
581
  "id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
582
  "metadata": {},
583
  "outputs": [
 
607
  },
608
  {
609
  "cell_type": "code",
610
+ "execution_count": 16,
611
  "id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
612
  "metadata": {},
613
  "outputs": [],
 
617
  },
618
  {
619
  "cell_type": "code",
620
+ "execution_count": 17,
621
  "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
622
  "metadata": {},
623
  "outputs": [],
 
627
  },
628
  {
629
  "cell_type": "code",
630
+ "execution_count": 18,
631
+ "id": "399f4ace-6dc3-441f-972a-f7b3a103e239",
632
+ "metadata": {},
633
+ "outputs": [
634
+ {
635
+ "data": {
636
+ "text/plain": [
637
+ "2283641"
638
+ ]
639
+ },
640
+ "execution_count": 18,
641
+ "metadata": {},
642
+ "output_type": "execute_result"
643
+ }
644
+ ],
645
+ "source": [
646
+ "len(df_all)"
647
+ ]
648
+ },
649
+ {
650
+ "cell_type": "code",
651
+ "execution_count": 19,
652
  "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
653
  "metadata": {},
654
  "outputs": [],
 
659
  },
660
  {
661
  "cell_type": "code",
662
+ "execution_count": 25,
663
  "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
664
  "metadata": {},
665
  "outputs": [
666
  {
667
  "data": {
668
  "text/plain": [
669
+ "2277323"
670
  ]
671
  },
672
+ "execution_count": 25,
673
  "metadata": {},
674
  "output_type": "execute_result"
675
  }
 
680
  },
681
  {
682
  "cell_type": "code",
683
+ "execution_count": 26,
684
  "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
685
  "metadata": {},
686
  "outputs": [],
 
691
  },
692
  {
693
  "cell_type": "code",
694
+ "execution_count": 27,
695
  "id": "80c15210-1af3-436e-970b-f81fc596fb41",
696
  "metadata": {},
697
  "outputs": [],
 
701
  },
702
  {
703
  "cell_type": "code",
704
+ "execution_count": 28,
705
  "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
706
  "metadata": {},
707
  "outputs": [
 
717
  "dtype: object"
718
  ]
719
  },
720
+ "execution_count": 28,
721
  "metadata": {},
722
  "output_type": "execute_result"
723
  }
 
728
  },
729
  {
730
  "cell_type": "code",
731
+ "execution_count": 29,
732
  "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
733
  "metadata": {},
734
  "outputs": [],
 
738
  },
739
  {
740
  "cell_type": "code",
741
+ "execution_count": 30,
742
  "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
743
  "metadata": {},
744
  "outputs": [
 
848
  " <td>...</td>\n",
849
  " </tr>\n",
850
  " <tr>\n",
851
+ " <th>2277318</th>\n",
852
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
853
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
854
  " <td>0.0045</td>\n",
 
860
  " <td>252</td>\n",
861
  " </tr>\n",
862
  " <tr>\n",
863
+ " <th>2277319</th>\n",
864
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
865
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
866
  " <td>0.0045</td>\n",
 
872
  " <td>252</td>\n",
873
  " </tr>\n",
874
  " <tr>\n",
875
+ " <th>2277320</th>\n",
876
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
877
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
878
  " <td>125.0000</td>\n",
 
884
  " <td>124</td>\n",
885
  " </tr>\n",
886
  " <tr>\n",
887
+ " <th>2277321</th>\n",
888
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
889
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
890
  " <td>2.0000</td>\n",
 
896
  " <td>204</td>\n",
897
  " </tr>\n",
898
  " <tr>\n",
899
+ " <th>2277322</th>\n",
900
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
901
  " <td>CC[Se]C(=N)N</td>\n",
902
  " <td>0.0390</td>\n",
 
909
  " </tr>\n",
910
  " </tbody>\n",
911
  "</table>\n",
912
+ "<p>2277323 rows × 9 columns</p>\n",
913
  "</div>"
914
  ],
915
  "text/plain": [
 
920
  "3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
921
  "4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
922
  "... ... \n",
923
+ "2277318 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
924
+ "2277319 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
925
+ "2277320 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
926
+ "2277321 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
927
+ "2277322 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
928
  "\n",
929
  " smiles affinity_uM \\\n",
930
  "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
 
933
  "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
934
  "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
935
  "... ... ... \n",
936
+ "2277318 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
937
+ "2277319 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
938
+ "2277320 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
939
+ "2277321 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
940
+ "2277322 CC[Se]C(=N)N 0.0390 \n",
941
  "\n",
942
  " 0 1 2 3 4 5 \n",
943
  "0 0 0 805306368 272271360 890245320 136 \n",
 
946
  "3 0 6685696 2033191680 1345701844 2133187096 220 \n",
947
  "4 1048576 1107427332 2109513024 4081492984 4026260436 252 \n",
948
  "... ... ... ... ... ... ... \n",
949
+ "2277318 65536 393216 964698368 369403648 4284858000 252 \n",
950
+ "2277319 65536 393216 964698368 369403648 4284858000 252 \n",
951
+ "2277320 67108864 1115688962 1771869508 4018431718 3744193341 124 \n",
952
+ "2277321 2097152 137216 958148868 1746307978 2067783280 204 \n",
953
+ "2277322 16 6144 537396736 2170880 1510015504 192 \n",
954
  "\n",
955
+ "[2277323 rows x 9 columns]"
956
  ]
957
  },
958
+ "execution_count": 30,
959
  "metadata": {},
960
  "output_type": "execute_result"
961
  }
 
966
  },
967
  {
968
  "cell_type": "code",
969
+ "execution_count": 31,
970
  "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
971
  "metadata": {},
972
  "outputs": [
 
976
  "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
977
  ]
978
  },
979
+ "execution_count": 31,
980
  "metadata": {},
981
  "output_type": "execute_result"
982
  }
 
987
  },
988
  {
989
  "cell_type": "code",
990
+ "execution_count": 32,
991
  "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
992
  "metadata": {},
993
  "outputs": [],
 
997
  },
998
  {
999
  "cell_type": "code",
1000
+ "execution_count": 33,
1001
  "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
1002
  "metadata": {},
1003
  "outputs": [
 
1007
  "Index(['smiles', 'affinity_uM'], dtype='object')"
1008
  ]
1009
  },
1010
+ "execution_count": 33,
1011
  "metadata": {},
1012
  "output_type": "execute_result"
1013
  }
 
1018
  },
1019
  {
1020
  "cell_type": "code",
1021
+ "execution_count": 34,
1022
  "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
1023
  "metadata": {},
1024
  "outputs": [],
 
1029
  },
1030
  {
1031
  "cell_type": "code",
1032
+ "execution_count": 36,
1033
  "id": "6a704c5e-68a6-418f-bcad-8688a13ca1d6",
1034
  "metadata": {},
1035
  "outputs": [],
 
1039
  },
1040
  {
1041
  "cell_type": "code",
1042
+ "execution_count": 37,
1043
  "id": "0cad3882-975d-4693-aad1-63ec26646bd0",
1044
  "metadata": {},
1045
  "outputs": [
 
1058
  },
1059
  {
1060
  "cell_type": "code",
1061
+ "execution_count": 38,
1062
  "id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
1063
  "metadata": {},
1064
  "outputs": [
 
1133
  " <td>...</td>\n",
1134
  " </tr>\n",
1135
  " <tr>\n",
1136
+ " <th>1838495</th>\n",
1137
  " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1138
  " <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
1139
  " <td>8.0000</td>\n",
1140
  " <td>5.096910</td>\n",
1141
  " </tr>\n",
1142
  " <tr>\n",
1143
+ " <th>1838496</th>\n",
1144
  " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1145
  " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
1146
  " <td>8.0000</td>\n",
1147
  " <td>5.096910</td>\n",
1148
  " </tr>\n",
1149
  " <tr>\n",
1150
+ " <th>1838497</th>\n",
1151
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
1152
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
1153
  " <td>0.0045</td>\n",
1154
  " <td>8.346787</td>\n",
1155
  " </tr>\n",
1156
  " <tr>\n",
1157
+ " <th>1838498</th>\n",
1158
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
1159
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
1160
  " <td>2.0000</td>\n",
1161
  " <td>5.698970</td>\n",
1162
  " </tr>\n",
1163
  " <tr>\n",
1164
+ " <th>1838499</th>\n",
1165
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
1166
  " <td>CC[Se]C(=N)N</td>\n",
1167
  " <td>0.0390</td>\n",
 
1169
  " </tr>\n",
1170
  " </tbody>\n",
1171
  "</table>\n",
1172
+ "<p>1838500 rows × 4 columns</p>\n",
1173
  "</div>"
1174
  ],
1175
  "text/plain": [
 
1180
  "3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
1181
  "4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
1182
  "... ... \n",
1183
+ "1838495 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1184
+ "1838496 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1185
+ "1838497 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
1186
+ "1838498 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
1187
+ "1838499 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
1188
  "\n",
1189
  " smiles affinity_uM \\\n",
1190
  "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
 
1193
  "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
1194
  "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
1195
  "... ... ... \n",
1196
+ "1838495 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.0000 \n",
1197
+ "1838496 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.0000 \n",
1198
+ "1838497 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
1199
+ "1838498 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
1200
+ "1838499 CC[Se]C(=N)N 0.0390 \n",
1201
  "\n",
1202
  " neg_log10_affinity_M \n",
1203
  "0 7.585027 \n",
 
1206
  "3 5.191789 \n",
1207
  "4 6.732828 \n",
1208
  "... ... \n",
1209
+ "1838495 5.096910 \n",
1210
+ "1838496 5.096910 \n",
1211
+ "1838497 8.346787 \n",
1212
+ "1838498 5.698970 \n",
1213
+ "1838499 7.408935 \n",
1214
  "\n",
1215
+ "[1838500 rows x 4 columns]"
1216
  ]
1217
  },
1218
+ "execution_count": 38,
1219
  "metadata": {},
1220
  "output_type": "execute_result"
1221
  }
 
1226
  },
1227
  {
1228
  "cell_type": "code",
1229
+ "execution_count": 52,
1230
  "id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
1231
  "metadata": {},
1232
  "outputs": [],
 
1236
  },
1237
  {
1238
  "cell_type": "code",
1239
+ "execution_count": 53,
1240
  "id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
1241
  "metadata": {},
1242
  "outputs": [],
 
1251
  },
1252
  {
1253
  "cell_type": "code",
1254
+ "execution_count": 54,
1255
  "id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
1256
  "metadata": {},
1257
  "outputs": [],
 
1261
  },
1262
  {
1263
  "cell_type": "code",
1264
+ "execution_count": 55,
1265
  "id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
1266
  "metadata": {},
1267
  "outputs": [],
 
1271
  },
1272
  {
1273
  "cell_type": "code",
1274
+ "execution_count": 56,
1275
  "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
1276
  "metadata": {},
1277
  "outputs": [],
 
1281
  },
1282
  {
1283
  "cell_type": "code",
1284
+ "execution_count": 57,
1285
  "id": "0c027988-0b44-4010-ad61-7d70eead1654",
1286
  "metadata": {},
1287
  "outputs": [],
 
1291
  },
1292
  {
1293
  "cell_type": "code",
1294
+ "execution_count": 58,
1295
  "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
1296
  "metadata": {},
1297
  "outputs": [],
 
1301
  },
1302
  {
1303
  "cell_type": "code",
1304
+ "execution_count": 59,
1305
  "id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
1306
  "metadata": {},
1307
  "outputs": [
1308
  {
1309
  "data": {
1310
  "text/plain": [
1311
+ "(array([6.50604534]), array([2.43319576]))"
1312
  ]
1313
  },
1314
+ "execution_count": 59,
1315
  "metadata": {},
1316
  "output_type": "execute_result"
1317
  }
 
1322
  },
1323
  {
1324
  "cell_type": "code",
1325
+ "execution_count": 60,
1326
  "id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
1327
  "metadata": {},
1328
  "outputs": [],
 
1332
  },
1333
  {
1334
  "cell_type": "code",
1335
+ "execution_count": 61,
1336
  "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
1337
  "metadata": {},
1338
  "outputs": [],
1339
  "source": [
1340
  "#df.to_parquet('data/all.parquet')\n",
1341
+ "#df = pd.read_parquet('data/all.parquet')"
1342
  ]
1343
  },
1344
  {
1345
  "cell_type": "code",
1346
+ "execution_count": 62,
1347
  "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
1348
  "metadata": {},
1349
  "outputs": [
 
1355
  " dtype='object')"
1356
  ]
1357
  },
1358
+ "execution_count": 62,
1359
  "metadata": {},
1360
  "output_type": "execute_result"
1361
  }
 
1366
  },
1367
  {
1368
  "cell_type": "code",
1369
+ "execution_count": 63,
1370
  "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
1371
  "metadata": {},
1372
  "outputs": [
1373
  {
1374
  "data": {
1375
+ "image/png": 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\n",
1376
  "text/plain": [
1377
  "<Figure size 432x288 with 1 Axes>"
1378
  ]
 
1392
  },
1393
  {
1394
  "cell_type": "code",
1395
+ "execution_count": 64,
1396
  "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
1397
  "metadata": {},
1398
  "outputs": [
1399
  {
1400
  "data": {
1401
  "text/plain": [
1402
+ "1836729"
1403
  ]
1404
  },
1405
+ "execution_count": 64,
1406
  "metadata": {},
1407
  "output_type": "execute_result"
1408
  }
 
1413
  },
1414
  {
1415
  "cell_type": "code",
1416
+ "execution_count": 65,
1417
  "id": "3af855d3-a943-4574-985c-540d3f6b6f80",
1418
  "metadata": {},
1419
  "outputs": [
 
1424
  " 'with_std': True,\n",
1425
  " 'copy': True,\n",
1426
  " 'n_features_in_': 1,\n",
1427
+ " 'n_samples_seen_': 1836729,\n",
1428
+ " 'mean_': array([6.50604534]),\n",
1429
+ " 'var_': array([2.43319576]),\n",
1430
+ " 'scale_': array([1.55987043])}"
1431
  ]
1432
  },
1433
+ "execution_count": 65,
1434
  "metadata": {},
1435
  "output_type": "execute_result"
1436
  }
 
1441
  },
1442
  {
1443
  "cell_type": "code",
1444
+ "execution_count": 66,
1445
  "id": "15f8d5b9-37d5-453e-a6df-df6510cc5c81",
1446
  "metadata": {},
1447
  "outputs": [],
 
1471
  },
1472
  {
1473
  "cell_type": "code",
1474
+ "execution_count": 67,
1475
  "id": "8dec95dc-a014-4d39-ae51-8de981173573",
1476
  "metadata": {},
1477
  "outputs": [],
 
1482
  },
1483
  {
1484
  "cell_type": "code",
1485
+ "execution_count": 68,
1486
  "id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
1487
  "metadata": {},
1488
  "outputs": [],
 
1492
  },
1493
  {
1494
  "cell_type": "code",
1495
+ "execution_count": 69,
1496
  "id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
1497
  "metadata": {},
1498
  "outputs": [
1499
  {
1500
  "data": {
1501
  "text/plain": [
1502
+ "1836326"
1503
  ]
1504
  },
1505
+ "execution_count": 69,
1506
  "metadata": {},
1507
  "output_type": "execute_result"
1508
  }
 
1513
  },
1514
  {
1515
  "cell_type": "code",
1516
+ "execution_count": 70,
1517
  "id": "47966268-c97c-4bd9-9c90-eb568249f2ef",
1518
  "metadata": {},
1519
  "outputs": [],
 
1531
  },
1532
  {
1533
  "cell_type": "code",
1534
+ "execution_count": 71,
1535
  "id": "c0d250a3-5680-446c-9c98-7d6623643304",
1536
  "metadata": {},
1537
  "outputs": [],
 
1542
  },
1543
  {
1544
  "cell_type": "code",
1545
+ "execution_count": 72,
1546
  "id": "0c7c0b26-1f2a-4b80-8117-f1e02719aac9",
1547
  "metadata": {},
1548
  "outputs": [
 
1550
  "name": "stderr",
1551
  "output_type": "stream",
1552
  "text": [
1553
+ "RDKit WARNING: [13:20:36] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1554
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1555
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1556
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1557
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1558
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1559
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
1560
+ "RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n"
1561
  ]
1562
  }
1563
  ],
 
1568
  },
1569
  {
1570
  "cell_type": "code",
1571
+ "execution_count": 74,
1572
  "id": "258f593c-1cba-45cb-936e-8c1360075926",
1573
  "metadata": {},
1574
  "outputs": [],
 
1578
  },
1579
  {
1580
  "cell_type": "code",
1581
+ "execution_count": 75,
1582
  "id": "ee3fa0bc-9ad3-4ea7-9393-cbc7504f634c",
1583
  "metadata": {},
1584
  "outputs": [],
 
1589
  {
1590
  "cell_type": "code",
1591
  "execution_count": null,
1592
+ "id": "5c12fedc-4236-4587-a744-c0c9ec21ceaa",
1593
  "metadata": {},
1594
  "outputs": [],
1595
+ "source": [
1596
+ "l"
1597
+ ]
1598
  }
1599
  ],
1600
  "metadata": {