update notebooks
Browse files- bindingdb_single.ipynb +1036 -0
- combine_dbs.ipynb +148 -125
bindingdb_single.ipynb
ADDED
@@ -0,0 +1,1036 @@
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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 |
+
},
|
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+
{
|
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 |
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"allseq = ['BindingDB Target Chain Sequence']+['BindingDB Target Chain Sequence.{}'.format(j) for j in range(1,13)]"
|
32 |
+
]
|
33 |
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},
|
34 |
+
{
|
35 |
+
"cell_type": "code",
|
36 |
+
"execution_count": 4,
|
37 |
+
"id": "54f0721e-1e36-48cc-a635-a1617a04f9e5",
|
38 |
+
"metadata": {},
|
39 |
+
"outputs": [],
|
40 |
+
"source": [
|
41 |
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"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 |
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"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 |
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" '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 |
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"outputs": [],
|
76 |
+
"source": [
|
77 |
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"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 |
+
{
|
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|
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"len(ddf[~ddf['BindingDB Target Chain Sequence.1'].isnull()])/len(ddf[~ddf['BindingDB Target Chain Sequence'].isnull()])"
|
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{
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|
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"source": [
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"# remove rows with more than one target\n",
|
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"ddf_prune = ddf[ddf['BindingDB Target Chain Sequence.1'].isnull()]\n",
|
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"ddf_prune = ddf_prune.rename(columns={'BindingDB Target Chain Sequence': 'seq'})"
|
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{
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"source": [
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"ddf_nonnull = ddf_prune[~ddf_prune.seq.isnull()].copy()"
|
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]
|
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|
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|
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|
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|
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|
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" </tr>\n",
|
273 |
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" <tr>\n",
|
274 |
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|
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|
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|
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|
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|
282 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
298 |
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],
|
299 |
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"text/plain": [
|
300 |
+
" Ligand SMILES Ki (nM) IC50 (nM) \\\n",
|
301 |
+
"0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 0.24 NaN \n",
|
302 |
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"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 |
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"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 |
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},
|
364 |
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"execution_count": 20,
|
365 |
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"metadata": {},
|
366 |
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"output_type": "execute_result"
|
367 |
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}
|
368 |
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],
|
369 |
+
"source": [
|
370 |
+
"ddf_nonnull.head()"
|
371 |
+
]
|
372 |
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},
|
373 |
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{
|
374 |
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"cell_type": "code",
|
375 |
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"execution_count": 21,
|
376 |
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"id": "7b423365-4989-4325-a5a5-845d852d52e9",
|
377 |
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"metadata": {},
|
378 |
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"outputs": [
|
379 |
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{
|
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"data": {
|
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"text/plain": [
|
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"2221761"
|
383 |
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]
|
384 |
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},
|
385 |
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"execution_count": 21,
|
386 |
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"metadata": {},
|
387 |
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"output_type": "execute_result"
|
388 |
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}
|
389 |
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],
|
390 |
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"source": [
|
391 |
+
"len(ddf_nonnull)"
|
392 |
+
]
|
393 |
+
},
|
394 |
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{
|
395 |
+
"cell_type": "code",
|
396 |
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"execution_count": 22,
|
397 |
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"id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
|
398 |
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"metadata": {},
|
399 |
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"outputs": [],
|
400 |
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"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 |
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"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 |
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"outputs": [],
|
833 |
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"source": [
|
834 |
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"df_pdb = df[~df['PDB ID(s) for Ligand-Target Complex'].isnull()][['PDB ID(s) for Ligand-Target Complex','Ligand SMILES']]"
|
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]
|
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"metadata": {},
|
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"outputs": [],
|
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"source": [
|
844 |
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"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 |
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},
|
850 |
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{
|
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|
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|
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" <th>0</th>\n",
|
885 |
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|
886 |
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" <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
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887 |
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" <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
|
888 |
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|
889 |
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|
890 |
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" <th>29</th>\n",
|
891 |
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" <td>1HWR</td>\n",
|
892 |
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" <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC=C)C(=O)...</td>\n",
|
893 |
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" <td>C=CCN1C(=O)N(CC=C)[C@H](Cc2ccccc2)[C@H](O)[C@@...</td>\n",
|
894 |
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" </tr>\n",
|
895 |
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" <tr>\n",
|
896 |
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" <th>34</th>\n",
|
897 |
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" <td>6DGY,6DH1,6DH4,6DH7,3O99</td>\n",
|
898 |
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" <td>CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O...</td>\n",
|
899 |
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" <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 |
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" <td>OCc1ccc(CN2[C@H](Cc3ccccc3)[C@H](O)[C@@H](O)[C...</td>\n",
|
905 |
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" <td>O=C1N(Cc2ccc(CO)cc2)[C@H](Cc2ccccc2)[C@H](O)[C...</td>\n",
|
906 |
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" </tr>\n",
|
907 |
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" <tr>\n",
|
908 |
+
" <th>130</th>\n",
|
909 |
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" <td>1MER,1DMP,1RQ9</td>\n",
|
910 |
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" <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 |
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|
915 |
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" <td>...</td>\n",
|
916 |
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|
917 |
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" <td>...</td>\n",
|
918 |
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|
919 |
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" <tr>\n",
|
920 |
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" <th>2333375</th>\n",
|
921 |
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" <td>1MUI,2RKG,2RKF,1RV7,2Q5K,2O4S,6DJ1,6DJ2,3OGQ,2...</td>\n",
|
922 |
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" <td>CC(C)[C@H](N1CCCNC1=O)C(=O)N[C@H](C[C@H](O)[C@...</td>\n",
|
923 |
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" <td>Cc1cccc(C)c1OCC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)...</td>\n",
|
924 |
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|
925 |
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|
926 |
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" <th>2333376</th>\n",
|
927 |
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" <td>4NPT,4DQH,4DQE,5E5J,3JW2,6OPU,6OPX,2HS2,2HS1,2...</td>\n",
|
928 |
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" <td>CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]...</td>\n",
|
929 |
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" <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 |
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" <th>2333384</th>\n",
|
939 |
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" <td>6EKZ,1DY4,5FUK,6PS5</td>\n",
|
940 |
+
" <td>CC(C)NCC(O)COc1cccc2ccccc12</td>\n",
|
941 |
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" <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 |
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" <td>CC(C)c1onc(-c2c(Cl)cccc2Cl)c1COc1ccc(/C=C/c2cc...</td>\n",
|
948 |
+
" </tr>\n",
|
949 |
+
" </tbody>\n",
|
950 |
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"</table>\n",
|
951 |
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"<p>123385 rows × 3 columns</p>\n",
|
952 |
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"</div>"
|
953 |
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],
|
954 |
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"text/plain": [
|
955 |
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" 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 |
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"129 1MES,1MEU,1MET,1BVG,1BVE,3JVW,1QBS \n",
|
960 |
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"130 1MER,1DMP,1RQ9 \n",
|
961 |
+
"... ... \n",
|
962 |
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"2333375 1MUI,2RKG,2RKF,1RV7,2Q5K,2O4S,6DJ1,6DJ2,3OGQ,2... \n",
|
963 |
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"2333376 4NPT,4DQH,4DQE,5E5J,3JW2,6OPU,6OPX,2HS2,2HS1,2... \n",
|
964 |
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"2333380 6EKZ,1DY4,5FUK,6PS5 \n",
|
965 |
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"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 |
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"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",
|
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+
"[123385 rows x 3 columns]"
|
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]
|
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},
|
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|
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"output_type": "execute_result"
|
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|
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|
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"source": [
|
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"df_pdb"
|
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|
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|
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{
|
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"cell_type": "code",
|
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"id": "593c9aec",
|
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"metadata": {},
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"source": []
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|
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"name": "ipython",
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"version": 3
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"file_extension": ".py",
|
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"mimetype": "text/x-python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"nbformat": 4,
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CHANGED
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"id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
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" <th>
|
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" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
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" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
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" <td>0.0045</td>\n",
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" </tr>\n",
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" <th>
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" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
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" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
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|
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|
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" </tr>\n",
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" <tr>\n",
|
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" <th>
|
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" <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
|
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" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
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" <td>125.0000</td>\n",
|
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|
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" </tr>\n",
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" <th>
|
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" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
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" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
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@@ -875,7 +896,7 @@
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|
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" </tr>\n",
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|
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" <th>
|
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" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
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" <td>CC[Se]C(=N)N</td>\n",
|
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" <td>0.0390</td>\n",
|
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|
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|
@@ -899,11 +920,11 @@
|
|
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"3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
|
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"4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
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" smiles affinity_uM \\\n",
|
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"0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
|
@@ -912,11 +933,11 @@
|
|
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"3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
|
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"4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
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|
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|
@@ -955,7 +976,7 @@
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"Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
|
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|
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|
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|
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"execution_count":
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|
@@ -1112,35 +1133,35 @@
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|
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|
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" </tr>\n",
|
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|
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" <th>
|
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" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
|
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" <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
|
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" <td>8.0000</td>\n",
|
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" <td>5.096910</td>\n",
|
1120 |
" </tr>\n",
|
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" <tr>\n",
|
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-
" <th>
|
1123 |
" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
|
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" <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",
|
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" <td>5.096910</td>\n",
|
1127 |
" </tr>\n",
|
1128 |
" <tr>\n",
|
1129 |
-
" <th>
|
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",
|
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" <td>8.346787</td>\n",
|
1134 |
" </tr>\n",
|
1135 |
" <tr>\n",
|
1136 |
-
" <th>
|
1137 |
" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
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" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
|
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" <td>2.0000</td>\n",
|
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" <td>5.698970</td>\n",
|
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" </tr>\n",
|
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" <tr>\n",
|
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-
" <th>
|
1144 |
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
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" <td>CC[Se]C(=N)N</td>\n",
|
1146 |
" <td>0.0390</td>\n",
|
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|
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" </tr>\n",
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" </tbody>\n",
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|
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],
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|
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"3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
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|
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|
|
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"3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
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"0 7.585027 \n",
|
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"3 5.191789 \n",
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|
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|
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|
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"df = pd.read_parquet('data/all.parquet')"
|
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"image/png": 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\n",
|
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"text/plain": [
|
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"<Figure size 432x288 with 1 Axes>"
|
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]
|
@@ -1371,17 +1392,17 @@
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
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"metadata": {},
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"outputs": [
|
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{
|
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"data": {
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"text/plain": [
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-
"
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},
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-
"execution_count":
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "3af855d3-a943-4574-985c-540d3f6b6f80",
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"metadata": {},
|
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"outputs": [
|
@@ -1403,13 +1424,13 @@
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" 'with_std': True,\n",
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" 'copy': True,\n",
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" 'n_features_in_': 1,\n",
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-
" 'n_samples_seen_':
|
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-
" 'mean_': array([6.
|
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-
" 'var_': array([2.
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-
" 'scale_': array([1.
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]
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},
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-
"execution_count":
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "15f8d5b9-37d5-453e-a6df-df6510cc5c81",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "8dec95dc-a014-4d39-ae51-8de981173573",
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"metadata": {},
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"outputs": [],
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@@ -1461,7 +1482,7 @@
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
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"metadata": {},
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"outputs": [],
|
@@ -1471,17 +1492,17 @@
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},
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
|
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"metadata": {},
|
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"outputs": [
|
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{
|
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"data": {
|
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"text/plain": [
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-
"
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]
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},
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-
"execution_count":
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"metadata": {},
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"output_type": "execute_result"
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}
|
@@ -1492,7 +1513,7 @@
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},
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "47966268-c97c-4bd9-9c90-eb568249f2ef",
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"metadata": {},
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"outputs": [],
|
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "c0d250a3-5680-446c-9c98-7d6623643304",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "0c7c0b26-1f2a-4b80-8117-f1e02719aac9",
|
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"metadata": {},
|
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"outputs": [
|
@@ -1529,14 +1550,14 @@
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"name": "stderr",
|
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"output_type": "stream",
|
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"text": [
|
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-
"RDKit WARNING: [
|
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-
"RDKit WARNING: [
|
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"RDKit WARNING: [
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"RDKit WARNING: [
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"RDKit WARNING: [
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"RDKit WARNING: [
|
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-
"RDKit WARNING: [
|
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"RDKit WARNING: [
|
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]
|
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}
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],
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@@ -1547,7 +1568,7 @@
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},
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "258f593c-1cba-45cb-936e-8c1360075926",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -1557,7 +1578,7 @@
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "ee3fa0bc-9ad3-4ea7-9393-cbc7504f634c",
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"metadata": {},
|
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"outputs": [],
|
@@ -1568,10 +1589,12 @@
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|
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{
|
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"cell_type": "code",
|
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"execution_count": null,
|
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-
"id": "
|
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"metadata": {},
|
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"outputs": [],
|
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-
"source": [
|
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}
|
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],
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"metadata": {
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},
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{
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"cell_type": "code",
|
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+
"execution_count": 7,
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"id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
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"metadata": {},
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"outputs": [],
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},
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{
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+
"execution_count": 8,
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"id": "25553199-1715-40fb-9260-427bdd6c3706",
|
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"metadata": {},
|
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"outputs": [
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"[25425 rows x 3 columns]"
|
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]
|
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},
|
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+
"execution_count": 8,
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"metadata": {},
|
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"output_type": "execute_result"
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}
|
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},
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{
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"cell_type": "code",
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+
"execution_count": 9,
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"id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
|
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"metadata": {},
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"outputs": [],
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},
|
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{
|
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"cell_type": "code",
|
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"execution_count": 10,
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"id": "cee93018-601d-458b-af44-bd978da7a2bc",
|
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"metadata": {},
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"outputs": [
|
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"[13645 rows x 3 columns]"
|
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]
|
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},
|
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+
"execution_count": 10,
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"metadata": {},
|
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|
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}
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 11,
|
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"id": "195f92db-fe06-4d03-8500-8d6c310a3347",
|
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"metadata": {},
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"outputs": [],
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 12,
|
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"id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
|
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"metadata": {},
|
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"outputs": [
|
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{
|
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"data": {
|
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"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 |
+
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"text/plain": [
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"<Figure size 432x288 with 1 Axes>"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 64,
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1396 |
"id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
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1397 |
"metadata": {},
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"outputs": [
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1399 |
{
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1400 |
"data": {
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"text/plain": [
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"1836729"
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1403 |
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"execution_count": 64,
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1408 |
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{
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"id": "3af855d3-a943-4574-985c-540d3f6b6f80",
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1418 |
"metadata": {},
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1419 |
"outputs": [
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1424 |
" 'with_std': True,\n",
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1425 |
" 'copy': True,\n",
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1426 |
" 'n_features_in_': 1,\n",
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1427 |
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" 'n_samples_seen_': 1836729,\n",
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" 'mean_': array([6.50604534]),\n",
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1429 |
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" 'var_': array([2.43319576]),\n",
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1430 |
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" 'scale_': array([1.55987043])}"
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1431 |
]
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1432 |
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{
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{
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"execution_count": 68,
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"id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
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{
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"execution_count": 69,
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"id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
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1497 |
"metadata": {},
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"outputs": [
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1499 |
{
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1500 |
"data": {
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"1836326"
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{
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"id": "47966268-c97c-4bd9-9c90-eb568249f2ef",
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{
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"execution_count": 71,
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"id": "c0d250a3-5680-446c-9c98-7d6623643304",
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{
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"execution_count": 72,
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"id": "0c7c0b26-1f2a-4b80-8117-f1e02719aac9",
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"outputs": [
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1550 |
"name": "stderr",
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1551 |
"output_type": "stream",
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1552 |
"text": [
|
1553 |
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"RDKit WARNING: [13:20:36] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
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1554 |
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"RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
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1555 |
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"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 |
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"RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
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1558 |
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"RDKit WARNING: [13:20:37] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
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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"
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1561 |
]
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1562 |
}
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1563 |
],
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{
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"id": "258f593c-1cba-45cb-936e-8c1360075926",
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"outputs": [],
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{
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1590 |
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"id": "5c12fedc-4236-4587-a744-c0c9ec21ceaa",
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"metadata": {},
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"source": [
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