!pip install -q mdtraj nglview
from google.colab import output
output.enable_custom_widget_manager()
! pip install rdkit
! pip install oddt
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 30.7 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.1/7.1 MB 78.1 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 92.5 MB/s eta 0:00:00 Building wheel for mdtraj (pyproject.toml) ... done Building wheel for nglview (pyproject.toml) ... done Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/ Collecting rdkit Downloading rdkit-2023.3.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.7/29.7 MB 63.6 MB/s eta 0:00:00 Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from rdkit) (1.22.4) Requirement already satisfied: Pillow in /usr/local/lib/python3.10/dist-packages (from rdkit) (8.4.0) Installing collected packages: rdkit Successfully installed rdkit-2023.3.1 Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/ Collecting oddt Downloading oddt-0.7.tar.gz (2.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 80.3 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Collecting numpydoc (from oddt) Downloading numpydoc-1.5.0-py3-none-any.whl (52 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.4/52.4 kB 7.5 MB/s eta 0:00:00 Requirement already satisfied: six in /usr/local/lib/python3.10/dist-packages (from oddt) (1.16.0) Requirement already satisfied: numpy>=1.11 in /usr/local/lib/python3.10/dist-packages (from oddt) (1.22.4) Requirement already satisfied: scipy>=0.17 in /usr/local/lib/python3.10/dist-packages (from oddt) (1.10.1) Requirement already satisfied: scikit-learn>=0.18 in /usr/local/lib/python3.10/dist-packages (from oddt) (1.2.2) Requirement already satisfied: joblib>=0.9.4 in /usr/local/lib/python3.10/dist-packages (from oddt) (1.2.0) Requirement already satisfied: pandas>=0.19.2 in /usr/local/lib/python3.10/dist-packages (from oddt) (1.5.3) Requirement already satisfied: python-dateutil>=2.8.1 in /usr/local/lib/python3.10/dist-packages (from pandas>=0.19.2->oddt) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas>=0.19.2->oddt) (2022.7.1) Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn>=0.18->oddt) (3.1.0) Collecting sphinx>=4.2 (from numpydoc->oddt) Downloading sphinx-7.0.0-py3-none-any.whl (3.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 118.3 MB/s eta 0:00:00 Requirement already satisfied: Jinja2>=2.10 in /usr/local/lib/python3.10/dist-packages (from numpydoc->oddt) (3.1.2) Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from Jinja2>=2.10->numpydoc->oddt) (2.1.2) Requirement already satisfied: sphinxcontrib-applehelp in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (1.0.4) Requirement already satisfied: sphinxcontrib-devhelp in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (1.0.2) Requirement already satisfied: sphinxcontrib-jsmath in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (2.0.1) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (1.1.5) Requirement already satisfied: sphinxcontrib-qthelp in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (1.0.3) Requirement already satisfied: Pygments>=2.13 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (2.14.0) Collecting docutils<0.20,>=0.18.1 (from sphinx>=4.2->numpydoc->oddt) Downloading docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 59.0 MB/s eta 0:00:00 Requirement already satisfied: snowballstemmer>=2.0 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (2.2.0) Requirement already satisfied: babel>=2.9 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (2.12.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (0.7.13) Requirement already satisfied: imagesize>=1.3 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (1.4.1) Requirement already satisfied: requests>=2.25.0 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (2.27.1) Requirement already satisfied: packaging>=21.0 in /usr/local/lib/python3.10/dist-packages (from sphinx>=4.2->numpydoc->oddt) (23.1) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests>=2.25.0->sphinx>=4.2->numpydoc->oddt) (1.26.15) Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests>=2.25.0->sphinx>=4.2->numpydoc->oddt) (2022.12.7) Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.10/dist-packages (from requests>=2.25.0->sphinx>=4.2->numpydoc->oddt) (2.0.12) Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests>=2.25.0->sphinx>=4.2->numpydoc->oddt) (3.4) Building wheels for collected packages: oddt Building wheel for oddt (setup.py) ... done Created wheel for oddt: filename=oddt-0.7-py2.py3-none-any.whl size=2409540 sha256=658f3bcae3ea70bd26fa606261bda0027f5658be54f40432b23b7995fb51a59b Stored in directory: /root/.cache/pip/wheels/56/d9/f0/0806faccf253c082ae93545eb3a2c0e39185304146433742ce Successfully built oddt Installing collected packages: docutils, sphinx, numpydoc, oddt Attempting uninstall: docutils Found existing installation: docutils 0.16 Uninstalling docutils-0.16: Successfully uninstalled docutils-0.16 Attempting uninstall: sphinx Found existing installation: Sphinx 3.5.4 Uninstalling Sphinx-3.5.4: Successfully uninstalled Sphinx-3.5.4 Successfully installed docutils-0.19 numpydoc-1.5.0 oddt-0.7 sphinx-7.0.0
%%bash
wget https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_linux_x86.tgz
tar xzvf autodock_vina_1_1_2_linux_x86.tgz
autodock_vina_1_1_2_linux_x86/ autodock_vina_1_1_2_linux_x86/LICENSE autodock_vina_1_1_2_linux_x86/bin/ autodock_vina_1_1_2_linux_x86/bin/vina autodock_vina_1_1_2_linux_x86/bin/vina_split
--2023-05-10 19:08:42-- https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_linux_x86.tgz
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HTTP request sent, awaiting response... 200 OK
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Saving to: ‘autodock_vina_1_1_2_linux_x86.tgz’
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import numpy as np
import copy
# Отображение структур
import IPython.display
import ipywidgets
from IPython.display import display,display_svg,SVG,Image
# Open Drug Discovery Toolkit
import oddt
import oddt.docking
import oddt.interactions
# Органика
from rdkit.Chem import Draw
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
import mdtraj as md
u = md.load('LYS_LAMBD.B99990001.pdb')
pdb = u.topology
for i,r in enumerate(pdb.atoms):
print(i,r)
0 MET1-N 1 MET1-CA 2 MET1-CB 3 MET1-CG 4 MET1-SD 5 MET1-CE 6 MET1-C 7 MET1-O 8 VAL2-N 9 VAL2-CA 10 VAL2-CB 11 VAL2-CG1 12 VAL2-CG2 13 VAL2-C 14 VAL2-O 15 GLU3-N 16 GLU3-CA 17 GLU3-CB 18 GLU3-CG 19 GLU3-CD 20 GLU3-OE1 21 GLU3-OE2 22 GLU3-C 23 GLU3-O 24 ILE4-N 25 ILE4-CA 26 ILE4-CB 27 ILE4-CG1 28 ILE4-CG2 29 ILE4-CD1 30 ILE4-C 31 ILE4-O 32 ASN5-N 33 ASN5-CA 34 ASN5-CB 35 ASN5-CG 36 ASN5-OD1 37 ASN5-ND2 38 ASN5-C 39 ASN5-O 40 ASN6-N 41 ASN6-CA 42 ASN6-CB 43 ASN6-CG 44 ASN6-OD1 45 ASN6-ND2 46 ASN6-C 47 ASN6-O 48 GLN7-N 49 GLN7-CA 50 GLN7-CB 51 GLN7-CG 52 GLN7-CD 53 GLN7-OE1 54 GLN7-NE2 55 GLN7-C 56 GLN7-O 57 ARG8-N 58 ARG8-CA 59 ARG8-CB 60 ARG8-CG 61 ARG8-CD 62 ARG8-NE 63 ARG8-CZ 64 ARG8-NH1 65 ARG8-NH2 66 ARG8-C 67 ARG8-O 68 LYS9-N 69 LYS9-CA 70 LYS9-CB 71 LYS9-CG 72 LYS9-CD 73 LYS9-CE 74 LYS9-NZ 75 LYS9-C 76 LYS9-O 77 ALA10-N 78 ALA10-CA 79 ALA10-CB 80 ALA10-C 81 ALA10-O 82 PHE11-N 83 PHE11-CA 84 PHE11-CB 85 PHE11-CG 86 PHE11-CD1 87 PHE11-CD2 88 PHE11-CE1 89 PHE11-CE2 90 PHE11-CZ 91 PHE11-C 92 PHE11-O 93 LEU12-N 94 LEU12-CA 95 LEU12-CB 96 LEU12-CG 97 LEU12-CD1 98 LEU12-CD2 99 LEU12-C 100 LEU12-O 101 ASP13-N 102 ASP13-CA 103 ASP13-CB 104 ASP13-CG 105 ASP13-OD1 106 ASP13-OD2 107 ASP13-C 108 ASP13-O 109 MET14-N 110 MET14-CA 111 MET14-CB 112 MET14-CG 113 MET14-SD 114 MET14-CE 115 MET14-C 116 MET14-O 117 LEU15-N 118 LEU15-CA 119 LEU15-CB 120 LEU15-CG 121 LEU15-CD1 122 LEU15-CD2 123 LEU15-C 124 LEU15-O 125 ALA16-N 126 ALA16-CA 127 ALA16-CB 128 ALA16-C 129 ALA16-O 130 TRP17-N 131 TRP17-CA 132 TRP17-CB 133 TRP17-CG 134 TRP17-CD2 135 TRP17-CD1 136 TRP17-NE1 137 TRP17-CE2 138 TRP17-CE3 139 TRP17-CZ2 140 TRP17-CZ3 141 TRP17-CH2 142 TRP17-C 143 TRP17-O 144 SER18-N 145 SER18-CA 146 SER18-CB 147 SER18-OG 148 SER18-C 149 SER18-O 150 GLU19-N 151 GLU19-CA 152 GLU19-CB 153 GLU19-CG 154 GLU19-CD 155 GLU19-OE1 156 GLU19-OE2 157 GLU19-C 158 GLU19-O 159 GLY20-N 160 GLY20-CA 161 GLY20-C 162 GLY20-O 163 THR21-N 164 THR21-CA 165 THR21-CB 166 THR21-OG1 167 THR21-CG2 168 THR21-C 169 THR21-O 170 ASP22-N 171 ASP22-CA 172 ASP22-CB 173 ASP22-CG 174 ASP22-OD1 175 ASP22-OD2 176 ASP22-C 177 ASP22-O 178 ASN23-N 179 ASN23-CA 180 ASN23-CB 181 ASN23-CG 182 ASN23-OD1 183 ASN23-ND2 184 ASN23-C 185 ASN23-O 186 GLY24-N 187 GLY24-CA 188 GLY24-C 189 GLY24-O 190 ARG25-N 191 ARG25-CA 192 ARG25-CB 193 ARG25-CG 194 ARG25-CD 195 ARG25-NE 196 ARG25-CZ 197 ARG25-NH1 198 ARG25-NH2 199 ARG25-C 200 ARG25-O 201 GLN26-N 202 GLN26-CA 203 GLN26-CB 204 GLN26-CG 205 GLN26-CD 206 GLN26-OE1 207 GLN26-NE2 208 GLN26-C 209 GLN26-O 210 LYS27-N 211 LYS27-CA 212 LYS27-CB 213 LYS27-CG 214 LYS27-CD 215 LYS27-CE 216 LYS27-NZ 217 LYS27-C 218 LYS27-O 219 THR28-N 220 THR28-CA 221 THR28-CB 222 THR28-OG1 223 THR28-CG2 224 THR28-C 225 THR28-O 226 ARG29-N 227 ARG29-CA 228 ARG29-CB 229 ARG29-CG 230 ARG29-CD 231 ARG29-NE 232 ARG29-CZ 233 ARG29-NH1 234 ARG29-NH2 235 ARG29-C 236 ARG29-O 237 ASN30-N 238 ASN30-CA 239 ASN30-CB 240 ASN30-CG 241 ASN30-OD1 242 ASN30-ND2 243 ASN30-C 244 ASN30-O 245 HIS31-N 246 HIS31-CA 247 HIS31-ND1 248 HIS31-CG 249 HIS31-CB 250 HIS31-NE2 251 HIS31-CD2 252 HIS31-CE1 253 HIS31-C 254 HIS31-O 255 GLY32-N 256 GLY32-CA 257 GLY32-C 258 GLY32-O 259 TYR33-N 260 TYR33-CA 261 TYR33-CB 262 TYR33-CG 263 TYR33-CD1 264 TYR33-CD2 265 TYR33-CE1 266 TYR33-CE2 267 TYR33-CZ 268 TYR33-OH 269 TYR33-C 270 TYR33-O 271 ASP34-N 272 ASP34-CA 273 ASP34-CB 274 ASP34-CG 275 ASP34-OD1 276 ASP34-OD2 277 ASP34-C 278 ASP34-O 279 VAL35-N 280 VAL35-CA 281 VAL35-CB 282 VAL35-CG1 283 VAL35-CG2 284 VAL35-C 285 VAL35-O 286 ILE36-N 287 ILE36-CA 288 ILE36-CB 289 ILE36-CG1 290 ILE36-CG2 291 ILE36-CD1 292 ILE36-C 293 ILE36-O 294 VAL37-N 295 VAL37-CA 296 VAL37-CB 297 VAL37-CG1 298 VAL37-CG2 299 VAL37-C 300 VAL37-O 301 GLY38-N 302 GLY38-CA 303 GLY38-C 304 GLY38-O 305 GLY39-N 306 GLY39-CA 307 GLY39-C 308 GLY39-O 309 GLU40-N 310 GLU40-CA 311 GLU40-CB 312 GLU40-CG 313 GLU40-CD 314 GLU40-OE1 315 GLU40-OE2 316 GLU40-C 317 GLU40-O 318 LEU41-N 319 LEU41-CA 320 LEU41-CB 321 LEU41-CG 322 LEU41-CD1 323 LEU41-CD2 324 LEU41-C 325 LEU41-O 326 PHE42-N 327 PHE42-CA 328 PHE42-CB 329 PHE42-CG 330 PHE42-CD1 331 PHE42-CD2 332 PHE42-CE1 333 PHE42-CE2 334 PHE42-CZ 335 PHE42-C 336 PHE42-O 337 THR43-N 338 THR43-CA 339 THR43-CB 340 THR43-OG1 341 THR43-CG2 342 THR43-C 343 THR43-O 344 ASP44-N 345 ASP44-CA 346 ASP44-CB 347 ASP44-CG 348 ASP44-OD1 349 ASP44-OD2 350 ASP44-C 351 ASP44-O 352 TYR45-N 353 TYR45-CA 354 TYR45-CB 355 TYR45-CG 356 TYR45-CD1 357 TYR45-CD2 358 TYR45-CE1 359 TYR45-CE2 360 TYR45-CZ 361 TYR45-OH 362 TYR45-C 363 TYR45-O 364 SER46-N 365 SER46-CA 366 SER46-CB 367 SER46-OG 368 SER46-C 369 SER46-O 370 ASP47-N 371 ASP47-CA 372 ASP47-CB 373 ASP47-CG 374 ASP47-OD1 375 ASP47-OD2 376 ASP47-C 377 ASP47-O 378 HIS48-N 379 HIS48-CA 380 HIS48-ND1 381 HIS48-CG 382 HIS48-CB 383 HIS48-NE2 384 HIS48-CD2 385 HIS48-CE1 386 HIS48-C 387 HIS48-O 388 PRO49-N 389 PRO49-CA 390 PRO49-CD 391 PRO49-CB 392 PRO49-CG 393 PRO49-C 394 PRO49-O 395 ARG50-N 396 ARG50-CA 397 ARG50-CB 398 ARG50-CG 399 ARG50-CD 400 ARG50-NE 401 ARG50-CZ 402 ARG50-NH1 403 ARG50-NH2 404 ARG50-C 405 ARG50-O 406 LYS51-N 407 LYS51-CA 408 LYS51-CB 409 LYS51-CG 410 LYS51-CD 411 LYS51-CE 412 LYS51-NZ 413 LYS51-C 414 LYS51-O 415 LEU52-N 416 LEU52-CA 417 LEU52-CB 418 LEU52-CG 419 LEU52-CD1 420 LEU52-CD2 421 LEU52-C 422 LEU52-O 423 VAL53-N 424 VAL53-CA 425 VAL53-CB 426 VAL53-CG1 427 VAL53-CG2 428 VAL53-C 429 VAL53-O 430 THR54-N 431 THR54-CA 432 THR54-CB 433 THR54-OG1 434 THR54-CG2 435 THR54-C 436 THR54-O 437 LEU55-N 438 LEU55-CA 439 LEU55-CB 440 LEU55-CG 441 LEU55-CD1 442 LEU55-CD2 443 LEU55-C 444 LEU55-O 445 ASN56-N 446 ASN56-CA 447 ASN56-CB 448 ASN56-CG 449 ASN56-OD1 450 ASN56-ND2 451 ASN56-C 452 ASN56-O 453 PRO57-N 454 PRO57-CA 455 PRO57-CD 456 PRO57-CB 457 PRO57-CG 458 PRO57-C 459 PRO57-O 460 LYS58-N 461 LYS58-CA 462 LYS58-CB 463 LYS58-CG 464 LYS58-CD 465 LYS58-CE 466 LYS58-NZ 467 LYS58-C 468 LYS58-O 469 LEU59-N 470 LEU59-CA 471 LEU59-CB 472 LEU59-CG 473 LEU59-CD1 474 LEU59-CD2 475 LEU59-C 476 LEU59-O 477 LYS60-N 478 LYS60-CA 479 LYS60-CB 480 LYS60-CG 481 LYS60-CD 482 LYS60-CE 483 LYS60-NZ 484 LYS60-C 485 LYS60-O 486 SER61-N 487 SER61-CA 488 SER61-CB 489 SER61-OG 490 SER61-C 491 SER61-O 492 THR62-N 493 THR62-CA 494 THR62-CB 495 THR62-OG1 496 THR62-CG2 497 THR62-C 498 THR62-O 499 GLY63-N 500 GLY63-CA 501 GLY63-C 502 GLY63-O 503 ALA64-N 504 ALA64-CA 505 ALA64-CB 506 ALA64-C 507 ALA64-O 508 GLY65-N 509 GLY65-CA 510 GLY65-C 511 GLY65-O 512 ARG66-N 513 ARG66-CA 514 ARG66-CB 515 ARG66-CG 516 ARG66-CD 517 ARG66-NE 518 ARG66-CZ 519 ARG66-NH1 520 ARG66-NH2 521 ARG66-C 522 ARG66-O 523 TYR67-N 524 TYR67-CA 525 TYR67-CB 526 TYR67-CG 527 TYR67-CD1 528 TYR67-CD2 529 TYR67-CE1 530 TYR67-CE2 531 TYR67-CZ 532 TYR67-OH 533 TYR67-C 534 TYR67-O 535 GLN68-N 536 GLN68-CA 537 GLN68-CB 538 GLN68-CG 539 GLN68-CD 540 GLN68-OE1 541 GLN68-NE2 542 GLN68-C 543 GLN68-O 544 LEU69-N 545 LEU69-CA 546 LEU69-CB 547 LEU69-CG 548 LEU69-CD1 549 LEU69-CD2 550 LEU69-C 551 LEU69-O 552 LEU70-N 553 LEU70-CA 554 LEU70-CB 555 LEU70-CG 556 LEU70-CD1 557 LEU70-CD2 558 LEU70-C 559 LEU70-O 560 SER71-N 561 SER71-CA 562 SER71-CB 563 SER71-OG 564 SER71-C 565 SER71-O 566 ARG72-N 567 ARG72-CA 568 ARG72-CB 569 ARG72-CG 570 ARG72-CD 571 ARG72-NE 572 ARG72-CZ 573 ARG72-NH1 574 ARG72-NH2 575 ARG72-C 576 ARG72-O 577 TRP73-N 578 TRP73-CA 579 TRP73-CB 580 TRP73-CG 581 TRP73-CD2 582 TRP73-CD1 583 TRP73-NE1 584 TRP73-CE2 585 TRP73-CE3 586 TRP73-CZ2 587 TRP73-CZ3 588 TRP73-CH2 589 TRP73-C 590 TRP73-O 591 TRP74-N 592 TRP74-CA 593 TRP74-CB 594 TRP74-CG 595 TRP74-CD2 596 TRP74-CD1 597 TRP74-NE1 598 TRP74-CE2 599 TRP74-CE3 600 TRP74-CZ2 601 TRP74-CZ3 602 TRP74-CH2 603 TRP74-C 604 TRP74-O 605 ASP75-N 606 ASP75-CA 607 ASP75-CB 608 ASP75-CG 609 ASP75-OD1 610 ASP75-OD2 611 ASP75-C 612 ASP75-O 613 ALA76-N 614 ALA76-CA 615 ALA76-CB 616 ALA76-C 617 ALA76-O 618 TYR77-N 619 TYR77-CA 620 TYR77-CB 621 TYR77-CG 622 TYR77-CD1 623 TYR77-CD2 624 TYR77-CE1 625 TYR77-CE2 626 TYR77-CZ 627 TYR77-OH 628 TYR77-C 629 TYR77-O 630 ARG78-N 631 ARG78-CA 632 ARG78-CB 633 ARG78-CG 634 ARG78-CD 635 ARG78-NE 636 ARG78-CZ 637 ARG78-NH1 638 ARG78-NH2 639 ARG78-C 640 ARG78-O 641 LYS79-N 642 LYS79-CA 643 LYS79-CB 644 LYS79-CG 645 LYS79-CD 646 LYS79-CE 647 LYS79-NZ 648 LYS79-C 649 LYS79-O 650 GLN80-N 651 GLN80-CA 652 GLN80-CB 653 GLN80-CG 654 GLN80-CD 655 GLN80-OE1 656 GLN80-NE2 657 GLN80-C 658 GLN80-O 659 LEU81-N 660 LEU81-CA 661 LEU81-CB 662 LEU81-CG 663 LEU81-CD1 664 LEU81-CD2 665 LEU81-C 666 LEU81-O 667 GLY82-N 668 GLY82-CA 669 GLY82-C 670 GLY82-O 671 LEU83-N 672 LEU83-CA 673 LEU83-CB 674 LEU83-CG 675 LEU83-CD1 676 LEU83-CD2 677 LEU83-C 678 LEU83-O 679 LYS84-N 680 LYS84-CA 681 LYS84-CB 682 LYS84-CG 683 LYS84-CD 684 LYS84-CE 685 LYS84-NZ 686 LYS84-C 687 LYS84-O 688 ASP85-N 689 ASP85-CA 690 ASP85-CB 691 ASP85-CG 692 ASP85-OD1 693 ASP85-OD2 694 ASP85-C 695 ASP85-O 696 PHE86-N 697 PHE86-CA 698 PHE86-CB 699 PHE86-CG 700 PHE86-CD1 701 PHE86-CD2 702 PHE86-CE1 703 PHE86-CE2 704 PHE86-CZ 705 PHE86-C 706 PHE86-O 707 SER87-N 708 SER87-CA 709 SER87-CB 710 SER87-OG 711 SER87-C 712 SER87-O 713 PRO88-N 714 PRO88-CA 715 PRO88-CD 716 PRO88-CB 717 PRO88-CG 718 PRO88-C 719 PRO88-O 720 LYS89-N 721 LYS89-CA 722 LYS89-CB 723 LYS89-CG 724 LYS89-CD 725 LYS89-CE 726 LYS89-NZ 727 LYS89-C 728 LYS89-O 729 SER90-N 730 SER90-CA 731 SER90-CB 732 SER90-OG 733 SER90-C 734 SER90-O 735 GLN91-N 736 GLN91-CA 737 GLN91-CB 738 GLN91-CG 739 GLN91-CD 740 GLN91-OE1 741 GLN91-NE2 742 GLN91-C 743 GLN91-O 744 ASP92-N 745 ASP92-CA 746 ASP92-CB 747 ASP92-CG 748 ASP92-OD1 749 ASP92-OD2 750 ASP92-C 751 ASP92-O 752 ALA93-N 753 ALA93-CA 754 ALA93-CB 755 ALA93-C 756 ALA93-O 757 VAL94-N 758 VAL94-CA 759 VAL94-CB 760 VAL94-CG1 761 VAL94-CG2 762 VAL94-C 763 VAL94-O 764 ALA95-N 765 ALA95-CA 766 ALA95-CB 767 ALA95-C 768 ALA95-O 769 LEU96-N 770 LEU96-CA 771 LEU96-CB 772 LEU96-CG 773 LEU96-CD1 774 LEU96-CD2 775 LEU96-C 776 LEU96-O 777 GLN97-N 778 GLN97-CA 779 GLN97-CB 780 GLN97-CG 781 GLN97-CD 782 GLN97-OE1 783 GLN97-NE2 784 GLN97-C 785 GLN97-O 786 GLN98-N 787 GLN98-CA 788 GLN98-CB 789 GLN98-CG 790 GLN98-CD 791 GLN98-OE1 792 GLN98-NE2 793 GLN98-C 794 GLN98-O 795 ILE99-N 796 ILE99-CA 797 ILE99-CB 798 ILE99-CG1 799 ILE99-CG2 800 ILE99-CD1 801 ILE99-C 802 ILE99-O 803 LYS100-N 804 LYS100-CA 805 LYS100-CB 806 LYS100-CG 807 LYS100-CD 808 LYS100-CE 809 LYS100-NZ 810 LYS100-C 811 LYS100-O 812 GLU101-N 813 GLU101-CA 814 GLU101-CB 815 GLU101-CG 816 GLU101-CD 817 GLU101-OE1 818 GLU101-OE2 819 GLU101-C 820 GLU101-O 821 ARG102-N 822 ARG102-CA 823 ARG102-CB 824 ARG102-CG 825 ARG102-CD 826 ARG102-NE 827 ARG102-CZ 828 ARG102-NH1 829 ARG102-NH2 830 ARG102-C 831 ARG102-O 832 GLY103-N 833 GLY103-CA 834 GLY103-C 835 GLY103-O 836 ALA104-N 837 ALA104-CA 838 ALA104-CB 839 ALA104-C 840 ALA104-O 841 LEU105-N 842 LEU105-CA 843 LEU105-CB 844 LEU105-CG 845 LEU105-CD1 846 LEU105-CD2 847 LEU105-C 848 LEU105-O 849 PRO106-N 850 PRO106-CA 851 PRO106-CD 852 PRO106-CB 853 PRO106-CG 854 PRO106-C 855 PRO106-O 856 MET107-N 857 MET107-CA 858 MET107-CB 859 MET107-CG 860 MET107-SD 861 MET107-CE 862 MET107-C 863 MET107-O 864 ILE108-N 865 ILE108-CA 866 ILE108-CB 867 ILE108-CG1 868 ILE108-CG2 869 ILE108-CD1 870 ILE108-C 871 ILE108-O 872 ASP109-N 873 ASP109-CA 874 ASP109-CB 875 ASP109-CG 876 ASP109-OD1 877 ASP109-OD2 878 ASP109-C 879 ASP109-O 880 ARG110-N 881 ARG110-CA 882 ARG110-CB 883 ARG110-CG 884 ARG110-CD 885 ARG110-NE 886 ARG110-CZ 887 ARG110-NH1 888 ARG110-NH2 889 ARG110-C 890 ARG110-O 891 GLY111-N 892 GLY111-CA 893 GLY111-C 894 GLY111-O 895 ASP112-N 896 ASP112-CA 897 ASP112-CB 898 ASP112-CG 899 ASP112-OD1 900 ASP112-OD2 901 ASP112-C 902 ASP112-O 903 ILE113-N 904 ILE113-CA 905 ILE113-CB 906 ILE113-CG1 907 ILE113-CG2 908 ILE113-CD1 909 ILE113-C 910 ILE113-O 911 ARG114-N 912 ARG114-CA 913 ARG114-CB 914 ARG114-CG 915 ARG114-CD 916 ARG114-NE 917 ARG114-CZ 918 ARG114-NH1 919 ARG114-NH2 920 ARG114-C 921 ARG114-O 922 GLN115-N 923 GLN115-CA 924 GLN115-CB 925 GLN115-CG 926 GLN115-CD 927 GLN115-OE1 928 GLN115-NE2 929 GLN115-C 930 GLN115-O 931 ALA116-N 932 ALA116-CA 933 ALA116-CB 934 ALA116-C 935 ALA116-O 936 ILE117-N 937 ILE117-CA 938 ILE117-CB 939 ILE117-CG1 940 ILE117-CG2 941 ILE117-CD1 942 ILE117-C 943 ILE117-O 944 ASP118-N 945 ASP118-CA 946 ASP118-CB 947 ASP118-CG 948 ASP118-OD1 949 ASP118-OD2 950 ASP118-C 951 ASP118-O 952 ARG119-N 953 ARG119-CA 954 ARG119-CB 955 ARG119-CG 956 ARG119-CD 957 ARG119-NE 958 ARG119-CZ 959 ARG119-NH1 960 ARG119-NH2 961 ARG119-C 962 ARG119-O 963 CYS120-N 964 CYS120-CA 965 CYS120-CB 966 CYS120-SG 967 CYS120-C 968 CYS120-O 969 SER121-N 970 SER121-CA 971 SER121-CB 972 SER121-OG 973 SER121-C 974 SER121-O 975 ASN122-N 976 ASN122-CA 977 ASN122-CB 978 ASN122-CG 979 ASN122-OD1 980 ASN122-ND2 981 ASN122-C 982 ASN122-O 983 ILE123-N 984 ILE123-CA 985 ILE123-CB 986 ILE123-CG1 987 ILE123-CG2 988 ILE123-CD1 989 ILE123-C 990 ILE123-O 991 TRP124-N 992 TRP124-CA 993 TRP124-CB 994 TRP124-CG 995 TRP124-CD2 996 TRP124-CD1 997 TRP124-NE1 998 TRP124-CE2 999 TRP124-CE3 1000 TRP124-CZ2 1001 TRP124-CZ3 1002 TRP124-CH2 1003 TRP124-C 1004 TRP124-O 1005 ALA125-N 1006 ALA125-CA 1007 ALA125-CB 1008 ALA125-C 1009 ALA125-O 1010 SER126-N 1011 SER126-CA 1012 SER126-CB 1013 SER126-OG 1014 SER126-C 1015 SER126-O 1016 LEU127-N 1017 LEU127-CA 1018 LEU127-CB 1019 LEU127-CG 1020 LEU127-CD1 1021 LEU127-CD2 1022 LEU127-C 1023 LEU127-O 1024 PRO128-N 1025 PRO128-CA 1026 PRO128-CD 1027 PRO128-CB 1028 PRO128-CG 1029 PRO128-C 1030 PRO128-O 1031 GLY129-N 1032 GLY129-CA 1033 GLY129-C 1034 GLY129-O 1035 ALA130-N 1036 ALA130-CA 1037 ALA130-CB 1038 ALA130-C 1039 ALA130-O 1040 GLY131-N 1041 GLY131-CA 1042 GLY131-C 1043 GLY131-O 1044 TYR132-N 1045 TYR132-CA 1046 TYR132-CB 1047 TYR132-CG 1048 TYR132-CD1 1049 TYR132-CD2 1050 TYR132-CE1 1051 TYR132-CE2 1052 TYR132-CZ 1053 TYR132-OH 1054 TYR132-C 1055 TYR132-O 1056 GLY133-N 1057 GLY133-CA 1058 GLY133-C 1059 GLY133-O 1060 GLN134-N 1061 GLN134-CA 1062 GLN134-CB 1063 GLN134-CG 1064 GLN134-CD 1065 GLN134-OE1 1066 GLN134-NE2 1067 GLN134-C 1068 GLN134-O 1069 PHE135-N 1070 PHE135-CA 1071 PHE135-CB 1072 PHE135-CG 1073 PHE135-CD1 1074 PHE135-CD2 1075 PHE135-CE1 1076 PHE135-CE2 1077 PHE135-CZ 1078 PHE135-C 1079 PHE135-O 1080 GLU136-N 1081 GLU136-CA 1082 GLU136-CB 1083 GLU136-CG 1084 GLU136-CD 1085 GLU136-OE1 1086 GLU136-OE2 1087 GLU136-C 1088 GLU136-O 1089 HIS137-N 1090 HIS137-CA 1091 HIS137-ND1 1092 HIS137-CG 1093 HIS137-CB 1094 HIS137-NE2 1095 HIS137-CD2 1096 HIS137-CE1 1097 HIS137-C 1098 HIS137-O 1099 LYS138-N 1100 LYS138-CA 1101 LYS138-CB 1102 LYS138-CG 1103 LYS138-CD 1104 LYS138-CE 1105 LYS138-NZ 1106 LYS138-C 1107 LYS138-O 1108 ALA139-N 1109 ALA139-CA 1110 ALA139-CB 1111 ALA139-C 1112 ALA139-O 1113 ASP140-N 1114 ASP140-CA 1115 ASP140-CB 1116 ASP140-CG 1117 ASP140-OD1 1118 ASP140-OD2 1119 ASP140-C 1120 ASP140-O 1121 SER141-N 1122 SER141-CA 1123 SER141-CB 1124 SER141-OG 1125 SER141-C 1126 SER141-O 1127 LEU142-N 1128 LEU142-CA 1129 LEU142-CB 1130 LEU142-CG 1131 LEU142-CD1 1132 LEU142-CD2 1133 LEU142-C 1134 LEU142-O 1135 ILE143-N 1136 ILE143-CA 1137 ILE143-CB 1138 ILE143-CG1 1139 ILE143-CG2 1140 ILE143-CD1 1141 ILE143-C 1142 ILE143-O 1143 ALA144-N 1144 ALA144-CA 1145 ALA144-CB 1146 ALA144-C 1147 ALA144-O 1148 LYS145-N 1149 LYS145-CA 1150 LYS145-CB 1151 LYS145-CG 1152 LYS145-CD 1153 LYS145-CE 1154 LYS145-NZ 1155 LYS145-C 1156 LYS145-O 1157 PHE146-N 1158 PHE146-CA 1159 PHE146-CB 1160 PHE146-CG 1161 PHE146-CD1 1162 PHE146-CD2 1163 PHE146-CE1 1164 PHE146-CE2 1165 PHE146-CZ 1166 PHE146-C 1167 PHE146-O 1168 LYS147-N 1169 LYS147-CA 1170 LYS147-CB 1171 LYS147-CG 1172 LYS147-CD 1173 LYS147-CE 1174 LYS147-NZ 1175 LYS147-C 1176 LYS147-O 1177 GLU148-N 1178 GLU148-CA 1179 GLU148-CB 1180 GLU148-CG 1181 GLU148-CD 1182 GLU148-OE1 1183 GLU148-OE2 1184 GLU148-C 1185 GLU148-O 1186 ALA149-N 1187 ALA149-CA 1188 ALA149-CB 1189 ALA149-C 1190 ALA149-O 1191 GLY150-N 1192 GLY150-CA 1193 GLY150-C 1194 GLY150-O 1195 GLY151-N 1196 GLY151-CA 1197 GLY151-C 1198 GLY151-O 1199 THR152-N 1200 THR152-CA 1201 THR152-CB 1202 THR152-OG1 1203 THR152-CG2 1204 THR152-C 1205 THR152-O 1206 VAL153-N 1207 VAL153-CA 1208 VAL153-CB 1209 VAL153-CG1 1210 VAL153-CG2 1211 VAL153-C 1212 VAL153-O 1213 ARG154-N 1214 ARG154-CA 1215 ARG154-CB 1216 ARG154-CG 1217 ARG154-CD 1218 ARG154-NE 1219 ARG154-CZ 1220 ARG154-NH1 1221 ARG154-NH2 1222 ARG154-C 1223 ARG154-O 1224 GLU155-N 1225 GLU155-CA 1226 GLU155-CB 1227 GLU155-CG 1228 GLU155-CD 1229 GLU155-OE1 1230 GLU155-OE2 1231 GLU155-C 1232 GLU155-O 1233 ILE156-N 1234 ILE156-CA 1235 ILE156-CB 1236 ILE156-CG1 1237 ILE156-CG2 1238 ILE156-CD1 1239 ILE156-C 1240 ILE156-O 1241 ASP157-N 1242 ASP157-CA 1243 ASP157-CB 1244 ASP157-CG 1245 ASP157-OD1 1246 ASP157-OD2 1247 ASP157-C 1248 ASP157-O 1249 VAL158-N 1250 VAL158-CA 1251 VAL158-CB 1252 VAL158-CG1 1253 VAL158-CG2 1254 VAL158-C 1255 VAL158-O 1256 VAL158-OXT 1257 NDG159-C1 1258 NDG159-C2 1259 NDG159-C3 1260 NDG159-C4 1261 NDG159-C5 1262 NDG159-C6 1263 NDG159-C7 1264 NDG159-C8 1265 NDG159-O5 1266 NDG159-O3 1267 NDG159-O4 1268 NDG159-O6 1269 NDG159-O7 1270 NDG159-N2 1271 NDG159-O1 1272 NAG160-C1 1273 NAG160-C2 1274 NAG160-C3 1275 NAG160-C4 1276 NAG160-C5 1277 NAG160-C6 1278 NAG160-C7 1279 NAG160-C8 1280 NAG160-N2 1281 NAG160-O3 1282 NAG160-O4 1283 NAG160-O5 1284 NAG160-O6 1285 NAG160-O7 1286 NAG161-C1 1287 NAG161-C2 1288 NAG161-C3 1289 NAG161-C4 1290 NAG161-C5 1291 NAG161-C6 1292 NAG161-C7 1293 NAG161-C8 1294 NAG161-N2 1295 NAG161-O3 1296 NAG161-O4 1297 NAG161-O5 1298 NAG161-O6 1299 NAG161-O7
u2 = u.atom_slice(range(1257))
u2.save_pdb('clean.pdb', force_overwrite=True)
pdb = u2.topology
lig = u.atom_slice(range(1096,1138))
lig_center = np.mean(lig.xyz[0], axis=0) * 10
lig_center
array([51.096794, 42.11686 , 16.71131 ], dtype=float32)
prot = next(oddt.toolkit.readfile('pdb', 'clean.pdb'))
print('is it the first mol in 1lmp is protein?',prot.protein,':) and MW of this mol is:', prot.molwt )
is it the first mol in 1lmp is protein? False :) and MW of this mol is: 17825.262999999977
NAG = "C(=O)NC1C(O)OC(CO)C(O)C1O"
smiles = ['c1cccc(O)c1', 'c1c(O)ccc(O)c1','c1(O)cc(c2ccccc2)cc(O)c1']
mols= []
images =[]
smiles = ["C", # NAG
"O", # OH
"[NH3+]", # NH3+
"", # H
"C=1(C=CC=CC1)", # Ph
"OC([O-])"] # COO-
for s in smiles:
smi = s + NAG
print(smi)
m = oddt.toolkit.readstring('smi', smi)
m.make3D(forcefield='mmff94', steps=150)
mols.append(m)
images.append((SVG(copy.deepcopy(m).write('svg'))))
display_svg(*images)
CC(=O)NC1C(O)OC(CO)C(O)C1O OC(=O)NC1C(O)OC(CO)C(O)C1O [NH3+]C(=O)NC1C(O)OC(CO)C(O)C1O C(=O)NC1C(O)OC(CO)C(O)C1O C=1(C=CC=CC1)C(=O)NC1C(O)OC(CO)C(O)C1O OC([O-])C(=O)NC1C(O)OC(CO)C(O)C1O
[18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs() [18:48:50] Molecule does not have explicit Hs. Consider calling AddHs()
dock_obj= oddt.docking.AutodockVina.autodock_vina(
protein=prot,size=(20,20,20),center=lig_center,
executable='/content/autodock_vina_1_1_2_linux_x86/bin/vina',autocleanup=True, num_modes=9)
#пришлось Вину самостоятельно ставить, но вроде работает
print(dock_obj.tmp_dir)
print(" ".join(dock_obj.params))
/tmp/autodock_vina_je33lm4l --center_x 51.096794 --center_y 42.11686 --center_z 16.71131 --size_x 20 --size_y 20 --size_z 20 --exhaustiveness 8 --num_modes 9 --energy_range 3
Создан файл для докинга. Заданы центр и размеры в декартовой системе координат для коробки докинга. Полнота 8 - будет предлагать несколько поз с менее благоприятной энергией. 9 конформаций, созданных Autodock Vina. 3 - отсечка диапазона энергии между ллучшим и худшим вариантом связывания.
res = dock_obj.dock(mols, prot)
print('num\tformula\taffin\trmsd\tresidue')
for i,r in enumerate(res):
### Узнаем дескриптор "формула"
formula = Chem.rdMolDescriptors.CalcMolFormula(r.Mol)
print("%4d%10s%8s%8s%8s" %(i, formula, r.data['vina_affinity'], r.data['vina_rmsd_ub'], r.residues[0].name))
data = []
for i,r in enumerate(res):
data.append([
Chem.rdMolDescriptors.CalcMolFormula(r.Mol),
r.data['vina_affinity'],
r.data['vina_rmsd_ub'],
len(oddt.interactions.hbonds(prot,r)[0]),
len(oddt.interactions.pi_stacking(prot,r)[0]),
len(oddt.interactions.hydrophobic_contacts(prot,r)[0])
])
import pandas as pd
table = pd.DataFrame(data, columns=['Formula', 'Affinity', 'RMSD', 'H bonds', 'Stacking', 'Hydrophobic contacts'])
table.sort_values('Affinity', ascending=False)
| Formula | Affinity | RMSD | H bonds | Stacking | Hydrophobic contacts | |
|---|---|---|---|---|---|---|
| 36 | C13H17NO6 | -6.9 | 0.000 | 3 | 0 | 5 |
| 37 | C13H17NO6 | -6.6 | 2.048 | 1 | 0 | 3 |
| 38 | C13H17NO6 | -6.6 | 14.573 | 4 | 1 | 12 |
| 39 | C13H17NO6 | -6.5 | 16.650 | 3 | 0 | 4 |
| 40 | C13H17NO6 | -6.2 | 15.325 | 2 | 0 | 2 |
| 41 | C13H17NO6 | -6.2 | 7.020 | 5 | 0 | 6 |
| 42 | C13H17NO6 | -6.2 | 2.730 | 0 | 1 | 3 |
| 43 | C13H17NO6 | -5.9 | 2.288 | 2 | 0 | 4 |
| 44 | C13H17NO6 | -5.9 | 6.993 | 3 | 0 | 5 |
| 45 | C8H14NO8- | -5.7 | 0.000 | 2 | 0 | 0 |
| 46 | C8H14NO8- | -5.6 | 2.991 | 4 | 0 | 0 |
| 47 | C8H14NO8- | -5.5 | 1.844 | 4 | 0 | 0 |
| 48 | C8H14NO8- | -5.4 | 13.977 | 5 | 0 | 0 |
| 0 | C8H15NO6 | -5.3 | 0.000 | 3 | 0 | 1 |
| 2 | C8H15NO6 | -5.3 | 13.909 | 6 | 0 | 3 |
| 1 | C8H15NO6 | -5.3 | 4.703 | 4 | 0 | 0 |
| 4 | C8H15NO6 | -5.2 | 4.358 | 6 | 0 | 0 |
| 3 | C8H15NO6 | -5.2 | 2.472 | 5 | 0 | 0 |
| 49 | C8H14NO8- | -5.1 | 14.342 | 4 | 0 | 0 |
| 50 | C8H14NO8- | -5.1 | 5.809 | 1 | 0 | 0 |
| 51 | C8H14NO8- | -5.1 | 15.457 | 4 | 0 | 0 |
| 5 | C8H15NO6 | -5.1 | 14.662 | 1 | 0 | 0 |
| 9 | C7H13NO7 | -5.0 | 0.000 | 5 | 0 | 0 |
| 18 | C7H15N2O6+ | -5.0 | 0.000 | 2 | 0 | 0 |
| 19 | C7H15N2O6+ | -5.0 | 5.244 | 2 | 0 | 0 |
| 20 | C7H15N2O6+ | -5.0 | 4.977 | 3 | 0 | 0 |
| 21 | C7H15N2O6+ | -5.0 | 5.100 | 1 | 0 | 0 |
| 52 | C8H14NO8- | -4.9 | 13.778 | 3 | 0 | 0 |
| 53 | C8H14NO8- | -4.9 | 14.781 | 1 | 0 | 0 |
| 22 | C7H15N2O6+ | -4.9 | 5.254 | 4 | 0 | 0 |
| 6 | C8H15NO6 | -4.9 | 2.503 | 1 | 0 | 1 |
| 10 | C7H13NO7 | -4.9 | 4.837 | 3 | 0 | 0 |
| 25 | C7H15N2O6+ | -4.9 | 2.356 | 1 | 0 | 0 |
| 24 | C7H15N2O6+ | -4.9 | 15.586 | 2 | 0 | 0 |
| 23 | C7H15N2O6+ | -4.9 | 14.522 | 4 | 0 | 0 |
| 15 | C7H13NO7 | -4.8 | 15.308 | 3 | 0 | 0 |
| 7 | C8H15NO6 | -4.8 | 15.773 | 3 | 0 | 0 |
| 8 | C8H15NO6 | -4.8 | 14.779 | 2 | 0 | 1 |
| 11 | C7H13NO7 | -4.8 | 4.571 | 4 | 0 | 0 |
| 12 | C7H13NO7 | -4.8 | 4.446 | 2 | 0 | 0 |
| 26 | C7H15N2O6+ | -4.8 | 5.544 | 9 | 0 | 0 |
| 13 | C7H13NO7 | -4.8 | 14.874 | 7 | 0 | 0 |
| 14 | C7H13NO7 | -4.8 | 4.979 | 4 | 0 | 0 |
| 27 | C7H13NO6 | -4.7 | 0.000 | 3 | 0 | 0 |
| 16 | C7H13NO7 | -4.7 | 14.586 | 6 | 0 | 0 |
| 17 | C7H13NO7 | -4.7 | 3.427 | 4 | 0 | 0 |
| 28 | C7H13NO6 | -4.6 | 2.910 | 0 | 0 | 0 |
| 29 | C7H13NO6 | -4.6 | 4.711 | 6 | 0 | 0 |
| 30 | C7H13NO6 | -4.5 | 13.898 | 3 | 0 | 0 |
| 32 | C7H13NO6 | -4.5 | 4.468 | 5 | 0 | 0 |
| 31 | C7H13NO6 | -4.5 | 3.968 | 1 | 0 | 0 |
| 35 | C7H13NO6 | -4.4 | 2.683 | 4 | 0 | 0 |
| 34 | C7H13NO6 | -4.4 | 13.816 | 4 | 0 | 0 |
| 33 | C7H13NO6 | -4.4 | 16.393 | 2 | 0 | 0 |
Лучшую афинность по оценке Вина показал C13H17NO6 (фенил), причем во всех девяти позах - полагаю, очень хороший результат. Судя по всему, этот результат достигается по большей части за счет гидрофобных контактов внесенного фенольного кольца, а не коровой части молекулы. Следом идет COO- радикал и изначальный лиганд.
Худшим оказалось лучшее предсказание для C7H13NO6 (водород). Похоже, заменяемый остаток был ключевым в полярных взаимодействиях, хоть по числу водородных связей этого и не скажешь.
#посмотрим на лучшие
for i,r in enumerate(res):
if i%9 == 0:
r.write(filename='r%s.pdb' % i, format='pdb', overwrite=True)
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd
from IPython.display import Image
pymol.cmd.reinitialize()
for i in range(6):
pymol.cmd.load('r' + str(i*9) + '.pdb')
pymol.cmd.do('''
load LYS_LAMBD.B99990001.pdb
show cartoon, LYS_LAMBD.B99990001
hide lines, LYS_LAMBD.B99990001
orient r0
zoom r0, 9
set stick_transparency, 0.6
ray
png pic0.png
''')
Image(filename='pic0.png')
Засели довольно плотно, примерно одинаково ориентированы.
Предложите методы из статьи про ODDT (пакет Sklearn), которые можно было бы использовать в Вашем упражнении Я почитал - ну мы буквально используем какую-то имплементацию первого примера. Для второго и третьего можно было бы поискать данные в литературе, но на основании чисто нынешних данных их не реализуешь - машинное обучение любит массивы даных)