File size: 26,806 Bytes
b3c2eb7 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 |
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: rdkit in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (2022.3.5)\n",
"Requirement already satisfied: Pillow in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from rdkit) (9.2.0)\n",
"Requirement already satisfied: numpy in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from rdkit) (1.23.3)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"pip install rdkit"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: torch in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (1.13.1)\n",
"Requirement already satisfied: typing-extensions in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from torch) (4.3.0)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"pip install torch"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: pytorch_lightning in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (1.7.7)\n",
"Requirement already satisfied: fsspec[http]!=2021.06.0,>=2021.05.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (2022.8.2)\n",
"Requirement already satisfied: tensorboard>=2.9.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (2.10.1)\n",
"Requirement already satisfied: torch>=1.9.* in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (1.13.1)\n",
"Requirement already satisfied: torchmetrics>=0.7.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (0.9.3)\n",
"Requirement already satisfied: PyYAML>=5.4 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (6.0)\n",
"Requirement already satisfied: typing-extensions>=4.0.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (4.3.0)\n",
"Requirement already satisfied: numpy>=1.17.2 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (1.23.3)\n",
"Requirement already satisfied: tqdm>=4.57.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (4.64.1)\n",
"Requirement already satisfied: pyDeprecate>=0.3.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pytorch_lightning) (0.3.2)\n",
"Requirement already satisfied: packaging>=17.0 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from pytorch_lightning) (21.3)\n",
"Requirement already satisfied: requests in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (2.28.1)\n",
"Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (3.8.3)\n",
"Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from packaging>=17.0->pytorch_lightning) (3.0.9)\n",
"Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (0.4.6)\n",
"Requirement already satisfied: markdown>=2.6.8 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (3.4.1)\n",
"Requirement already satisfied: protobuf<3.20,>=3.9.2 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (3.19.5)\n",
"Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (1.8.1)\n",
"Requirement already satisfied: grpcio>=1.24.3 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (1.49.1)\n",
"Requirement already satisfied: werkzeug>=1.0.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (2.2.2)\n",
"Requirement already satisfied: setuptools>=41.0.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (56.0.0)\n",
"Requirement already satisfied: wheel>=0.26 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (0.37.1)\n",
"Requirement already satisfied: google-auth<3,>=1.6.3 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (2.12.0)\n",
"Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (0.6.1)\n",
"Requirement already satisfied: absl-py>=0.4 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from tensorboard>=2.9.1->pytorch_lightning) (1.2.0)\n",
"Requirement already satisfied: colorama in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from tqdm>=4.57.0->pytorch_lightning) (0.4.5)\n",
"Requirement already satisfied: attrs>=17.3.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (22.1.0)\n",
"Requirement already satisfied: multidict<7.0,>=4.5 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (6.0.2)\n",
"Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (4.0.2)\n",
"Requirement already satisfied: yarl<2.0,>=1.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (1.8.1)\n",
"Requirement already satisfied: charset-normalizer<3.0,>=2.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (2.1.1)\n",
"Requirement already satisfied: aiosignal>=1.1.2 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (1.2.0)\n",
"Requirement already satisfied: frozenlist>=1.1.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (1.3.1)\n",
"Requirement already satisfied: rsa<5,>=3.1.4 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from google-auth<3,>=1.6.3->tensorboard>=2.9.1->pytorch_lightning) (4.9)\n",
"Requirement already satisfied: six>=1.9.0 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from google-auth<3,>=1.6.3->tensorboard>=2.9.1->pytorch_lightning) (1.16.0)\n",
"Requirement already satisfied: pyasn1-modules>=0.2.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from google-auth<3,>=1.6.3->tensorboard>=2.9.1->pytorch_lightning) (0.2.8)\n",
"Requirement already satisfied: cachetools<6.0,>=2.0.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from google-auth<3,>=1.6.3->tensorboard>=2.9.1->pytorch_lightning) (5.2.0)\n",
"Requirement already satisfied: requests-oauthlib>=0.7.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard>=2.9.1->pytorch_lightning) (1.3.1)\n",
"Requirement already satisfied: importlib-metadata>=4.4 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from markdown>=2.6.8->tensorboard>=2.9.1->pytorch_lightning) (4.12.0)\n",
"Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (1.26.12)\n",
"Requirement already satisfied: idna<4,>=2.5 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (3.4)\n",
"Requirement already satisfied: certifi>=2017.4.17 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch_lightning) (2022.9.24)\n",
"Requirement already satisfied: MarkupSafe>=2.1.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from werkzeug>=1.0.1->tensorboard>=2.9.1->pytorch_lightning) (2.1.1)\n",
"Requirement already satisfied: zipp>=0.5 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard>=2.9.1->pytorch_lightning) (3.8.1)\n",
"Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pyasn1-modules>=0.2.1->google-auth<3,>=1.6.3->tensorboard>=2.9.1->pytorch_lightning) (0.4.8)\n",
"Requirement already satisfied: oauthlib>=3.0.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard>=2.9.1->pytorch_lightning) (3.2.1)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"pip install pytorch_lightning"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: subword_nmt in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (0.3.8)Note: you may need to restart the kernel to use updated packages.\n",
"\n",
"Requirement already satisfied: tqdm in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from subword_nmt) (4.64.1)\n",
"Requirement already satisfied: mock in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from subword_nmt) (4.0.3)\n",
"Requirement already satisfied: colorama in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from tqdm->subword_nmt) (0.4.5)\n"
]
}
],
"source": [
"pip install subword_nmt"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: pandas in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (1.5.0)\n",
"Requirement already satisfied: numpy>=1.20.3 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pandas) (1.23.3)\n",
"Requirement already satisfied: pytz>=2020.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pandas) (2022.2.1)\n",
"Requirement already satisfied: python-dateutil>=2.8.1 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from pandas) (2.8.2)\n",
"Requirement already satisfied: six>=1.5 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from python-dateutil>=2.8.1->pandas) (1.16.0)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"pip install pandas"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Could not fetch URL https://pypi.org/simple/deepchem/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/deepchem/ (Caused by SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")) - skipping\n",
"Could not fetch URL https://pypi.org/simple/pip/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/pip/ (Caused by SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")) - skipping\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING: pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.\n",
"WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")': /simple/deepchem/\n",
"WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")': /simple/deepchem/\n",
"WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")': /simple/deepchem/\n",
"WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")': /simple/deepchem/\n",
"WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(\"Can't connect to HTTPS URL because the SSL module is not available.\")': /simple/deepchem/\n",
"ERROR: Could not find a version that satisfies the requirement deepchem\n",
"ERROR: No matching distribution found for deepchem\n",
"WARNING: pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.\n"
]
}
],
"source": [
"!pip install deepchem"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: pip in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (23.0.1)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"pip install --upgrade pip"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: deepchem in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (2.6.1)\n",
"Requirement already satisfied: scipy in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from deepchem) (1.9.1)\n",
"Requirement already satisfied: pandas in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from deepchem) (1.5.0)\n",
"Requirement already satisfied: joblib in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from deepchem) (1.2.0)\n",
"Requirement already satisfied: rdkit-pypi in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from deepchem) (2022.3.5)\n",
"Requirement already satisfied: scikit-learn in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from deepchem) (1.1.2)\n",
"Requirement already satisfied: numpy>=1.21 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from deepchem) (1.23.3)\n",
"Requirement already satisfied: pytz>=2020.1 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from pandas->deepchem) (2022.2.1)\n",
"Requirement already satisfied: python-dateutil>=2.8.1 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from pandas->deepchem) (2.8.2)\n",
"Requirement already satisfied: Pillow in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from rdkit-pypi->deepchem) (9.2.0)\n",
"Requirement already satisfied: threadpoolctl>=2.0.0 in c:\\users\\prajwal\\appdata\\local\\programs\\python\\python39\\lib\\site-packages (from scikit-learn->deepchem) (3.1.0)\n",
"Requirement already satisfied: six>=1.5 in c:\\users\\prajwal\\appdata\\roaming\\python\\python39\\site-packages (from python-dateutil>=2.8.1->pandas->deepchem) (1.16.0)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"source": [
"pip install deepchem --user"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"c:\\Users\\Prajwal\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\tqdm\\auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
" from .autonotebook import tqdm as notebook_tqdm\n"
]
}
],
"source": [
"from train_cli import FsrFgLightning\n",
"from rdkit import Chem\n",
"import codecs\n",
"import numpy as np\n",
"import pandas as pd\n",
"from rdkit.Chem import Descriptors\n",
"from subword_nmt.apply_bpe import BPE"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"c:\\Users\\Prajwal\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\torchmetrics\\utilities\\prints.py:36: UserWarning: Metric `AUROC` will save all targets and predictions in buffer. For large datasets this may lead to large memory footprint.\n",
" warnings.warn(*args, **kwargs)\n"
]
},
{
"data": {
"text/plain": [
"FsrFgLightning(\n",
" (net): FsrFgModel(\n",
" (encoder): Sequential(\n",
" (0): Linear(in_features=5372, out_features=500, bias=True)\n",
" (1): SELU()\n",
" (2): Linear(in_features=500, out_features=100, bias=True)\n",
" )\n",
" (decoder): Sequential(\n",
" (0): Linear(in_features=100, out_features=500, bias=True)\n",
" (1): SELU()\n",
" (2): Linear(in_features=500, out_features=5372, bias=True)\n",
" )\n",
" (dropout): Dropout(p=0.8, inplace=False)\n",
" (batch_norm): BatchNorm1d(100, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
" (predictor): Sequential(\n",
" (0): Linear(in_features=100, out_features=200, bias=True)\n",
" (1): SELU()\n",
" (2): BatchNorm1d(200, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
" (3): Linear(in_features=200, out_features=100, bias=True)\n",
" (4): SELU()\n",
" (5): BatchNorm1d(100, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
" (6): Linear(in_features=100, out_features=50, bias=True)\n",
" (7): SELU()\n",
" (8): BatchNorm1d(50, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
" (9): Dropout(p=0.8, inplace=False)\n",
" (10): Linear(in_features=50, out_features=2, bias=True)\n",
" )\n",
" )\n",
" (criterion): CrossEntropyLoss()\n",
" (recon_loss): BCEWithLogitsLoss()\n",
" (softmax): Softmax(dim=1)\n",
" (train_auc): AUROC()\n",
" (valid_auc): AUROC()\n",
" (test_auc): AUROC()\n",
")"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"model = FsrFgLightning.load_from_checkpoint('epoch=22-step=5359.ckpt')\n",
"model.eval()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def smiles2index(s1, words2idx, bpe):\n",
" t1 = bpe.process_line(s1).split()\n",
" i1 = [words2idx[i] for i in t1]\n",
" return i1\n",
"\n",
"\n",
"def index2multi_hot(i1, idx2word):\n",
" v1 = np.zeros(len(idx2word))\n",
" v1[i1] = 1\n",
" return v1\n",
"\n",
"\n",
"def index2multi_hot_fg(molecule, fgroups_list):\n",
" v1 = np.zeros(len(fgroups_list))\n",
" for idx in range(len(fgroups_list)):\n",
" if molecule.HasSubstructMatch(fgroups_list[idx]):\n",
" v1[idx] = 1\n",
" return v1\n",
"\n",
"\n",
"def smiles2vector_fgr(s1, words2idx, bpe, idx2word, fgroups_list):\n",
" i1 = smiles2index(s1, words2idx, bpe)\n",
" mfg = index2multi_hot(i1, idx2word)\n",
" molecule = Chem.MolFromSmiles(s1)\n",
" fg = index2multi_hot_fg(molecule, fgroups_list)\n",
" return fg, mfg"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"fgroups = pd.read_csv('Functional_groups_filtered.csv')\n",
"fgroups_list = list(map(lambda x: Chem.MolFromSmarts(x), fgroups['SMARTS'].tolist()))\n",
"fgroups_list = [i for i in fgroups_list if i]\n",
"descriptor_funcs = {name: func for name, func in Descriptors.descList}\n",
"\n",
"vocab_path = 'codes_drug_chembl_1500.txt'\n",
"bpe_codes_fin = codecs.open(vocab_path)\n",
"bpe = BPE(bpe_codes_fin, merges=-1, separator='')\n",
"vocab_map = pd.read_csv('subword_units_map_drug_chembl_1500.csv')\n",
"idx2word = vocab_map['index'].values\n",
"words2idx = dict(zip(idx2word, range(0, len(idx2word))))"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"f = open('saff_gen_gpt.txt')\n",
"smiles = f.read().splitlines()\n",
"\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 30/30 [00:01<00:00, 25.86it/s]\n"
]
}
],
"source": [
"from tqdm.auto import tqdm\n",
"import torch\n",
"sm = torch.nn.Softmax(dim = 1)\n",
"preds = []\n",
"probab = []\n",
"for smile in tqdm(smiles):\n",
" fg, mfg = smiles2vector_fgr(smile, words2idx, bpe, idx2word, fgroups_list)\n",
" y_pred, _ = model(fg=torch.Tensor(fg).unsqueeze(0),mfg=torch.Tensor(mfg).unsqueeze(0),num_features=None)\n",
" probabilities = sm(y_pred) \n",
" # print(y_pred)\n",
" # print(probabilities.detach().max().item())\n",
" probab.append(probabilities.detach().max().item())\n",
" # print(int(torch.argmax(y_pred)))\n",
" preds.append(int(torch.argmax(y_pred)))"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"data = {'SMILES': smiles,'Predicted_activity':preds, 'Probability': probab}"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"pd.DataFrame(data).to_csv('moses250.csv',index=False)"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"0 30\n",
"Name: Predicted_activity, dtype: int64"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pd.DataFrame(data)['Predicted_activity'].value_counts()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.9.5 64-bit",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.5"
},
"vscode": {
"interpreter": {
"hash": "a4329ea539b1232b51730207fd9c93849c82cf9ff2a2d6356a1e6b85d15167f8"
}
}
},
"nbformat": 4,
"nbformat_minor": 0
}
|