├── Automated DFT (1).ipynb ├── Building a Simple Decision Tree.ipynb ├── Building a Simple Regression Model.ipynb ├── Ewald Electrostastic Energy.ipynb ├── Exploratory Data Analysis.ipynb ├── Exploring New Alloy Systems with Pymatgen.ipynb ├── ML Band Structure.ipynb ├── ML for Materials Science 1.ipynb ├── ML using CrystalFeatures to predict the bandgap (1).ipynb ├── ML using pymatgen.ipynb ├── MSEML-Linear Regression.ipynb ├── Materials API.ipynb ├── Pandas for Cheminformatics.ipynb ├── Pymatgen_foundations.ipynb ├── RDKit for Cheminformatics.ipynb ├── README.md ├── Working with Surfaces using ML.ipynb ├── curated-solubility-dataset.csv ├── delaney.csv ├── example_compounds.sdf ├── mol_formula.csv └── solubility_data_ok.csv /Automated DFT (1).ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "id": "961c80e3", 7 | "metadata": {}, 8 | "outputs": [], 9 | "source": [ 10 | "from pymatgen import Structure" 11 | ] 12 | }, 13 | { 14 | "cell_type": "code", 15 | "execution_count": 11, 16 | "id": "bf2f9e04", 17 | "metadata": {}, 18 | "outputs": [], 19 | "source": [ 20 | "struc = Structure.from_file(\"Al16Cr10.cif\")" 21 | ] 22 | }, 23 | { 24 | "cell_type": "code", 25 | "execution_count": 12, 26 | "id": "0749abe9", 27 | "metadata": {}, 28 | "outputs": [ 29 | { 30 | "data": { 31 | "text/plain": [ 32 | "Structure Summary\n", 33 | "Lattice\n", 34 | " abc : 7.87891373 7.87891356 7.87891376\n", 35 | " angles : 109.69518779 109.69519443 109.69518692000001\n", 36 | " volume : 373.3557970242865\n", 37 | " A : 7.4179879378990465 0.0 -2.6553223002051487\n", 38 | " B : -3.7708043655287886 6.388081220096889 -2.6553213832427804\n", 39 | " C : 0.0 0.0 7.87891376\n", 40 | "PeriodicSite: Al (2.5401, 4.4490, 1.7887) [0.6965, 0.6965, 0.6965]\n", 41 | "PeriodicSite: Al (4.7885, 0.0131, 3.3720) [0.6466, 0.0020, 0.6466]\n", 42 | "PeriodicSite: Al (2.3581, 4.1303, -3.4176) [0.6466, 0.6466, 0.0020]\n", 43 | "PeriodicSite: Al (-2.4229, 4.1303, 3.3720) [0.0020, 0.6466, 0.6466]\n", 44 | "PeriodicSite: Al (0.3901, 3.5682, 0.2747) [0.3365, 0.5586, 0.3365]\n", 45 | "PeriodicSite: Al (1.2274, 2.1497, 2.6138) [0.3365, 0.3365, 0.5586]\n", 46 | "PeriodicSite: Al (2.8745, 2.1497, 0.2747) [0.5586, 0.3365, 0.3365]\n", 47 | "PeriodicSite: Al (4.0040, 2.4506, 2.8195) [0.7348, 0.3836, 0.7348]\n", 48 | "PeriodicSite: Al (2.6798, 4.6938, -0.8796) [0.7348, 0.7348, 0.3836]\n", 49 | "PeriodicSite: Al (0.0750, 4.6938, 2.8195) [0.3836, 0.7348, 0.7348]\n", 50 | "PeriodicSite: Al (-0.4312, 4.2592, -2.2162) [0.2808, 0.6667, 0.0381]\n", 51 | "PeriodicSite: Al (-0.7766, 1.7938, 4.4066) [0.0381, 0.2808, 0.6667]\n", 52 | "PeriodicSite: Al (4.8024, 0.2431, 0.3409) [0.6667, 0.0381, 0.2808]\n", 53 | "PeriodicSite: Al (3.8871, 1.7938, -2.2162) [0.6667, 0.2808, 0.0381]\n", 54 | "PeriodicSite: Al (-2.2319, 4.2592, 0.3409) [0.0381, 0.6667, 0.2808]\n", 55 | "PeriodicSite: Al (1.9395, 0.2431, 4.4066) [0.2808, 0.0381, 0.6667]\n", 56 | "PeriodicSite: Cr (0.5512, 0.9654, 0.3881) [0.1511, 0.1511, 0.1511]\n", 57 | "PeriodicSite: Cr (-2.8925, 5.0930, -2.0369) [0.0153, 0.7973, 0.0153]\n", 58 | "PeriodicSite: Cr (0.0560, 0.0980, 6.2001) [0.0153, 0.0153, 0.7973]\n", 59 | "PeriodicSite: Cr (5.8563, 0.0980, -2.0369) [0.7973, 0.0153, 0.0153]\n", 60 | "PeriodicSite: Cr (6.0694, 2.1316, 4.2740) [0.9878, 0.3337, 0.9878]\n", 61 | "PeriodicSite: Cr (3.6028, 6.3103, -2.6169) [0.9878, 0.9878, 0.3337]\n", 62 | "PeriodicSite: Cr (-1.2496, 6.3103, 4.2740) [0.3337, 0.9878, 0.9878]\n", 63 | "PeriodicSite: Cr (2.6477, 0.1018, 1.8644) [0.3650, 0.0159, 0.3650]\n", 64 | "PeriodicSite: Cr (1.3313, 2.3318, -1.8130) [0.3650, 0.3650, 0.0159]\n", 65 | "PeriodicSite: Cr (-1.2582, 2.3318, 1.8644) [0.0159, 0.3650, 0.3650]" 66 | ] 67 | }, 68 | "execution_count": 12, 69 | "metadata": {}, 70 | "output_type": "execute_result" 71 | } 72 | ], 73 | "source": [ 74 | "struc" 75 | ] 76 | }, 77 | { 78 | "cell_type": "code", 79 | "execution_count": 13, 80 | "id": "b3f5e64c", 81 | "metadata": {}, 82 | "outputs": [], 83 | "source": [ 84 | "import pymatgen.io" 85 | ] 86 | }, 87 | { 88 | "cell_type": "code", 89 | "execution_count": 14, 90 | "id": "322952d2", 91 | "metadata": {}, 92 | "outputs": [], 93 | "source": [ 94 | "from pymatgen.io.vasp.inputs import Poscar" 95 | ] 96 | }, 97 | { 98 | "cell_type": "code", 99 | "execution_count": 15, 100 | "id": "124b386d", 101 | "metadata": {}, 102 | "outputs": [], 103 | "source": [ 104 | "my_poscar = Poscar(structure=struc)" 105 | ] 106 | }, 107 | { 108 | "cell_type": "code", 109 | "execution_count": 16, 110 | "id": "883ddc4d", 111 | "metadata": {}, 112 | "outputs": [ 113 | { 114 | "name": "stdout", 115 | "output_type": "stream", 116 | "text": [ 117 | "Al16 Cr10\n", 118 | "1.0\n", 119 | "7.417988 0.000000 -2.655322\n", 120 | "-3.770804 6.388081 -2.655321\n", 121 | "0.000000 0.000000 7.878914\n", 122 | "Al Cr\n", 123 | "16 10\n", 124 | "direct\n", 125 | "0.696455 0.696455 0.696455 Al\n", 126 | "0.646563 0.002044 0.646563 Al\n", 127 | "0.646563 0.646563 0.002044 Al\n", 128 | "0.002044 0.646563 0.646563 Al\n", 129 | "0.336523 0.558569 0.336523 Al\n", 130 | "0.336523 0.336523 0.558569 Al\n", 131 | "0.558569 0.336523 0.336523 Al\n", 132 | "0.734771 0.383622 0.734771 Al\n", 133 | "0.734771 0.734771 0.383622 Al\n", 134 | "0.383622 0.734771 0.734771 Al\n", 135 | "0.280797 0.666745 0.038053 Al\n", 136 | "0.038053 0.280797 0.666745 Al\n", 137 | "0.666745 0.038053 0.280797 Al\n", 138 | "0.666745 0.280797 0.038053 Al\n", 139 | "0.038053 0.666745 0.280797 Al\n", 140 | "0.280797 0.038053 0.666745 Al\n", 141 | "0.151124 0.151124 0.151124 Cr\n", 142 | "0.015343 0.797266 0.015343 Cr\n", 143 | "0.015343 0.015343 0.797266 Cr\n", 144 | "0.797266 0.015343 0.015343 Cr\n", 145 | "0.987828 0.333690 0.987828 Cr\n", 146 | "0.987828 0.987828 0.333690 Cr\n", 147 | "0.333690 0.987828 0.987828 Cr\n", 148 | "0.365023 0.015932 0.365023 Cr\n", 149 | "0.365023 0.365023 0.015932 Cr\n", 150 | "0.015932 0.365023 0.365023 Cr\n", 151 | "\n" 152 | ] 153 | } 154 | ], 155 | "source": [ 156 | "print(my_poscar)" 157 | ] 158 | }, 159 | { 160 | "cell_type": "code", 161 | "execution_count": 18, 162 | "id": "ae347f69", 163 | "metadata": {}, 164 | "outputs": [], 165 | "source": [ 166 | "example_poscar = Poscar.from_file(\"./POSCAR.gz\")" 167 | ] 168 | }, 169 | { 170 | "cell_type": "code", 171 | "execution_count": 19, 172 | "id": "bc5c5550", 173 | "metadata": {}, 174 | "outputs": [ 175 | { 176 | "name": "stdout", 177 | "output_type": "stream", 178 | "text": [ 179 | "Al16 Cr10\n", 180 | "1.0\n", 181 | "7.417988 0.000000 -2.655322\n", 182 | "-3.770804 6.388081 -2.655321\n", 183 | "0.000000 0.000000 7.878914\n", 184 | "Al Cr\n", 185 | "16 10\n", 186 | "direct\n", 187 | "0.696455 0.696455 0.696455 Al\n", 188 | "0.646563 0.002044 0.646563 Al\n", 189 | "0.646563 0.646563 0.002044 Al\n", 190 | "0.002044 0.646563 0.646563 Al\n", 191 | "0.336523 0.558569 0.336523 Al\n", 192 | "0.336523 0.336523 0.558569 Al\n", 193 | "0.558569 0.336523 0.336523 Al\n", 194 | "0.734771 0.383622 0.734771 Al\n", 195 | "0.734771 0.734771 0.383622 Al\n", 196 | "0.383622 0.734771 0.734771 Al\n", 197 | "0.280797 0.666745 0.038053 Al\n", 198 | "0.038053 0.280797 0.666745 Al\n", 199 | "0.666745 0.038053 0.280797 Al\n", 200 | "0.666745 0.280797 0.038053 Al\n", 201 | "0.038053 0.666745 0.280797 Al\n", 202 | "0.280797 0.038053 0.666745 Al\n", 203 | "0.151124 0.151124 0.151124 Cr\n", 204 | "0.015343 0.797266 0.015343 Cr\n", 205 | "0.015343 0.015343 0.797266 Cr\n", 206 | "0.797266 0.015343 0.015343 Cr\n", 207 | "0.987828 0.333690 0.987828 Cr\n", 208 | "0.987828 0.987828 0.333690 Cr\n", 209 | "0.333690 0.987828 0.987828 Cr\n", 210 | "0.365023 0.015932 0.365023 Cr\n", 211 | "0.365023 0.365023 0.015932 Cr\n", 212 | "0.015932 0.365023 0.365023 Cr\n", 213 | "\n" 214 | ] 215 | } 216 | ], 217 | "source": [ 218 | "print(example_poscar)" 219 | ] 220 | }, 221 | { 222 | "cell_type": "code", 223 | "execution_count": 20, 224 | "id": "101cbe1b", 225 | "metadata": {}, 226 | "outputs": [ 227 | { 228 | "data": { 229 | "text/plain": [ 230 | "Structure Summary\n", 231 | "Lattice\n", 232 | " abc : 7.878913687293953 7.87891307745034 7.878914\n", 233 | " angles : 109.69518608598659 109.6951922224134 109.69518763777374\n", 234 | " volume : 373.35579865899433\n", 235 | " A : 7.417988 0.0 -2.655322\n", 236 | " B : -3.770804 6.388081 -2.655321\n", 237 | " C : 0.0 0.0 7.878914\n", 238 | "PeriodicSite: Al (2.5401, 4.4490, 1.7887) [0.6965, 0.6965, 0.6965]\n", 239 | "PeriodicSite: Al (4.7885, 0.0131, 3.3720) [0.6466, 0.0020, 0.6466]\n", 240 | "PeriodicSite: Al (2.3581, 4.1303, -3.4176) [0.6466, 0.6466, 0.0020]\n", 241 | "PeriodicSite: Al (-2.4229, 4.1303, 3.3720) [0.0020, 0.6466, 0.6466]\n", 242 | "PeriodicSite: Al (0.3901, 3.5682, 0.2747) [0.3365, 0.5586, 0.3365]\n", 243 | "PeriodicSite: Al (1.2274, 2.1497, 2.6138) [0.3365, 0.3365, 0.5586]\n", 244 | "PeriodicSite: Al (2.8745, 2.1497, 0.2747) [0.5586, 0.3365, 0.3365]\n", 245 | "PeriodicSite: Al (4.0040, 2.4506, 2.8195) [0.7348, 0.3836, 0.7348]\n", 246 | "PeriodicSite: Al (2.6798, 4.6938, -0.8796) [0.7348, 0.7348, 0.3836]\n", 247 | "PeriodicSite: Al (0.0750, 4.6938, 2.8195) [0.3836, 0.7348, 0.7348]\n", 248 | "PeriodicSite: Al (-0.4312, 4.2592, -2.2162) [0.2808, 0.6667, 0.0381]\n", 249 | "PeriodicSite: Al (-0.7766, 1.7938, 4.4066) [0.0381, 0.2808, 0.6667]\n", 250 | "PeriodicSite: Al (4.8024, 0.2431, 0.3409) [0.6667, 0.0381, 0.2808]\n", 251 | "PeriodicSite: Al (3.8871, 1.7938, -2.2162) [0.6667, 0.2808, 0.0381]\n", 252 | "PeriodicSite: Al (-2.2319, 4.2592, 0.3409) [0.0381, 0.6667, 0.2808]\n", 253 | "PeriodicSite: Al (1.9395, 0.2431, 4.4066) [0.2808, 0.0381, 0.6667]\n", 254 | "PeriodicSite: Cr (0.5512, 0.9654, 0.3881) [0.1511, 0.1511, 0.1511]\n", 255 | "PeriodicSite: Cr (-2.8925, 5.0930, -2.0369) [0.0153, 0.7973, 0.0153]\n", 256 | "PeriodicSite: Cr (0.0560, 0.0980, 6.2001) [0.0153, 0.0153, 0.7973]\n", 257 | "PeriodicSite: Cr (5.8563, 0.0980, -2.0369) [0.7973, 0.0153, 0.0153]\n", 258 | "PeriodicSite: Cr (6.0694, 2.1316, 4.2740) [0.9878, 0.3337, 0.9878]\n", 259 | "PeriodicSite: Cr (3.6028, 6.3103, -2.6169) [0.9878, 0.9878, 0.3337]\n", 260 | "PeriodicSite: Cr (-1.2496, 6.3103, 4.2740) [0.3337, 0.9878, 0.9878]\n", 261 | "PeriodicSite: Cr (2.6477, 0.1018, 1.8644) [0.3650, 0.0159, 0.3650]\n", 262 | "PeriodicSite: Cr (1.3313, 2.3318, -1.8130) [0.3650, 0.3650, 0.0159]\n", 263 | "PeriodicSite: Cr (-1.2582, 2.3318, 1.8644) [0.0159, 0.3650, 0.3650]" 264 | ] 265 | }, 266 | "execution_count": 20, 267 | "metadata": {}, 268 | "output_type": "execute_result" 269 | } 270 | ], 271 | "source": [ 272 | "example_poscar.structure" 273 | ] 274 | }, 275 | { 276 | "cell_type": "code", 277 | "execution_count": 21, 278 | "id": "8fb04009", 279 | "metadata": {}, 280 | "outputs": [ 281 | { 282 | "name": "stdout", 283 | "output_type": "stream", 284 | "text": [ 285 | "Full Formula (H4 C3 O3)\n", 286 | "Reduced Formula: H4(CO)3\n", 287 | "Charge = 0, Spin Mult = 1\n", 288 | "Sites (10)\n", 289 | "0 O 0.310287 -1.176345 -0.374099\n", 290 | "1 C -0.682156 -0.509251 0.347984\n", 291 | "2 C 1.528121 -0.493823 -0.092251\n", 292 | "3 O -1.901588 -0.631984 -0.015154\n", 293 | "4 O -0.247010 0.912691 0.370073\n", 294 | "5 C 1.108528 0.972764 -0.081946\n", 295 | "6 H 2.251945 -0.729522 -0.871996\n", 296 | "7 H 1.920141 -0.804271 0.883050\n", 297 | "8 H 1.141868 1.409846 -1.084537\n", 298 | "9 H 1.702594 1.580992 0.602886\n" 299 | ] 300 | } 301 | ], 302 | "source": [ 303 | "from pymatgen import Molecule\n", 304 | "\n", 305 | "mol = Molecule.from_file(\"ethylene_carbonate.xyz\")\n", 306 | "print(mol)" 307 | ] 308 | }, 309 | { 310 | "cell_type": "code", 311 | "execution_count": 22, 312 | "id": "6f945e07", 313 | "metadata": {}, 314 | "outputs": [], 315 | "source": [ 316 | "import pymatgen.io.qchem.inputs" 317 | ] 318 | }, 319 | { 320 | "cell_type": "code", 321 | "execution_count": 24, 322 | "id": "3808259e", 323 | "metadata": {}, 324 | "outputs": [ 325 | { 326 | "data": { 327 | "text/plain": [ 328 | "pymatgen.io.qchem.inputs.QCInput" 329 | ] 330 | }, 331 | "execution_count": 24, 332 | "metadata": {}, 333 | "output_type": "execute_result" 334 | } 335 | ], 336 | "source": [ 337 | "pymatgen.io.qchem.inputs.QCInput" 338 | ] 339 | }, 340 | { 341 | "cell_type": "code", 342 | "execution_count": 25, 343 | "id": "5cb034d6", 344 | "metadata": {}, 345 | "outputs": [ 346 | { 347 | "name": "stdout", 348 | "output_type": "stream", 349 | "text": [ 350 | "Full Formula (H4 C3 O3)\n", 351 | "Reduced Formula: H4(CO)3\n", 352 | "Charge = 0.0, Spin Mult = 1\n", 353 | "Sites (10)\n", 354 | "0 O 0.310287 -1.176345 -0.374099\n", 355 | "1 C -0.682156 -0.509251 0.347984\n", 356 | "2 C 1.528121 -0.493823 -0.092251\n", 357 | "3 O -1.901588 -0.631984 -0.015154\n", 358 | "4 O -0.247010 0.912691 0.370073\n", 359 | "5 C 1.108528 0.972764 -0.081946\n", 360 | "6 H 2.251945 -0.729522 -0.871996\n", 361 | "7 H 1.920141 -0.804271 0.883050\n", 362 | "8 H 1.141868 1.409846 -1.084537\n", 363 | "9 H 1.702594 1.580992 0.602886\n" 364 | ] 365 | } 366 | ], 367 | "source": [ 368 | "from pymatgen.io.qchem.inputs import QCInput\n", 369 | "\n", 370 | "qcinp = QCInput.from_file(\"./mol.qin.gz\")\n", 371 | "print(qcinp.molecule)" 372 | ] 373 | }, 374 | { 375 | "cell_type": "code", 376 | "execution_count": 26, 377 | "id": "75169718", 378 | "metadata": {}, 379 | "outputs": [], 380 | "source": [ 381 | "import pymatgen.io.qchem.outputs" 382 | ] 383 | }, 384 | { 385 | "cell_type": "code", 386 | "execution_count": 27, 387 | "id": "28fa349f", 388 | "metadata": {}, 389 | "outputs": [ 390 | { 391 | "data": { 392 | "text/plain": [ 393 | "pymatgen.io.qchem.outputs.QCOutput" 394 | ] 395 | }, 396 | "execution_count": 27, 397 | "metadata": {}, 398 | "output_type": "execute_result" 399 | } 400 | ], 401 | "source": [ 402 | "pymatgen.io.qchem.outputs.QCOutput" 403 | ] 404 | }, 405 | { 406 | "cell_type": "code", 407 | "execution_count": 28, 408 | "id": "13630c87", 409 | "metadata": {}, 410 | "outputs": [], 411 | "source": [ 412 | "from pymatgen.io.qchem.outputs import QCOutput\n", 413 | "\n", 414 | "qcoutput = QCOutput(filename=\"./mol.qout.gz\")" 415 | ] 416 | }, 417 | { 418 | "cell_type": "code", 419 | "execution_count": 29, 420 | "id": "544c9f5c", 421 | "metadata": {}, 422 | "outputs": [ 423 | { 424 | "data": { 425 | "text/plain": [ 426 | "dict_keys(['errors', 'warnings', 'multiple_outputs', 'charge', 'multiplicity', 'point_group', 'species', 'initial_geometry', 'initial_molecule', 'completion', 'walltime', 'cputime', 'unrestricted', 'using_GEN_SCFMAN', 'SCF', 'SCF_energy_in_the_final_basis_set', 'Total_energy_in_the_final_basis_set', 'Mulliken', 'RESP', 'solvent_method', 'solvent_data', 'final_energy', 'using_dft_d3', 'optimization', 'energy_trajectory', 'geometries', 'last_geometry', 'molecule_from_last_geometry', 'optimized_geometry', 'molecule_from_optimized_geometry', 'gradients', 'pcm_gradients', 'CDS_gradients', 'opt_constraint', 'frequency_job', 'single_point_job', 'force_job'])" 427 | ] 428 | }, 429 | "execution_count": 29, 430 | "metadata": {}, 431 | "output_type": "execute_result" 432 | } 433 | ], 434 | "source": [ 435 | "qcoutput.data.keys()" 436 | ] 437 | }, 438 | { 439 | "cell_type": "code", 440 | "execution_count": 30, 441 | "id": "b0248ff3", 442 | "metadata": {}, 443 | "outputs": [ 444 | { 445 | "data": { 446 | "text/plain": [ 447 | "Molecule Summary\n", 448 | "Site: O (0.2918, -1.1858, -0.2649)\n", 449 | "Site: C (-0.7138, -0.3636, 0.0702)\n", 450 | "Site: C (1.5471, -0.4958, -0.0800)\n", 451 | "Site: O (-1.8614, -0.6985, 0.1528)\n", 452 | "Site: O (-0.2714, 0.8816, 0.3009)\n", 453 | "Site: C (1.1213, 0.9646, -0.0719)\n", 454 | "Site: H (2.2107, -0.7524, -0.9034)\n", 455 | "Site: H (1.9781, -0.8165, 0.8703)\n", 456 | "Site: H (1.1856, 1.4299, -1.0573)\n", 457 | "Site: H (1.6448, 1.5675, 0.6674)" 458 | ] 459 | }, 460 | "execution_count": 30, 461 | "metadata": {}, 462 | "output_type": "execute_result" 463 | } 464 | ], 465 | "source": [ 466 | "qcoutput.data['molecule_from_optimized_geometry']" 467 | ] 468 | }, 469 | { 470 | "cell_type": "code", 471 | "execution_count": 31, 472 | "id": "e986b863", 473 | "metadata": {}, 474 | "outputs": [], 475 | "source": [ 476 | "import pymatgen.io.vasp.sets" 477 | ] 478 | }, 479 | { 480 | "cell_type": "code", 481 | "execution_count": 33, 482 | "id": "e8e8ee27", 483 | "metadata": {}, 484 | "outputs": [], 485 | "source": [ 486 | "from pymatgen.io.vasp.sets import MPRelaxSet" 487 | ] 488 | }, 489 | { 490 | "cell_type": "code", 491 | "execution_count": 34, 492 | "id": "6f4ab194", 493 | "metadata": {}, 494 | "outputs": [], 495 | "source": [ 496 | "relax_set = MPRelaxSet(structure=struc)" 497 | ] 498 | }, 499 | { 500 | "cell_type": "code", 501 | "execution_count": 35, 502 | "id": "8b12c046", 503 | "metadata": {}, 504 | "outputs": [ 505 | { 506 | "name": "stdout", 507 | "output_type": "stream", 508 | "text": [ 509 | "ALGO = Fast\n", 510 | "EDIFF = 0.0013000000000000002\n", 511 | "ENCUT = 520\n", 512 | "IBRION = 2\n", 513 | "ISIF = 3\n", 514 | "ISMEAR = -5\n", 515 | "ISPIN = 2\n", 516 | "LASPH = True\n", 517 | "LORBIT = 11\n", 518 | "LREAL = Auto\n", 519 | "LWAVE = False\n", 520 | "MAGMOM = 16*0.6 10*5.0\n", 521 | "NELM = 100\n", 522 | "NSW = 99\n", 523 | "PREC = Accurate\n", 524 | "SIGMA = 0.05\n", 525 | "\n" 526 | ] 527 | }, 528 | { 529 | "name": "stderr", 530 | "output_type": "stream", 531 | "text": [ 532 | "/home/max/.virtualenvs/aiida/lib/python3.7/site-packages/pymatgen/io/vasp/sets.py:613: BadInputSetWarning: Relaxation of likely metal with ISMEAR < 1 detected. Please see VASP recommendations on ISMEAR for metals.\n", 533 | " BadInputSetWarning,\n" 534 | ] 535 | } 536 | ], 537 | "source": [ 538 | "print(relax_set.incar)" 539 | ] 540 | }, 541 | { 542 | "cell_type": "code", 543 | "execution_count": 36, 544 | "id": "7474f004", 545 | "metadata": {}, 546 | "outputs": [], 547 | "source": [ 548 | "from pymatgen.io.vasp.sets import MPMetalRelaxSet" 549 | ] 550 | }, 551 | { 552 | "cell_type": "code", 553 | "execution_count": 37, 554 | "id": "dbad54b0", 555 | "metadata": {}, 556 | "outputs": [ 557 | { 558 | "name": "stdout", 559 | "output_type": "stream", 560 | "text": [ 561 | "ALGO = Fast\n", 562 | "EDIFF = 0.0013000000000000002\n", 563 | "ENCUT = 520\n", 564 | "IBRION = 2\n", 565 | "ISIF = 3\n", 566 | "ISMEAR = 1\n", 567 | "ISPIN = 2\n", 568 | "LASPH = True\n", 569 | "LORBIT = 11\n", 570 | "LREAL = Auto\n", 571 | "LWAVE = False\n", 572 | "MAGMOM = 16*0.6 10*5.0\n", 573 | "NELM = 100\n", 574 | "NSW = 99\n", 575 | "PREC = Accurate\n", 576 | "SIGMA = 0.2\n", 577 | "\n" 578 | ] 579 | } 580 | ], 581 | "source": [ 582 | "metal_relax_set = MPMetalRelaxSet(structure=struc)\n", 583 | "print(metal_relax_set.incar)" 584 | ] 585 | }, 586 | { 587 | "cell_type": "code", 588 | "execution_count": 38, 589 | "id": "d59de9de", 590 | "metadata": {}, 591 | "outputs": [], 592 | "source": [ 593 | "import pymatgen.io.qchem.sets" 594 | ] 595 | }, 596 | { 597 | "cell_type": "code", 598 | "execution_count": 39, 599 | "id": "2b85ab17", 600 | "metadata": {}, 601 | "outputs": [ 602 | { 603 | "data": { 604 | "text/plain": [ 605 | "pymatgen.io.qchem.sets.OptSet" 606 | ] 607 | }, 608 | "execution_count": 39, 609 | "metadata": {}, 610 | "output_type": "execute_result" 611 | } 612 | ], 613 | "source": [ 614 | "pymatgen.io.qchem.sets.OptSet" 615 | ] 616 | }, 617 | { 618 | "cell_type": "code", 619 | "execution_count": 41, 620 | "id": "7a7de7e7", 621 | "metadata": {}, 622 | "outputs": [], 623 | "source": [ 624 | "from pymatgen.io.qchem.sets import OptSet" 625 | ] 626 | }, 627 | { 628 | "cell_type": "code", 629 | "execution_count": 42, 630 | "id": "a3e111a1", 631 | "metadata": {}, 632 | "outputs": [ 633 | { 634 | "name": "stdout", 635 | "output_type": "stream", 636 | "text": [ 637 | "$molecule\n", 638 | " 0 1\n", 639 | " O 0.3102870000 -1.1763450000 -0.3740990000\n", 640 | " C -0.6821560000 -0.5092510000 0.3479840000\n", 641 | " C 1.5281210000 -0.4938230000 -0.0922510000\n", 642 | " O -1.9015880000 -0.6319840000 -0.0151540000\n", 643 | " O -0.2470100000 0.9126910000 0.3700730000\n", 644 | " C 1.1085280000 0.9727640000 -0.0819460000\n", 645 | " H 2.2519450000 -0.7295220000 -0.8719960000\n", 646 | " H 1.9201410000 -0.8042710000 0.8830500000\n", 647 | " H 1.1418680000 1.4098460000 -1.0845370000\n", 648 | " H 1.7025940000 1.5809920000 0.6028860000\n", 649 | "$end\n", 650 | "\n", 651 | "$rem\n", 652 | " job_type = opt\n", 653 | " basis = def2-tzvppd\n", 654 | " max_scf_cycles = 200\n", 655 | " gen_scfman = true\n", 656 | " xc_grid = 3\n", 657 | " scf_algorithm = diis\n", 658 | " resp_charges = true\n", 659 | " symmetry = false\n", 660 | " sym_ignore = true\n", 661 | " method = wb97xd\n", 662 | " geom_opt_max_cycles = 200\n", 663 | "$end\n", 664 | "\n" 665 | ] 666 | } 667 | ], 668 | "source": [ 669 | "opt_set = OptSet(molecule=mol)\n", 670 | "print(opt_set)" 671 | ] 672 | }, 673 | { 674 | "cell_type": "code", 675 | "execution_count": 43, 676 | "id": "606853bc", 677 | "metadata": {}, 678 | "outputs": [], 679 | "source": [ 680 | "from pymatgen.io.qchem.sets import FreqSet" 681 | ] 682 | }, 683 | { 684 | "cell_type": "code", 685 | "execution_count": 44, 686 | "id": "ca13182d", 687 | "metadata": {}, 688 | "outputs": [ 689 | { 690 | "name": "stdout", 691 | "output_type": "stream", 692 | "text": [ 693 | "$molecule\n", 694 | " 0 1\n", 695 | " O 0.3102870000 -1.1763450000 -0.3740990000\n", 696 | " C -0.6821560000 -0.5092510000 0.3479840000\n", 697 | " C 1.5281210000 -0.4938230000 -0.0922510000\n", 698 | " O -1.9015880000 -0.6319840000 -0.0151540000\n", 699 | " O -0.2470100000 0.9126910000 0.3700730000\n", 700 | " C 1.1085280000 0.9727640000 -0.0819460000\n", 701 | " H 2.2519450000 -0.7295220000 -0.8719960000\n", 702 | " H 1.9201410000 -0.8042710000 0.8830500000\n", 703 | " H 1.1418680000 1.4098460000 -1.0845370000\n", 704 | " H 1.7025940000 1.5809920000 0.6028860000\n", 705 | "$end\n", 706 | "\n", 707 | "$rem\n", 708 | " job_type = freq\n", 709 | " basis = def2-tzvppd\n", 710 | " max_scf_cycles = 200\n", 711 | " gen_scfman = true\n", 712 | " xc_grid = 3\n", 713 | " scf_algorithm = diis\n", 714 | " resp_charges = true\n", 715 | " symmetry = false\n", 716 | " sym_ignore = true\n", 717 | " method = wb97xd\n", 718 | "$end\n", 719 | "\n" 720 | ] 721 | } 722 | ], 723 | "source": [ 724 | "freq_set = FreqSet(mol)\n", 725 | "print(freq_set)" 726 | ] 727 | }, 728 | { 729 | "cell_type": "code", 730 | "execution_count": 45, 731 | "id": "8be044ad", 732 | "metadata": {}, 733 | "outputs": [ 734 | { 735 | "name": "stdout", 736 | "output_type": "stream", 737 | "text": [ 738 | "$molecule\n", 739 | " 0 1\n", 740 | " O 0.3102870000 -1.1763450000 -0.3740990000\n", 741 | " C -0.6821560000 -0.5092510000 0.3479840000\n", 742 | " C 1.5281210000 -0.4938230000 -0.0922510000\n", 743 | " O -1.9015880000 -0.6319840000 -0.0151540000\n", 744 | " O -0.2470100000 0.9126910000 0.3700730000\n", 745 | " C 1.1085280000 0.9727640000 -0.0819460000\n", 746 | " H 2.2519450000 -0.7295220000 -0.8719960000\n", 747 | " H 1.9201410000 -0.8042710000 0.8830500000\n", 748 | " H 1.1418680000 1.4098460000 -1.0845370000\n", 749 | " H 1.7025940000 1.5809920000 0.6028860000\n", 750 | "$end\n", 751 | "\n", 752 | "$rem\n", 753 | " job_type = freq\n", 754 | " basis = def2-tzvppd\n", 755 | " max_scf_cycles = 200\n", 756 | " gen_scfman = true\n", 757 | " xc_grid = 3\n", 758 | " scf_algorithm = diis\n", 759 | " resp_charges = true\n", 760 | " symmetry = false\n", 761 | " sym_ignore = true\n", 762 | " method = b3lyp\n", 763 | "$end\n", 764 | "\n" 765 | ] 766 | } 767 | ], 768 | "source": [ 769 | "freq_set = FreqSet(mol, dft_rung=1)\n", 770 | "print(freq_set)" 771 | ] 772 | }, 773 | { 774 | "cell_type": "code", 775 | "execution_count": 54, 776 | "id": "0ac29d56", 777 | "metadata": {}, 778 | "outputs": [ 779 | { 780 | "name": "stdout", 781 | "output_type": "stream", 782 | "text": [ 783 | "Existing /home/max/.pmgrc.yaml backed up to /home/max/.pmgrc.yaml.bak\n", 784 | "New /home/max/.pmgrc.yaml written!\n" 785 | ] 786 | } 787 | ], 788 | "source": [ 789 | "!pmg config --add PMG_VASP_PSP_DIR /home/user/python_module/Automated_DFT/POTCAR" 790 | ] 791 | }, 792 | { 793 | "cell_type": "code", 794 | "execution_count": 55, 795 | "id": "5eaf5038", 796 | "metadata": {}, 797 | "outputs": [], 798 | "source": [ 799 | "si = Structure.from_file(\"Si.CIF\")" 800 | ] 801 | }, 802 | { 803 | "cell_type": "code", 804 | "execution_count": 59, 805 | "id": "f1274012", 806 | "metadata": {}, 807 | "outputs": [ 808 | { 809 | "name": "stdout", 810 | "output_type": 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kB)\n", 902 | "Requirement already satisfied: cffi in ./.virtualenvs/aiida/lib/python3.7/site-packages (from pynng>=0.5.0->maggma>=0.26.0->atomate) (1.14.5)\n", 903 | "Requirement already satisfied: ruamel.yaml.clib>=0.1.2 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from ruamel.yaml>=0.15.6->custodian>=2019.8.24->atomate) (0.2.2)\n", 904 | "Requirement already satisfied: urllib3>=1.10.0 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from sentry-sdk>=0.8.0->custodian>=2019.8.24->atomate) (1.26.5)\n", 905 | "Requirement already satisfied: certifi in ./.virtualenvs/aiida/lib/python3.7/site-packages (from sentry-sdk>=0.8.0->custodian>=2019.8.24->atomate) (2021.5.30)\n", 906 | "Requirement already satisfied: paramiko>=2.7.2 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from sshtunnel>=0.1.5->maggma>=0.26.0->atomate) (2.7.2)\n", 907 | "Requirement already satisfied: pynacl>=1.0.1 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from 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pytz>=2017.3 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from pandas->pymatgen>=2020.9.14->atomate) (2019.3)\n", 914 | "Requirement already satisfied: chardet<5,>=3.0.2 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from requests->mongogrant>=0.3.1->maggma>=0.26.0->atomate) (4.0.0)\n", 915 | "Requirement already satisfied: idna<3,>=2.5 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from requests->mongogrant>=0.3.1->maggma>=0.26.0->atomate) (2.10)\n", 916 | "Requirement already satisfied: mpmath>=0.19 in ./.virtualenvs/aiida/lib/python3.7/site-packages (from sympy->pymatgen>=2020.9.14->atomate) (1.2.1)\n", 917 | "Building wheels for collected packages: atomate, custodian, FireWorks, sentinels\n", 918 | " Building wheel for atomate (setup.py) ... \u001b[?25ldone\n", 919 | "\u001b[?25h Created wheel for atomate: filename=atomate-0.9.9-py3-none-any.whl size=234532 sha256=d0d7d337dcf0ee53b5c901818ae6bf1da348943e8b6fa5d98cc6ecdca576d23d\n", 920 | " Stored in directory: /home/max/.cache/pip/wheels/ec/8d/96/4707ae6e25baff8b01d99ecfacf77f569c5ed648eff2e25dc8\n", 921 | " Building wheel for custodian (PEP 517) ... \u001b[?25ldone\n", 922 | "\u001b[?25h Created wheel for custodian: filename=custodian-2021.2.8-py3-none-any.whl size=73532 sha256=73433325519550dde91f0d9efe63b42d84ba4d9875ee4db1cd694620188e3027\n", 923 | " Stored in directory: /home/max/.cache/pip/wheels/d2/f7/2f/b43a6da861cd2bef7e2e811a6a5e8935a7b6873ae4992528d7\n", 924 | " Building wheel for FireWorks (setup.py) ... \u001b[?25ldone\n", 925 | "\u001b[?25h Created wheel for FireWorks: filename=FireWorks-1.9.7-py3-none-any.whl size=451553 sha256=e94de97535d772d9c73b8a1cc3d7f487e18b344afee3214ce51c59d73f56991b\n", 926 | " Stored in directory: /home/max/.cache/pip/wheels/61/a3/c8/22ff04f2964bc4de48e6034574799418ed76c19d718d384e58\n", 927 | " Building wheel for sentinels (setup.py) ... \u001b[?25ldone\n", 928 | "\u001b[?25h Created wheel for sentinels: filename=sentinels-1.0.0-py3-none-any.whl size=3186 sha256=c5560e1696233fc106c5d3df31a71b7ad7e3ed2bfdd20fa93b4a7ea26fb4cf27\n", 929 | " Stored in directory: /home/max/.cache/pip/wheels/24/4b/6f/cceb54c29f42b50b5d11b8196eab1de6707c5742beac65f52b\n", 930 | "Successfully built atomate custodian FireWorks sentinels\n", 931 | "Installing collected packages: sniffio, sentinels, pymongo, sshtunnel, sentry-sdk, pynng, pydash, mongomock, mongogrant, gunicorn, flask-paginate, aioitertools, pymatgen-diffusion, maggma, FireWorks, custodian, atomate\n", 932 | "Successfully installed FireWorks-1.9.7 aioitertools-0.7.1 atomate-0.9.9 custodian-2021.2.8 flask-paginate-0.8.1 gunicorn-20.1.0 maggma-0.30.0 mongogrant-0.3.3 mongomock-3.23.0 pydash-5.0.1 pymatgen-diffusion-2020.10.8 pymongo-3.11.4 pynng-0.7.1 sentinels-1.0.0 sentry-sdk-1.3.0 sniffio-1.2.0 sshtunnel-0.4.0\n", 933 | "\u001b[33mWARNING: You are using pip version 20.3.4; however, version 21.1.3 is available.\n", 934 | "You should consider upgrading via the '/home/max/.virtualenvs/aiida/bin/python -m pip install --upgrade pip' command.\u001b[0m\n", 935 | "Note: you may need to restart the kernel to use updated packages.\n" 936 | ] 937 | } 938 | ], 939 | "source": [ 940 | "pip install atomate" 941 | ] 942 | }, 943 | { 944 | "cell_type": "code", 945 | "execution_count": 60, 946 | "id": "2b6ad404", 947 | "metadata": {}, 948 | "outputs": [ 949 | { 950 | "name": "stderr", 951 | "output_type": "stream", 952 | "text": [ 953 | "/home/max/.virtualenvs/aiida/lib/python3.7/site-packages/maggma/utils.py:20: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n", 954 | " from tqdm.autonotebook import tqdm\n" 955 | ] 956 | } 957 | ], 958 | "source": [ 959 | "from atomate.vasp.workflows import wf_structure_optimization" 960 | ] 961 | }, 962 | { 963 | "cell_type": "code", 964 | "execution_count": 61, 965 | "id": "97cc8706", 966 | "metadata": {}, 967 | "outputs": [ 968 | { 969 | "name": "stdout", 970 | "output_type": "stream", 971 | "text": [ 972 | "Workflow object: (fw_ids: odict_keys([-1]) , name: Si)\n" 973 | ] 974 | } 975 | ], 976 | "source": [ 977 | "wf = wf_structure_optimization(structure=si)\n", 978 | "print(wf)" 979 | ] 980 | }, 981 | { 982 | "cell_type": "code", 983 | "execution_count": 62, 984 | "id": "4263fd2d", 985 | "metadata": {}, 986 | "outputs": [ 987 | { 988 | "data": { 989 | "text/plain": [ 990 | "{'fws': [{'spec': {'_tasks': [{'files_to_write': [{'filename': 'FW--Si-structure_optimization',\n", 991 | " 'contents': ''}],\n", 992 | " '_fw_name': 'FileWriteTask'},\n", 993 | " {'structure': {'@module': 'pymatgen.core.structure',\n", 994 | " '@class': 'Structure',\n", 995 | " 'charge': None,\n", 996 | " 'lattice': {'matrix': [[5.523145, 0.0, 3.3819509227383545e-16],\n", 997 | " [8.794385361720813e-16, 5.468728, 3.348630120303753e-16],\n", 998 | " [0.0, 0.0, 5.468728]],\n", 999 | " 'a': 5.523145,\n", 1000 | " 'b': 5.468728,\n", 1001 | " 'c': 5.468728,\n", 1002 | " 'alpha': 90.0,\n", 1003 | " 'beta': 90.0,\n", 1004 | " 'gamma': 90.0,\n", 1005 | " 'volume': 165.1806198484466},\n", 1006 | " 'sites': [{'species': [{'element': 'Si', 'occu': 1.0}],\n", 1007 | " 'abc': [0.25, 0.25, 0.25],\n", 1008 | " 'xyz': [1.3807862500000003, 1.367182, 1.3671820000000001],\n", 1009 | " 'label': 'Si',\n", 1010 | " 'properties': {}},\n", 1011 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1012 | " 'abc': [0.5, 0.5, 0.0],\n", 1013 | " 'xyz': [2.7615725000000007, 2.734364, 3.365290521521054e-16],\n", 1014 | " 'label': 'Si',\n", 1015 | " 'properties': {}},\n", 1016 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1017 | " 'abc': [0.25, 0.75, 0.75],\n", 1018 | " 'xyz': [1.3807862500000008, 4.101546, 4.101546],\n", 1019 | " 'label': 'Si',\n", 1020 | " 'properties': {}},\n", 1021 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1022 | " 'abc': [0.5, 0.0, 0.5],\n", 1023 | " 'xyz': [2.7615725, 0.0, 2.734364],\n", 1024 | " 'label': 'Si',\n", 1025 | " 'properties': {}},\n", 1026 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1027 | " 'abc': [0.75, 0.25, 0.75],\n", 1028 | " 'xyz': [4.1423587500000005, 1.367182, 4.101546],\n", 1029 | " 'label': 'Si',\n", 1030 | " 'properties': {}},\n", 1031 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1032 | " 'abc': [0.0, 0.5, 0.5],\n", 1033 | " 'xyz': [4.3971926808604063e-16, 2.734364, 2.734364],\n", 1034 | " 'label': 'Si',\n", 1035 | " 'properties': {}},\n", 1036 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1037 | " 'abc': [0.75, 0.75, 0.25],\n", 1038 | " 'xyz': [4.142358750000001, 4.101546, 1.3671820000000003],\n", 1039 | " 'label': 'Si',\n", 1040 | " 'properties': {}},\n", 1041 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1042 | " 'abc': [0.0, 0.0, 0.0],\n", 1043 | " 'xyz': [0.0, 0.0, 0.0],\n", 1044 | " 'label': 'Si',\n", 1045 | " 'properties': {}}]},\n", 1046 | " 'vasp_input_set': {'@module': 'pymatgen.io.vasp.sets',\n", 1047 | " '@class': 'MPRelaxSet',\n", 1048 | " '@version': '2020.12.3',\n", 1049 | " 'structure': {'@module': 'pymatgen.core.structure',\n", 1050 | " '@class': 'Structure',\n", 1051 | " 'charge': None,\n", 1052 | " 'lattice': {'matrix': [[5.523145, 0.0, 3.3819509227383545e-16],\n", 1053 | " [8.794385361720813e-16, 5.468728, 3.348630120303753e-16],\n", 1054 | " [0.0, 0.0, 5.468728]],\n", 1055 | " 'a': 5.523145,\n", 1056 | " 'b': 5.468728,\n", 1057 | " 'c': 5.468728,\n", 1058 | " 'alpha': 90.0,\n", 1059 | " 'beta': 90.0,\n", 1060 | " 'gamma': 90.0,\n", 1061 | " 'volume': 165.1806198484466},\n", 1062 | " 'sites': [{'species': [{'element': 'Si', 'occu': 1.0}],\n", 1063 | " 'abc': [0.25, 0.25, 0.25],\n", 1064 | " 'xyz': [1.3807862500000003, 1.367182, 1.3671820000000001],\n", 1065 | " 'label': 'Si',\n", 1066 | " 'properties': {}},\n", 1067 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1068 | " 'abc': [0.5, 0.5, 0.0],\n", 1069 | " 'xyz': [2.7615725000000007, 2.734364, 3.365290521521054e-16],\n", 1070 | " 'label': 'Si',\n", 1071 | " 'properties': {}},\n", 1072 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1073 | " 'abc': [0.25, 0.75, 0.75],\n", 1074 | " 'xyz': [1.3807862500000008, 4.101546, 4.101546],\n", 1075 | " 'label': 'Si',\n", 1076 | " 'properties': {}},\n", 1077 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1078 | " 'abc': [0.5, 0.0, 0.5],\n", 1079 | " 'xyz': [2.7615725, 0.0, 2.734364],\n", 1080 | " 'label': 'Si',\n", 1081 | " 'properties': {}},\n", 1082 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1083 | " 'abc': [0.75, 0.25, 0.75],\n", 1084 | " 'xyz': [4.1423587500000005, 1.367182, 4.101546],\n", 1085 | " 'label': 'Si',\n", 1086 | " 'properties': {}},\n", 1087 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1088 | " 'abc': [0.0, 0.5, 0.5],\n", 1089 | " 'xyz': [4.3971926808604063e-16, 2.734364, 2.734364],\n", 1090 | " 'label': 'Si',\n", 1091 | " 'properties': {}},\n", 1092 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1093 | " 'abc': [0.75, 0.75, 0.25],\n", 1094 | " 'xyz': [4.142358750000001, 4.101546, 1.3671820000000003],\n", 1095 | " 'label': 'Si',\n", 1096 | " 'properties': {}},\n", 1097 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1098 | " 'abc': [0.0, 0.0, 0.0],\n", 1099 | " 'xyz': [0.0, 0.0, 0.0],\n", 1100 | " 'label': 'Si',\n", 1101 | " 'properties': {}}]},\n", 1102 | " 'force_gamma': True,\n", 1103 | " 'user_incar_settings': None},\n", 1104 | " '_fw_name': '{{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}'},\n", 1105 | " {'vasp_cmd': '>>vasp_cmd<<',\n", 1106 | " 'job_type': 'double_relaxation_run',\n", 1107 | " 'max_force_threshold': 0.25,\n", 1108 | " 'ediffg': None,\n", 1109 | " 'auto_npar': '>>auto_npar<<',\n", 1110 | " 'half_kpts_first_relax': False,\n", 1111 | " 'scratch_dir': '>>scratch_dir<<',\n", 1112 | " 'gamma_vasp_cmd': '>>gamma_vasp_cmd<<',\n", 1113 | " '_fw_name': '{{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}'},\n", 1114 | " {'name': 'structure optimization',\n", 1115 | " '_fw_name': '{{atomate.common.firetasks.glue_tasks.PassCalcLocs}}'},\n", 1116 | " {'db_file': '>>db_file<<',\n", 1117 | " 'additional_fields': {'task_label': 'structure optimization'},\n", 1118 | " '_fw_name': '{{atomate.vasp.firetasks.parse_outputs.VaspToDb}}'}]},\n", 1119 | " 'fw_id': -1,\n", 1120 | " 'created_on': '2021-07-08T12:49:56.022432',\n", 1121 | " 'updated_on': '2021-07-08T12:49:56.022435',\n", 1122 | " 'name': 'Si-structure optimization'}],\n", 1123 | " 'links': {'-1': []},\n", 1124 | " 'name': 'Si',\n", 1125 | " 'metadata': {'structure': {'@module': 'pymatgen.core.structure',\n", 1126 | " '@class': 'Structure',\n", 1127 | " 'charge': None,\n", 1128 | " 'lattice': {'matrix': [[5.523145, 0.0, 3.3819509227383545e-16],\n", 1129 | " [8.794385361720813e-16, 5.468728, 3.348630120303753e-16],\n", 1130 | " [0.0, 0.0, 5.468728]],\n", 1131 | " 'a': 5.523145,\n", 1132 | " 'b': 5.468728,\n", 1133 | " 'c': 5.468728,\n", 1134 | " 'alpha': 90.0,\n", 1135 | " 'beta': 90.0,\n", 1136 | " 'gamma': 90.0,\n", 1137 | " 'volume': 165.1806198484466},\n", 1138 | " 'sites': [{'species': [{'element': 'Si', 'occu': 1.0}],\n", 1139 | " 'abc': [0.25, 0.25, 0.25],\n", 1140 | " 'xyz': [1.3807862500000003, 1.367182, 1.3671820000000001],\n", 1141 | " 'label': 'Si',\n", 1142 | " 'properties': {}},\n", 1143 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1144 | " 'abc': [0.5, 0.5, 0.0],\n", 1145 | " 'xyz': [2.7615725000000007, 2.734364, 3.365290521521054e-16],\n", 1146 | " 'label': 'Si',\n", 1147 | " 'properties': {}},\n", 1148 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1149 | " 'abc': [0.25, 0.75, 0.75],\n", 1150 | " 'xyz': [1.3807862500000008, 4.101546, 4.101546],\n", 1151 | " 'label': 'Si',\n", 1152 | " 'properties': {}},\n", 1153 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1154 | " 'abc': [0.5, 0.0, 0.5],\n", 1155 | " 'xyz': [2.7615725, 0.0, 2.734364],\n", 1156 | " 'label': 'Si',\n", 1157 | " 'properties': {}},\n", 1158 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1159 | " 'abc': [0.75, 0.25, 0.75],\n", 1160 | " 'xyz': [4.1423587500000005, 1.367182, 4.101546],\n", 1161 | " 'label': 'Si',\n", 1162 | " 'properties': {}},\n", 1163 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1164 | " 'abc': [0.0, 0.5, 0.5],\n", 1165 | " 'xyz': [4.3971926808604063e-16, 2.734364, 2.734364],\n", 1166 | " 'label': 'Si',\n", 1167 | " 'properties': {}},\n", 1168 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1169 | " 'abc': [0.75, 0.75, 0.25],\n", 1170 | " 'xyz': [4.142358750000001, 4.101546, 1.3671820000000003],\n", 1171 | " 'label': 'Si',\n", 1172 | " 'properties': {}},\n", 1173 | " {'species': [{'element': 'Si', 'occu': 1.0}],\n", 1174 | " 'abc': [0.0, 0.0, 0.0],\n", 1175 | " 'xyz': [0.0, 0.0, 0.0],\n", 1176 | " 'label': 'Si',\n", 1177 | " 'properties': {}}]},\n", 1178 | " 'nsites': 8,\n", 1179 | " 'elements': ['Si'],\n", 1180 | " 'nelements': 1,\n", 1181 | " 'formula': 'Si8',\n", 1182 | " 'formula_pretty': 'Si',\n", 1183 | " 'formula_reduced_abc': 'Si1',\n", 1184 | " 'formula_anonymous': 'A',\n", 1185 | " 'chemsys': 'Si',\n", 1186 | " 'is_ordered': True,\n", 1187 | " 'is_valid': True},\n", 1188 | " 'updated_on': datetime.datetime(2021, 7, 8, 12, 49, 56, 22876),\n", 1189 | " 'created_on': datetime.datetime(2021, 7, 8, 12, 49, 56, 22874)}" 1190 | ] 1191 | }, 1192 | "execution_count": 62, 1193 | "metadata": {}, 1194 | "output_type": "execute_result" 1195 | } 1196 | ], 1197 | "source": [ 1198 | "wf.as_dict()" 1199 | ] 1200 | }, 1201 | { 1202 | "cell_type": "code", 1203 | "execution_count": 63, 1204 | "id": "c6686cf7", 1205 | "metadata": {}, 1206 | "outputs": [], 1207 | "source": [ 1208 | "from atomate.vasp.workflows import wf_bandstructure" 1209 | ] 1210 | }, 1211 | { 1212 | "cell_type": "code", 1213 | "execution_count": 65, 1214 | "id": "73ef6f14", 1215 | "metadata": {}, 1216 | "outputs": [], 1217 | "source": [ 1218 | "wf = wf_bandstructure(structure=si)" 1219 | ] 1220 | }, 1221 | { 1222 | "cell_type": "code", 1223 | "execution_count": 66, 1224 | "id": "7ec136b3", 1225 | "metadata": {}, 1226 | "outputs": [ 1227 | { 1228 | "name": "stdout", 1229 | "output_type": "stream", 1230 | "text": [ 1231 | "Workflow object: (fw_ids: odict_keys([-2, -3, -4, -5]) , name: Si)\n" 1232 | ] 1233 | } 1234 | ], 1235 | "source": [ 1236 | "print(wf)" 1237 | ] 1238 | } 1239 | ], 1240 | "metadata": { 1241 | "kernelspec": { 1242 | "display_name": "Python 3", 1243 | "language": "python", 1244 | "name": "python3" 1245 | }, 1246 | "language_info": { 1247 | "codemirror_mode": { 1248 | "name": "ipython", 1249 | "version": 3 1250 | }, 1251 | "file_extension": ".py", 1252 | "mimetype": "text/x-python", 1253 | "name": "python", 1254 | "nbconvert_exporter": "python", 1255 | "pygments_lexer": "ipython3", 1256 | "version": "3.7.10" 1257 | } 1258 | }, 1259 | "nbformat": 4, 1260 | "nbformat_minor": 5 1261 | } 1262 | -------------------------------------------------------------------------------- /Ewald Electrostastic Energy.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "id": "d453f679", 7 | "metadata": {}, 8 | "outputs": [], 9 | "source": [ 10 | "import numpy as np\n", 11 | "from pymatgen.analysis.energy_models import EwaldElectrostaticModel\n", 12 | "from pymatgen.core.structure import Structure" 13 | ] 14 | }, 15 | { 16 | "cell_type": "code", 17 | "execution_count": 3, 18 | "id": "b68d88df", 19 | "metadata": {}, 20 | "outputs": [ 21 | { 22 | "name": "stdout", 23 | "output_type": "stream", 24 | "text": [ 25 | "-1178.7058972857396\n" 26 | ] 27 | } 28 | ], 29 | "source": [ 30 | "structure_file = 'Li10Ge(PS6)2_mp-696128_conventional_standard.cif'\n", 31 | "\n", 32 | "structure = Structure.from_file(structure_file)\n", 33 | "structure.add_oxidation_state_by_element({\"Li\":1,\"Ge\":4,\"P\":5,\"S\":-2})\n", 34 | "ewald = EwaldElectrostaticModel()\n", 35 | "print(ewald.get_energy(structure))" 36 | ] 37 | }, 38 | { 39 | "cell_type": "code", 40 | "execution_count": null, 41 | "id": "24fda845", 42 | "metadata": {}, 43 | "outputs": [], 44 | "source": [] 45 | } 46 | ], 47 | "metadata": { 48 | "kernelspec": { 49 | "display_name": "Python 3", 50 | "language": "python", 51 | "name": "python3" 52 | }, 53 | "language_info": { 54 | "codemirror_mode": { 55 | "name": "ipython", 56 | "version": 3 57 | }, 58 | "file_extension": ".py", 59 | "mimetype": "text/x-python", 60 | "name": "python", 61 | "nbconvert_exporter": "python", 62 | "pygments_lexer": "ipython3", 63 | "version": "3.7.10" 64 | } 65 | }, 66 | "nbformat": 4, 67 | "nbformat_minor": 5 68 | } 69 | -------------------------------------------------------------------------------- /ML Band Structure.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 2, 6 | "id": "e06b5270", 7 | "metadata": {}, 8 | "outputs": [ 9 | { 10 | "name": "stdout", 11 | "output_type": "stream", 12 | "text": [ 13 | "mp-66 is a p type: \n" 14 | ] 15 | } 16 | ], 17 | "source": [ 18 | "from pymatgen.ext.matproj import MPRester\n", 19 | "m = MPRester(\"H8NcXtxiApE6LBhM\") \n", 20 | "material = 'mp-66' # Diamond\n", 21 | "try:\n", 22 | " bs = m.get_bandstructure_by_material_id(material)\n", 23 | " if bs:\n", 24 | " vbm = bs.get_vbm()['energy']\n", 25 | " cbm = bs.get_cbm()['energy']\n", 26 | " fermi = bs.efermi\n", 27 | " \n", 28 | " if fermi < (vbm + cbm)/2:\n", 29 | " print(material, ' is a p type: ')\n", 30 | " else:\n", 31 | " print(material, ' is an n type: ')\n", 32 | " else:\n", 33 | " print(\"MP doesn't have that bandstructure\")\n", 34 | "except:\n", 35 | " print(\"Can't get bandstructure\")" 36 | ] 37 | }, 38 | { 39 | "cell_type": "code", 40 | "execution_count": null, 41 | "id": "c419c997", 42 | "metadata": {}, 43 | "outputs": [], 44 | "source": [] 45 | } 46 | ], 47 | "metadata": { 48 | "kernelspec": { 49 | "display_name": "Python 3", 50 | "language": "python", 51 | "name": "python3" 52 | }, 53 | "language_info": { 54 | "codemirror_mode": { 55 | "name": "ipython", 56 | "version": 3 57 | }, 58 | "file_extension": ".py", 59 | "mimetype": "text/x-python", 60 | "name": "python", 61 | "nbconvert_exporter": "python", 62 | "pygments_lexer": "ipython3", 63 | "version": "3.7.10" 64 | } 65 | }, 66 | "nbformat": 4, 67 | "nbformat_minor": 5 68 | } 69 | -------------------------------------------------------------------------------- /ML using CrystalFeatures to predict the bandgap (1).ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "id": "85d67a5c", 7 | "metadata": {}, 8 | "outputs": [], 9 | "source": [ 10 | "import pymatgen\n", 11 | "from pymatgen import Structure" 12 | ] 13 | }, 14 | { 15 | "cell_type": "code", 16 | "execution_count": 2, 17 | "id": "b1d7ea22", 18 | "metadata": {}, 19 | "outputs": [], 20 | "source": [ 21 | "Structure = Structure.from_file(\"Li10Ge(PS6)2_mp-696128_conventional_standard.cif\")" 22 | ] 23 | }, 24 | { 25 | "cell_type": "code", 26 | "execution_count": 3, 27 | "id": "24b3427f", 28 | "metadata": {}, 29 | "outputs": [ 30 | { 31 | "name": "stdout", 32 | "output_type": "stream", 33 | "text": [ 34 | "Full Formula (Li20 Ge2 P4 S24)\n", 35 | "Reduced Formula: Li10Ge(PS6)2\n", 36 | "abc : 8.787646 8.787646 12.657546\n", 37 | "angles: 90.000000 90.000000 90.000000\n", 38 | "Sites (50)\n", 39 | " # SP a b c\n", 40 | "--- ---- -------- -------- --------\n", 41 | " 0 Li 0.228698 0.27295 0.294563\n", 42 | " 1 Li 0.771302 0.72705 0.294563\n", 43 | " 2 Li 0.27295 0.771302 0.794563\n", 44 | " 3 Li 0.72705 0.228698 0.794563\n", 45 | " 4 Li 0.228698 0.72705 0.294563\n", 46 | " 5 Li 0.771302 0.27295 0.294563\n", 47 | " 6 Li 0.27295 0.228698 0.794563\n", 48 | " 7 Li 0.72705 0.771302 0.794563\n", 49 | " 8 Li 0 0 0.93973\n", 50 | " 9 Li 0 0 0.43973\n", 51 | " 10 Li 0.5 0.5 0.54802\n", 52 | " 11 Li 0.5 0.5 0.04802\n", 53 | " 12 Li 0.256318 0.724772 0.036663\n", 54 | " 13 Li 0.743682 0.275228 0.036663\n", 55 | " 14 Li 0.275228 0.256318 0.536663\n", 56 | " 15 Li 0.724772 0.743682 0.536663\n", 57 | " 16 Li 0.275228 0.743682 0.536663\n", 58 | " 17 Li 0.724772 0.256318 0.536663\n", 59 | " 18 Li 0.256318 0.275228 0.036663\n", 60 | " 19 Li 0.743682 0.724772 0.036663\n", 61 | " 20 Ge 0.5 0.5 0.801028\n", 62 | " 21 Ge 0.5 0.5 0.301028\n", 63 | " 22 P 0 0 0.686051\n", 64 | " 23 P 0 0 0.186051\n", 65 | " 24 P 0 0.5 0.504073\n", 66 | " 25 P 0.5 0 0.004073\n", 67 | " 26 S 0 0.694431 0.412071\n", 68 | " 27 S 0 0.305569 0.412071\n", 69 | " 28 S 0.305569 0 0.912071\n", 70 | " 29 S 0.694431 0 0.912071\n", 71 | " 30 S 0.5 0.189848 0.097057\n", 72 | " 31 S 0.5 0.810152 0.097057\n", 73 | " 32 S 0.189848 0.5 0.597057\n", 74 | " 33 S 0.810152 0.5 0.597057\n", 75 | " 34 S 0 0.804708 0.094096\n", 76 | " 35 S 0 0.195292 0.094096\n", 77 | " 36 S 0.195292 0 0.594096\n", 78 | " 37 S 0.804708 0 0.594096\n", 79 | " 38 S 0.5 0.290002 0.403242\n", 80 | " 39 S 0.5 0.709998 0.403242\n", 81 | " 40 S 0.290002 0.5 0.903242\n", 82 | " 41 S 0.709998 0.5 0.903242\n", 83 | " 42 S 0 0.19195 0.777069\n", 84 | " 43 S 0 0.80805 0.777069\n", 85 | " 44 S 0.80805 0 0.277069\n", 86 | " 45 S 0.19195 0 0.277069\n", 87 | " 46 S 0.5 0.707378 0.698166\n", 88 | " 47 S 0.5 0.292622 0.698166\n", 89 | " 48 S 0.707378 0.5 0.198166\n", 90 | " 49 S 0.292622 0.5 0.198166\n" 91 | ] 92 | } 93 | ], 94 | "source": [ 95 | "print(Structure)" 96 | ] 97 | }, 98 | { 99 | "cell_type": "code", 100 | "execution_count": 4, 101 | "id": "b759ed22", 102 | "metadata": {}, 103 | "outputs": [ 104 | { 105 | "name": "stdout", 106 | "output_type": "stream", 107 | "text": [ 108 | "8.787646 0.000000 0.000000\n", 109 | "0.000000 8.787646 0.000000\n", 110 | "0.000000 0.000000 12.657546\n", 111 | "[Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Ge, Element Ge, Element P, Element P, Element P, Element P, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S, Element S]\n", 112 | "0.0\n", 113 | "[[2.00971706e+00 2.39858798e+00 3.72844472e+00]\n", 114 | " [6.77792894e+00 6.38905802e+00 3.72844472e+00]\n", 115 | " [2.39858798e+00 6.77792894e+00 1.00572177e+01]\n", 116 | " [6.38905802e+00 2.00971706e+00 1.00572177e+01]\n", 117 | " [2.00971706e+00 6.38905802e+00 3.72844472e+00]\n", 118 | " [6.77792894e+00 2.39858798e+00 3.72844472e+00]\n", 119 | " [2.39858798e+00 2.00971706e+00 1.00572177e+01]\n", 120 | " [6.38905802e+00 6.77792894e+00 1.00572177e+01]\n", 121 | " [0.00000000e+00 0.00000000e+00 1.18946757e+01]\n", 122 | " [0.00000000e+00 0.00000000e+00 5.56590270e+00]\n", 123 | " [4.39382300e+00 4.39382300e+00 6.93658836e+00]\n", 124 | " [4.39382300e+00 4.39382300e+00 6.07815359e-01]\n", 125 | " [2.25243185e+00 6.36903977e+00 4.64063609e-01]\n", 126 | " [6.53521415e+00 2.41860623e+00 4.64063609e-01]\n", 127 | " [2.41860623e+00 2.25243185e+00 6.79283661e+00]\n", 128 | " [6.36903977e+00 6.53521415e+00 6.79283661e+00]\n", 129 | " [2.41860623e+00 6.53521415e+00 6.79283661e+00]\n", 130 | " [6.36903977e+00 2.25243185e+00 6.79283661e+00]\n", 131 | " [2.25243185e+00 2.41860623e+00 4.64063609e-01]\n", 132 | " [6.53521415e+00 6.36903977e+00 4.64063609e-01]\n", 133 | " [4.39382300e+00 4.39382300e+00 1.01390488e+01]\n", 134 | " [4.39382300e+00 4.39382300e+00 3.81027576e+00]\n", 135 | " [0.00000000e+00 0.00000000e+00 8.68372209e+00]\n", 136 | " [0.00000000e+00 0.00000000e+00 2.35494909e+00]\n", 137 | " [7.06580628e-16 4.39382300e+00 6.38032718e+00]\n", 138 | " [4.39382300e+00 0.00000000e+00 5.15541849e-02]\n", 139 | " [9.81342985e-16 6.10241380e+00 5.21580764e+00]\n", 140 | " [4.31818272e-16 2.68523220e+00 5.21580764e+00]\n", 141 | " [2.68523220e+00 0.00000000e+00 1.15445806e+01]\n", 142 | " [6.10241380e+00 0.00000000e+00 1.15445806e+01]\n", 143 | " [4.39382300e+00 1.66831702e+00 1.22850344e+00]\n", 144 | " [4.39382300e+00 7.11932898e+00 1.22850344e+00]\n", 145 | " [1.66831702e+00 4.39382300e+00 7.55727644e+00]\n", 146 | " [7.11932898e+00 4.39382300e+00 7.55727644e+00]\n", 147 | " [1.13718217e-15 7.07148904e+00 1.19102445e+00]\n", 148 | " [2.75979088e-16 1.71615696e+00 1.19102445e+00]\n", 149 | " [1.71615696e+00 0.00000000e+00 7.51979745e+00]\n", 150 | " [7.07148904e+00 0.00000000e+00 7.51979745e+00]\n", 151 | " [4.39382300e+00 2.54843492e+00 5.10405416e+00]\n", 152 | " [4.39382300e+00 6.23921108e+00 5.10405416e+00]\n", 153 | " [2.54843492e+00 4.39382300e+00 1.14328272e+01]\n", 154 | " [6.23921108e+00 4.39382300e+00 1.14328272e+01]\n", 155 | " [2.71256303e-16 1.68678865e+00 9.83578661e+00]\n", 156 | " [1.14190495e-15 7.10085735e+00 9.83578661e+00]\n", 157 | " [7.10085735e+00 0.00000000e+00 3.50701361e+00]\n", 158 | " [1.68678865e+00 0.00000000e+00 3.50701361e+00]\n", 159 | " [4.39382300e+00 6.21618745e+00 8.83706826e+00]\n", 160 | " [4.39382300e+00 2.57145855e+00 8.83706826e+00]\n", 161 | " [6.21618745e+00 4.39382300e+00 2.50829526e+00]\n", 162 | " [2.57145855e+00 4.39382300e+00 2.50829526e+00]]\n", 163 | "(3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 32, 32, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16)\n", 164 | "[[0. 5.66389459 7.70605058 ... 5.64020211 4.81291187 2.40526111]\n", 165 | " [5.66389459 0. 7.70605058 ... 6.80852857 2.40526111 4.81291187]\n", 166 | " [7.70605058 7.70605058 0. ... 4.81291187 6.80852857 5.64020211]\n", 167 | " ...\n", 168 | " [5.64020211 6.80852857 4.81291187 ... 0. 6.83340267 6.83340267]\n", 169 | " [4.81291187 2.40526111 6.80852857 ... 6.83340267 0. 3.6447289 ]\n", 170 | " [2.40526111 4.81291187 5.64020211 ... 6.83340267 3.6447289 0. ]]\n" 171 | ] 172 | } 173 | ], 174 | "source": [ 175 | "Structure = Structure\n", 176 | "\n", 177 | "print(Structure.lattice)\n", 178 | "print(Structure.species)\n", 179 | "print(Structure.charge)\n", 180 | "print(Structure.cart_coords)\n", 181 | "print(Structure.atomic_numbers)\n", 182 | "print(Structure.distance_matrix)" 183 | ] 184 | }, 185 | { 186 | "cell_type": "code", 187 | "execution_count": 5, 188 | "id": "0b13e7b6", 189 | "metadata": {}, 190 | "outputs": [], 191 | "source": [ 192 | "from pymatgen.ext.matproj import MPRester\n", 193 | "from pymatgen.ext.matproj import MPRestError\n", 194 | "\n", 195 | "m = MPRester(\"asFGTum1WzyZOxCr\")" 196 | ] 197 | }, 198 | { 199 | "cell_type": "code", 200 | "execution_count": 6, 201 | "id": "3ae48ce8", 202 | "metadata": {}, 203 | "outputs": [ 204 | { 205 | "data": { 206 | "application/vnd.jupyter.widget-view+json": { 207 | "model_id": "a51bdf492e3348e3abd8ca2287b9b84c", 208 | "version_major": 2, 209 | "version_minor": 0 210 | }, 211 | "text/plain": [ 212 | " 0%| | 0/918 [00:00" 440 | ] 441 | }, 442 | "execution_count": 28, 443 | "metadata": {}, 444 | "output_type": "execute_result" 445 | } 446 | ], 447 | "source": [ 448 | "def descriptors(cif):\n", 449 | "\n", 450 | " atomic_numbers = []\n", 451 | "\n", 452 | " distance_matrix = []\n", 453 | " van_der_waals_radius = []\n", 454 | " electrical_resistivity = []\n", 455 | " velocity_of_sound = []\n", 456 | " reflectivity = []\n", 457 | " poissons_ratio = []\n", 458 | " molar_volume = []\n", 459 | " thermal_conductivity = []\n", 460 | " melting_point = []\n", 461 | " critical_temperature = []\n", 462 | " superconduction_temperature = []\n", 463 | " liquid_range = []\n", 464 | " bulk_modulus = []\n", 465 | " youngs_modulus = []\n", 466 | " brinell_hardness = []\n", 467 | " rigidity_modulus = []\n", 468 | " mineral_hardness = []\n", 469 | " vickers_hardness = []\n", 470 | " density_of_solid = []\n", 471 | " coefficient_of_linear_thermal_expansion = []\n", 472 | " average_ionic_radius = []\n", 473 | " average_cationic_radius = []\n", 474 | " average_anionic_radius = []\n", 475 | " Structure = Structure.from_file(\"Li10Ge(PS6)2_mp-696128_conventional_standard.cif\")\n", 476 | " \n", 477 | " numElements = len(Structure.atomic_numbers)\n", 478 | "\n", 479 | " num_metals = 0\n", 480 | " for e in Structure.species:\n", 481 | " if e.Z in range(3, 4+1) or e.Z in range(11, 12+1) or e.Z in range(19, 30+1) or e.Z in range(37, 48+1) or e.Z in range(55, 80 + 1) or e.Z in range(87, 112+1):\n", 482 | " num_metals += 1\n", 483 | " metals_fraction = num_metals/numElements\n", 484 | "\n", 485 | " spg = Structure.get_space_group_info()\n", 486 | "\n", 487 | " spacegroup_numbers = {}\n", 488 | " for i in range(1, 231):\n", 489 | " spacegroup_numbers[i] = 0\n", 490 | "\n", 491 | " spacegroup_numbers[spg[1]] = 1\n", 492 | "\n", 493 | " spacegroup_numbers_list = []\n", 494 | " for i in range(1, 231):\n", 495 | " spacegroup_numbers_list += [spacegroup_numbers[i]]\n", 496 | "\n", 497 | " atomic_numbers = [np.mean(structure.atomic_numbers), np.max(structure.atomic_numbers), np.min(\n", 498 | " structure.atomic_numbers), np.std(structure.atomic_numbers)]\n", 499 | " a_parameters = Structure.lattice.abc[0]\n", 500 | " b_parameters = Structure.lattice.abc[1]\n", 501 | " c_parameters = Structure.lattice.abc[2]\n", 502 | " alpha_parameters = Structure.lattice.angles[0]\n", 503 | " beta_parameters = Structure.lattice.angles[1]\n", 504 | " gamma_parameters = Structure.lattice.angles[2]\n", 505 | "\n", 506 | " distance_matrix += [np.mean(Structure.distance_matrix), np.max(Structure.distance_matrix),\n", 507 | " np.min(Structure.distance_matrix), np.std(Structure.distance_matrix)]\n", 508 | "\n", 509 | " e1, e2, e3, e4, e5, e6, e7, e8, e9, e10, e11, e12, e13, e14, e15, e16, e17, e18, e19, e20, e21, e22, e23 = [\n", 510 | " ], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], [], []\n", 511 | " for e in Structure.species:\n", 512 | " e1 += [e.van_der_waals_radius]\n", 513 | " e2 += [e.electrical_resistivity]\n", 514 | " e3 += [e.velocity_of_sound]\n", 515 | " e4 += [e.reflectivity]\n", 516 | " e6 += [e.poissons_ratio]\n", 517 | " e7 += [e.molar_volume]\n", 518 | " e8 += [e.thermal_conductivity]\n", 519 | " e9 += [e.melting_point]\n", 520 | " e10 += [e.critical_temperature]\n", 521 | " e11 += [e.superconduction_temperature]\n", 522 | " e12 += [e.liquid_range]\n", 523 | " e13 += [e.bulk_modulus]\n", 524 | " e14 += [e.youngs_modulus]\n", 525 | " e15 += [e.brinell_hardness]\n", 526 | " e16 += [e.rigidity_modulus]\n", 527 | " e17 += [e.mineral_hardness ]\n", 528 | " e18 += [e.vickers_hardness]\n", 529 | " e19 += [e.density_of_solid]\n", 530 | " e20 += [e.coefficient_of_linear_thermal_expansion]\n", 531 | " e21 += [e.average_ionic_radius]\n", 532 | " e22 += [e.average_cationic_radius]\n", 533 | " e23 += [e.average_anionic_radius]\n", 534 | " \n", 535 | " e1 = [0 if v is None else v for v in e1]\n", 536 | " e2 = [0 if v is None else v for v in e2]\n", 537 | " e3 = [0 if v is None else v for v in e3]\n", 538 | " e4 = [0 if v is None else v for v in e4]\n", 539 | " e5 = [0 if v is None else v for v in e5]\n", 540 | " e6 = [0 if v is None else v for v in e6]\n", 541 | " e7 = [0 if v is None else v for v in e7]\n", 542 | " e8 = [0 if v is None else v for v in e8]\n", 543 | " e9 = [0 if v is None else v for v in e9]\n", 544 | " e10 = [0 if v is None else v for v in e10]\n", 545 | " e11 = [0 if v is None else v for v in e11]\n", 546 | " e12 = [0 if v is None else v for v in e12]\n", 547 | " e13 = [0 if v is None else v for v in e13]\n", 548 | " e14 = [0 if v is None else v for v in e14]\n", 549 | " e15 = [0 if v is None else v for v in e15]\n", 550 | " e16 = [0 if v is None else v for v in e16]\n", 551 | " e17 = [0 if v is None else v for v in e17]\n", 552 | " e18 = [0 if v is None else v for v in e18]\n", 553 | " e19 = [0 if v is None else v for v in e19]\n", 554 | " e20 = [0 if v is None else v for v in e20]\n", 555 | " e21 = [0 if v is None else v for v in e21]\n", 556 | " e22 = [0 if v is None else v for v in e22]\n", 557 | " e23 = [0 if v is None else v for v in e23]\n", 558 | " \n", 559 | " van_der_waals_radius = [np.mean(e1), np.max(e1), np.min(e1), np.std(e1)]\n", 560 | " electrical_resistivity = [np.mean(e2), np.max(e2), np.min(e2), np.std(e2)]\n", 561 | " velocity_of_sound = [np.mean(e3), np.max(e3), np.min(e3), np.std(e3)]\n", 562 | " reflectivity = [np.mean(e4), np.max(e4), np.min(e4), np.std(e4)]\n", 563 | " poissons_ratio = [np.mean(e6), np.max(e6), np.min(e6), np.std(e6)]\n", 564 | " molar_volume = [np.mean(e7), np.max(e7), np.min(e7), np.std(e7)]\n", 565 | " thermal_conductivity = [np.mean(e8), np.max(e8), np.min(e8), np.std(e8)]\n", 566 | " melting_point = [np.mean(e9), np.max(e9), np.min(e9), np.std(e9)]\n", 567 | " critical_temperature = [np.mean(e10), np.max(\n", 568 | " e10), np.min(e10), np.std(e10)]\n", 569 | " superconduction_temperature = [\n", 570 | " np.mean(e11), np.max(e11), np.min(e11), np.std(e11)]\n", 571 | " liquid_range = [np.mean(e12), np.max(e12), np.min(e12), np.std(e12)]\n", 572 | " bulk_modulus = [np.mean(e13), np.max(e13), np.min(e13), np.std(e13)]\n", 573 | " youngs_modulus = [np.mean(e14), np.max(e14), np.min(e14), np.std(e14)]\n", 574 | " brinell_hardness = [np.mean(e15), np.max(e15), np.min(e15), np.std(e15)]\n", 575 | " rigidity_modulus = [np.mean(e16), np.max(e16), np.min(e16), np.std(e16)]\n", 576 | " vickers_hardness = [np.mean(e18), np.max(e18), np.min(e18), np.std(e18)]\n", 577 | " density_of_solid = [np.mean(e19), np.max(e19), np.min(e19), np.std(e19)]\n", 578 | " coefficient_of_linear_thermal_expansion = [\n", 579 | " np.mean(e20), np.max(e20), np.min(e20), np.std(e20)]\n", 580 | " average_ionic_radius = [np.mean(e21), np.max(\n", 581 | " e21), np.min(e21), np.std(e21)]\n", 582 | " average_cationic_radius = [\n", 583 | " np.mean(e22), np.max(e22), np.min(e22), np.std(e22)]\n", 584 | " average_anionic_radius = [\n", 585 | " np.mean(e23), np.max(e23), np.min(e23), np.std(e23)]\n", 586 | " \n", 587 | " V = a_parameters*b_parameters*c_parameters\n", 588 | " Density = V / numElements\n", 589 | "\n", 590 | " descriptors_list = atomic_numbers +\\\n", 591 | " [Density] +\\\n", 592 | " [alpha_parameters] +\\\n", 593 | " [beta_parameters] +\\\n", 594 | " [gamma_parameters] +\\\n", 595 | " [metals_fraction] +\\\n", 596 | " distance_matrix +\\\n", 597 | " van_der_waals_radius +\\\n", 598 | " electrical_resistivity +\\\n", 599 | " velocity_of_sound +\\\n", 600 | " reflectivity +\\\n", 601 | " poissons_ratio +\\\n", 602 | " molar_volume +\\\n", 603 | " thermal_conductivity +\\\n", 604 | " melting_point +\\\n", 605 | " critical_temperature +\\\n", 606 | " superconduction_temperature +\\\n", 607 | " liquid_range +\\\n", 608 | " bulk_modulus +\\\n", 609 | " youngs_modulus +\\\n", 610 | " brinell_hardness +\\\n", 611 | " rigidity_modulus +\\\n", 612 | " vickers_hardness +\\\n", 613 | " density_of_solid +\\\n", 614 | " coefficient_of_linear_thermal_expansion +\\\n", 615 | " average_ionic_radius +\\\n", 616 | " average_cationic_radius +\\\n", 617 | " average_anionic_radius +\\\n", 618 | " spacegroup_numbers_list\n", 619 | " return descriptors_list\n", 620 | "\n", 621 | "descriptors" 622 | ] 623 | }, 624 | { 625 | "cell_type": "code", 626 | "execution_count": 26, 627 | "id": "ddffeaaa", 628 | "metadata": {}, 629 | "outputs": [ 630 | { 631 | "data": { 632 | "image/png": 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\n", 633 | "text/plain": [ 634 | "
" 635 | ] 636 | }, 637 | "metadata": { 638 | "needs_background": "light" 639 | }, 640 | "output_type": "display_data" 641 | } 642 | ], 643 | "source": [ 644 | "import matplotlib.pyplot as plt\n", 645 | "\n", 646 | "plt.rcParams.update({'font.size': 20})\n", 647 | "\n", 648 | "plt.figure(figsize=(10, 10))\n", 649 | "plt.hist(band_gaps, bins=100)\n", 650 | "plt.savefig('Histogram_PDF', bbox_inches='tight')" 651 | ] 652 | }, 653 | { 654 | "cell_type": "code", 655 | "execution_count": null, 656 | "id": "08c3e26f", 657 | "metadata": {}, 658 | "outputs": [], 659 | "source": [] 660 | } 661 | ], 662 | "metadata": { 663 | "kernelspec": { 664 | "display_name": "Python 3", 665 | "language": "python", 666 | "name": "python3" 667 | }, 668 | "language_info": { 669 | "codemirror_mode": { 670 | "name": "ipython", 671 | "version": 3 672 | }, 673 | "file_extension": ".py", 674 | "mimetype": "text/x-python", 675 | "name": "python", 676 | "nbconvert_exporter": "python", 677 | "pygments_lexer": "ipython3", 678 | "version": "3.7.10" 679 | } 680 | }, 681 | "nbformat": 4, 682 | "nbformat_minor": 5 683 | } 684 | -------------------------------------------------------------------------------- /Pymatgen_foundations.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 3, 6 | "id": "171bead9", 7 | "metadata": {}, 8 | "outputs": [], 9 | "source": [ 10 | "import pymatgen" 11 | ] 12 | }, 13 | { 14 | "cell_type": "code", 15 | "execution_count": 5, 16 | "id": "b31f15e3", 17 | "metadata": {}, 18 | "outputs": [ 19 | { 20 | "name": "stdout", 21 | "output_type": "stream", 22 | "text": [ 23 | "3.7.10 (default, May 3 2021, 02:48:31) \n", 24 | "[GCC 7.5.0]\n" 25 | ] 26 | } 27 | ], 28 | "source": [ 29 | "import sys\n", 30 | "print(sys.version)" 31 | ] 32 | }, 33 | { 34 | "cell_type": "code", 35 | "execution_count": 6, 36 | "id": "d995fe84", 37 | "metadata": {}, 38 | "outputs": [], 39 | "source": [ 40 | "from pymatgen import Molecule" 41 | ] 42 | }, 43 | { 44 | "cell_type": "code", 45 | "execution_count": 7, 46 | "id": "22eb5082", 47 | "metadata": {}, 48 | "outputs": [ 49 | { 50 | "name": "stdout", 51 | "output_type": "stream", 52 | "text": [ 53 | "Full Formula (C1 O1)\n", 54 | "Reduced Formula: CO\n", 55 | "Charge = 0.0, Spin Mult = 1\n", 56 | "Sites (2)\n", 57 | "0 C 0.000000 0.000000 0.000000\n", 58 | "1 O 0.000000 0.000000 1.200000\n" 59 | ] 60 | } 61 | ], 62 | "source": [ 63 | "c_monox = Molecule([\"C\", \"O\"], [[0., 0., 0.], [0., 0., 1.2]])\n", 64 | "print(c_monox)" 65 | ] 66 | }, 67 | { 68 | "cell_type": "code", 69 | "execution_count": 8, 70 | "id": "f3b98534", 71 | "metadata": {}, 72 | "outputs": [], 73 | "source": [ 74 | "oh_minus = Molecule([\"O\", \"H\"], [[0., 0., 0.], [0., 0., 1.0]], charge=-1, spin_multiplicity=3)" 75 | ] 76 | }, 77 | { 78 | "cell_type": "code", 79 | "execution_count": 9, 80 | "id": "a2b43fe3", 81 | "metadata": {}, 82 | "outputs": [ 83 | { 84 | "name": "stdout", 85 | "output_type": "stream", 86 | "text": [ 87 | "Full Formula (H1 O1)\n", 88 | "Reduced Formula: H2O2\n", 89 | "Charge = -1, Spin Mult = 3\n", 90 | "Sites (2)\n", 91 | "0 O 0.000000 0.000000 0.000000\n", 92 | "1 H 0.000000 0.000000 1.000000\n" 93 | ] 94 | } 95 | ], 96 | "source": [ 97 | "print(oh_minus)" 98 | ] 99 | }, 100 | { 101 | "cell_type": "code", 102 | "execution_count": 14, 103 | "id": "18c02690", 104 | "metadata": {}, 105 | "outputs": [ 106 | { 107 | "name": "stdout", 108 | "output_type": "stream", 109 | "text": [ 110 | "Full Formula (H2 O1)\n", 111 | "Reduced Formula: H2O\n", 112 | "Charge = 0, Spin Mult = 1\n", 113 | "Sites (3)\n", 114 | "0 O 0.000000 0.000000 0.117790\n", 115 | "1 H 0.000000 0.755450 -0.471160\n", 116 | "2 H 0.000000 -0.755450 -0.471160\n" 117 | ] 118 | } 119 | ], 120 | "source": [ 121 | "water = Molecule.from_file(\"water.xyz\")\n", 122 | "print(water)" 123 | ] 124 | }, 125 | { 126 | "cell_type": "code", 127 | "execution_count": 18, 128 | "id": "6283f30a", 129 | "metadata": {}, 130 | "outputs": [ 131 | { 132 | "data": { 133 | "text/plain": [ 134 | "Molecule Summary\n", 135 | "Site: H (0.0000, 0.0000, 0.0000)\n", 136 | "Site: H (0.1000, 0.0000, 0.0000)" 137 | ] 138 | }, 139 | "execution_count": 18, 140 | "metadata": {}, 141 | "output_type": "execute_result" 142 | } 143 | ], 144 | "source": [ 145 | "example = Molecule([\"H\", \"H\"], [[0.0, 0.0, 0.0], [0.1, 0.0, 0.0]], validate_proximity=False)\n", 146 | "example" 147 | ] 148 | }, 149 | { 150 | "cell_type": "code", 151 | "execution_count": 19, 152 | "id": "7a78dc1d", 153 | "metadata": {}, 154 | "outputs": [ 155 | { 156 | "data": { 157 | "text/plain": [ 158 | "Molecule Summary\n", 159 | "Site: H (0.0000, 0.0000, 0.0000)\n", 160 | "Site: H (0.1000, 0.0000, 0.0000)" 161 | ] 162 | }, 163 | "execution_count": 19, 164 | "metadata": {}, 165 | "output_type": "execute_result" 166 | } 167 | ], 168 | "source": [ 169 | "example_2 = Molecule([\"H\", \"H\"], [[0.0, 0.0, 0.0], [0.1, 0.0, 0.0]], validate_proximity=False,\n", 170 | " site_properties={\"num_neutrons\": [0,1]})\n", 171 | "example_2" 172 | ] 173 | }, 174 | { 175 | "cell_type": "code", 176 | "execution_count": 20, 177 | "id": "e7717662", 178 | "metadata": {}, 179 | "outputs": [ 180 | { 181 | "data": { 182 | "text/plain": [ 183 | "array([[ 0. , 0. , 0.11779],\n", 184 | " [ 0. , 0.75545, -0.47116],\n", 185 | " [ 0. , -0.75545, -0.47116]])" 186 | ] 187 | }, 188 | "execution_count": 20, 189 | "metadata": {}, 190 | "output_type": "execute_result" 191 | } 192 | ], 193 | "source": [ 194 | "water.cart_coords" 195 | ] 196 | }, 197 | { 198 | "cell_type": "code", 199 | "execution_count": 21, 200 | "id": "f28c8bc0", 201 | "metadata": {}, 202 | "outputs": [ 203 | { 204 | "data": { 205 | "text/plain": [ 206 | "array([0. , 0. , 0.05188747])" 207 | ] 208 | }, 209 | "execution_count": 21, 210 | "metadata": {}, 211 | "output_type": "execute_result" 212 | } 213 | ], 214 | "source": [ 215 | "water.center_of_mass" 216 | ] 217 | }, 218 | { 219 | "cell_type": "code", 220 | "execution_count": 22, 221 | "id": "cd8b5c4b", 222 | "metadata": {}, 223 | "outputs": [], 224 | "source": [ 225 | "water.set_charge_and_spin(1)" 226 | ] 227 | }, 228 | { 229 | "cell_type": "code", 230 | "execution_count": 23, 231 | "id": "c43a0f33", 232 | "metadata": {}, 233 | "outputs": [ 234 | { 235 | "name": "stdout", 236 | "output_type": "stream", 237 | "text": [ 238 | "Full Formula (H2 O1)\n", 239 | "Reduced Formula: H2O\n", 240 | "Charge = 1, Spin Mult = 2\n", 241 | "Sites (3)\n", 242 | "0 O 0.000000 0.000000 0.117790\n", 243 | "1 H 0.000000 0.755450 -0.471160\n", 244 | "2 H 0.000000 -0.755450 -0.471160\n" 245 | ] 246 | } 247 | ], 248 | "source": [ 249 | "print(water)" 250 | ] 251 | }, 252 | { 253 | "cell_type": "code", 254 | "execution_count": 24, 255 | "id": "f8d37538", 256 | "metadata": {}, 257 | "outputs": [ 258 | { 259 | "data": { 260 | "text/plain": [ 261 | "[Site: O (0.0000, 0.0000, 0.1178),\n", 262 | " Site: H (0.0000, 0.7554, -0.4712),\n", 263 | " Site: H (0.0000, -0.7554, -0.4712)]" 264 | ] 265 | }, 266 | "execution_count": 24, 267 | "metadata": {}, 268 | "output_type": "execute_result" 269 | } 270 | ], 271 | "source": [ 272 | "list(water)" 273 | ] 274 | }, 275 | { 276 | "cell_type": "code", 277 | "execution_count": 26, 278 | "id": "41debf3f", 279 | "metadata": {}, 280 | "outputs": [ 281 | { 282 | "name": "stdout", 283 | "output_type": "stream", 284 | "text": [ 285 | "[0. 0. 0.11779] O\n" 286 | ] 287 | } 288 | ], 289 | "source": [ 290 | "site_0 = water[0]\n", 291 | "print(site_0)" 292 | ] 293 | }, 294 | { 295 | "cell_type": "code", 296 | "execution_count": 27, 297 | "id": "07fc505e", 298 | "metadata": {}, 299 | "outputs": [ 300 | { 301 | "data": { 302 | "text/plain": [ 303 | "Molecule Summary\n", 304 | "Site: C (0.0000, 0.0000, 0.0000)\n", 305 | "Site: O (0.0000, 0.0000, 1.2000)" 306 | ] 307 | }, 308 | "execution_count": 27, 309 | "metadata": {}, 310 | "output_type": "execute_result" 311 | } 312 | ], 313 | "source": [ 314 | "c_monox" 315 | ] 316 | }, 317 | { 318 | "cell_type": "code", 319 | "execution_count": 29, 320 | "id": "84d4e6ba", 321 | "metadata": {}, 322 | "outputs": [ 323 | { 324 | "name": "stdout", 325 | "output_type": "stream", 326 | "text": [ 327 | "Full Formula (C1 O1)\n", 328 | "Reduced Formula: CO\n", 329 | "Charge = 0.0, Spin Mult = 1\n", 330 | "Sites (2)\n", 331 | "0 O 0.000000 0.000000 0.000000\n", 332 | "1 C 0.000000 0.000000 1.200000\n" 333 | ] 334 | } 335 | ], 336 | "source": [ 337 | "c_monox[0] = \"O\"\n", 338 | "c_monox[1] = \"C\"\n", 339 | "print(c_monox)" 340 | ] 341 | }, 342 | { 343 | "cell_type": "code", 344 | "execution_count": 30, 345 | "id": "9f3ef928", 346 | "metadata": {}, 347 | "outputs": [], 348 | "source": [ 349 | "c_monox.append(\"C\", [0., 0., -1.2])" 350 | ] 351 | }, 352 | { 353 | "cell_type": "code", 354 | "execution_count": 31, 355 | "id": "2793d9e7", 356 | "metadata": {}, 357 | "outputs": [ 358 | { 359 | "name": "stdout", 360 | "output_type": "stream", 361 | "text": [ 362 | "Full Formula (C2 O1)\n", 363 | "Reduced Formula: C2O\n", 364 | "Charge = 0.0, Spin Mult = 1\n", 365 | "Sites (3)\n", 366 | "0 O 0.000000 0.000000 0.000000\n", 367 | "1 C 0.000000 0.000000 1.200000\n", 368 | "2 C 0.000000 0.000000 -1.200000\n" 369 | ] 370 | } 371 | ], 372 | "source": [ 373 | "print(c_monox)" 374 | ] 375 | }, 376 | { 377 | "cell_type": "code", 378 | "execution_count": 32, 379 | "id": "57b7ac45", 380 | "metadata": {}, 381 | "outputs": [ 382 | { 383 | "data": { 384 | "text/plain": [ 385 | "Site: O (0.0000, 0.0000, 0.1178)" 386 | ] 387 | }, 388 | "execution_count": 32, 389 | "metadata": {}, 390 | "output_type": "execute_result" 391 | } 392 | ], 393 | "source": [ 394 | "site_0" 395 | ] 396 | }, 397 | { 398 | "cell_type": "code", 399 | "execution_count": 33, 400 | "id": "ca9bea38", 401 | "metadata": {}, 402 | "outputs": [ 403 | { 404 | "data": { 405 | "text/plain": [ 406 | "Element O" 407 | ] 408 | }, 409 | "execution_count": 33, 410 | "metadata": {}, 411 | "output_type": "execute_result" 412 | } 413 | ], 414 | "source": [ 415 | "site_0.specie" 416 | ] 417 | }, 418 | { 419 | "cell_type": "code", 420 | "execution_count": 34, 421 | "id": "18562910", 422 | "metadata": {}, 423 | "outputs": [ 424 | { 425 | "data": { 426 | "text/plain": [ 427 | "array([0. , 0. , 0.11779])" 428 | ] 429 | }, 430 | "execution_count": 34, 431 | "metadata": {}, 432 | "output_type": "execute_result" 433 | } 434 | ], 435 | "source": [ 436 | "site_0.coords" 437 | ] 438 | }, 439 | { 440 | "cell_type": "code", 441 | "execution_count": 35, 442 | "id": "8c50d2c0", 443 | "metadata": {}, 444 | "outputs": [], 445 | "source": [ 446 | "from pymatgen import Element, Specie, Composition" 447 | ] 448 | }, 449 | { 450 | "cell_type": "code", 451 | "execution_count": 36, 452 | "id": "5dee2c0e", 453 | "metadata": {}, 454 | "outputs": [], 455 | "source": [ 456 | "carbon = Element(\"C\")" 457 | ] 458 | }, 459 | { 460 | "cell_type": "code", 461 | "execution_count": 38, 462 | "id": "77f74438", 463 | "metadata": {}, 464 | "outputs": [ 465 | { 466 | "name": "stdout", 467 | "output_type": "stream", 468 | "text": [ 469 | "C\n" 470 | ] 471 | } 472 | ], 473 | "source": [ 474 | "print(carbon)" 475 | ] 476 | }, 477 | { 478 | "cell_type": "code", 479 | "execution_count": 40, 480 | "id": "78ca003e", 481 | "metadata": {}, 482 | "outputs": [ 483 | { 484 | "data": { 485 | "text/plain": [ 486 | "12.0107" 487 | ] 488 | }, 489 | "execution_count": 40, 490 | "metadata": {}, 491 | "output_type": "execute_result" 492 | } 493 | ], 494 | "source": [ 495 | "carbon.atomic_mass" 496 | ] 497 | }, 498 | { 499 | "cell_type": "code", 500 | "execution_count": 41, 501 | "id": "b368e738", 502 | "metadata": {}, 503 | "outputs": [ 504 | { 505 | "data": { 506 | "text/plain": [ 507 | "0.3" 508 | ] 509 | }, 510 | "execution_count": 41, 511 | "metadata": {}, 512 | "output_type": "execute_result" 513 | } 514 | ], 515 | "source": [ 516 | "carbon.average_ionic_radius" 517 | ] 518 | }, 519 | { 520 | "cell_type": "code", 521 | "execution_count": 43, 522 | "id": "d1c968c2", 523 | "metadata": {}, 524 | "outputs": [ 525 | { 526 | "name": "stdout", 527 | "output_type": "stream", 528 | "text": [ 529 | "O2-\n" 530 | ] 531 | } 532 | ], 533 | "source": [ 534 | "o2_minus = Specie(\"O\", oxidation_state=-2)\n", 535 | "print(o2_minus)" 536 | ] 537 | }, 538 | { 539 | "cell_type": "code", 540 | "execution_count": 49, 541 | "id": "e9169575", 542 | "metadata": {}, 543 | "outputs": [ 544 | { 545 | "data": { 546 | "text/plain": [ 547 | "15.9994" 548 | ] 549 | }, 550 | "execution_count": 49, 551 | "metadata": {}, 552 | "output_type": "execute_result" 553 | } 554 | ], 555 | "source": [ 556 | "o2_minus.atomic_mass" 557 | ] 558 | }, 559 | { 560 | "cell_type": "code", 561 | "execution_count": 45, 562 | "id": "728b4f18", 563 | "metadata": {}, 564 | "outputs": [ 565 | { 566 | "data": { 567 | "text/plain": [ 568 | "-2" 569 | ] 570 | }, 571 | "execution_count": 45, 572 | "metadata": {}, 573 | "output_type": "execute_result" 574 | } 575 | ], 576 | "source": [ 577 | "o2_minus.oxi" 578 | ] 579 | }, 580 | { 581 | "cell_type": "code", 582 | "execution_count": 50, 583 | "id": "90b938cc", 584 | "metadata": {}, 585 | "outputs": [ 586 | { 587 | "name": "stdout", 588 | "output_type": "stream", 589 | "text": [ 590 | "Au0.5 Cu0.5\n" 591 | ] 592 | } 593 | ], 594 | "source": [ 595 | "comp = Composition({\"Au\": 0.5, \"Cu\": 0.5})\n", 596 | "print(comp)" 597 | ] 598 | }, 599 | { 600 | "cell_type": "code", 601 | "execution_count": 51, 602 | "id": "075ef6be", 603 | "metadata": {}, 604 | "outputs": [ 605 | { 606 | "data": { 607 | "text/plain": [ 608 | "'Au-Cu'" 609 | ] 610 | }, 611 | "execution_count": 51, 612 | "metadata": {}, 613 | "output_type": "execute_result" 614 | } 615 | ], 616 | "source": [ 617 | "comp.chemical_system" 618 | ] 619 | }, 620 | { 621 | "cell_type": "code", 622 | "execution_count": 52, 623 | "id": "428ad67e", 624 | "metadata": {}, 625 | "outputs": [ 626 | { 627 | "data": { 628 | "text/plain": [ 629 | "False" 630 | ] 631 | }, 632 | "execution_count": 52, 633 | "metadata": {}, 634 | "output_type": "execute_result" 635 | } 636 | ], 637 | "source": [ 638 | "comp.contains_element_type(\"metalloid\")" 639 | ] 640 | }, 641 | { 642 | "cell_type": "markdown", 643 | "id": "b91c4967", 644 | "metadata": {}, 645 | "source": [ 646 | "HCN\n", 647 | "linear molecule\n", 648 | "H-C, C-N " 649 | ] 650 | }, 651 | { 652 | "cell_type": "code", 653 | "execution_count": 54, 654 | "id": "0ef319ba", 655 | "metadata": {}, 656 | "outputs": [], 657 | "source": [ 658 | "h = Element(\"H\")\n", 659 | "c = Element(\"C\")\n", 660 | "n = Element(\"N\")\n", 661 | "hc = h.atomic_radius + c.atomic_radius\n", 662 | "cn = c.atomic_radius + n.atomic_radius\n", 663 | "h_pos = 0.0\n", 664 | "c_pos = h_pos + hc\n", 665 | "n_pos = c_pos + cn" 666 | ] 667 | }, 668 | { 669 | "cell_type": "code", 670 | "execution_count": 55, 671 | "id": "b727d306", 672 | "metadata": {}, 673 | "outputs": [ 674 | { 675 | "data": { 676 | "text/plain": [ 677 | "0.95" 678 | ] 679 | }, 680 | "execution_count": 55, 681 | "metadata": {}, 682 | "output_type": "execute_result" 683 | } 684 | ], 685 | "source": [ 686 | "hc" 687 | ] 688 | }, 689 | { 690 | "cell_type": "code", 691 | "execution_count": 56, 692 | "id": "d48fa7b5", 693 | "metadata": {}, 694 | "outputs": [ 695 | { 696 | "data": { 697 | "text/plain": [ 698 | "1.35" 699 | ] 700 | }, 701 | "execution_count": 56, 702 | "metadata": {}, 703 | "output_type": "execute_result" 704 | } 705 | ], 706 | "source": [ 707 | "cn" 708 | ] 709 | }, 710 | { 711 | "cell_type": "code", 712 | "execution_count": 57, 713 | "id": "2fdd9098", 714 | "metadata": {}, 715 | "outputs": [], 716 | "source": [ 717 | "hcn = Molecule([\"H\", \"C\", \"N\"], [[0., 0., h_pos], [0., 0., c_pos], [0., 0., n_pos]])" 718 | ] 719 | }, 720 | { 721 | "cell_type": "code", 722 | "execution_count": 58, 723 | "id": "62632a98", 724 | "metadata": {}, 725 | "outputs": [ 726 | { 727 | "name": "stdout", 728 | "output_type": "stream", 729 | "text": [ 730 | "Full Formula (H1 C1 N1)\n", 731 | "Reduced Formula: HCN\n", 732 | "Charge = 0.0, Spin Mult = 1\n", 733 | "Sites (3)\n", 734 | "0 H 0.000000 0.000000 0.000000\n", 735 | "1 C 0.000000 0.000000 0.950000\n", 736 | "2 N 0.000000 0.000000 2.300000\n" 737 | ] 738 | } 739 | ], 740 | "source": [ 741 | "print(hcn)" 742 | ] 743 | }, 744 | { 745 | "cell_type": "code", 746 | "execution_count": 59, 747 | "id": "fa169149", 748 | "metadata": {}, 749 | "outputs": [], 750 | "source": [ 751 | "from pymatgen import Lattice" 752 | ] 753 | }, 754 | { 755 | "cell_type": "code", 756 | "execution_count": 60, 757 | "id": "d7a98394", 758 | "metadata": {}, 759 | "outputs": [], 760 | "source": [ 761 | "Lattice_1 = Lattice([[5.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 5.0]])" 762 | ] 763 | }, 764 | { 765 | "cell_type": "code", 766 | "execution_count": 61, 767 | "id": "8267c4f5", 768 | "metadata": {}, 769 | "outputs": [ 770 | { 771 | "name": "stdout", 772 | "output_type": "stream", 773 | "text": [ 774 | "5.000000 0.000000 0.000000\n", 775 | "0.000000 5.000000 0.000000\n", 776 | "0.000000 0.000000 5.000000\n" 777 | ] 778 | } 779 | ], 780 | "source": [ 781 | "print(Lattice_1)" 782 | ] 783 | }, 784 | { 785 | "cell_type": "code", 786 | "execution_count": 62, 787 | "id": "2a8cd852", 788 | "metadata": {}, 789 | "outputs": [], 790 | "source": [ 791 | "lattice_2 = Lattice.from_parameters(5.0, 5.0, 5.0, 90.0, 90.0, 90.0)" 792 | ] 793 | }, 794 | { 795 | "cell_type": "code", 796 | "execution_count": 63, 797 | "id": "7e71f97f", 798 | "metadata": {}, 799 | "outputs": [], 800 | "source": [ 801 | "lattice_3 = Lattice.cubic(5.0)" 802 | ] 803 | }, 804 | { 805 | "cell_type": "code", 806 | "execution_count": 65, 807 | "id": "31273b00", 808 | "metadata": {}, 809 | "outputs": [ 810 | { 811 | "data": { 812 | "text/plain": [ 813 | "True" 814 | ] 815 | }, 816 | "execution_count": 65, 817 | "metadata": {}, 818 | "output_type": "execute_result" 819 | } 820 | ], 821 | "source": [ 822 | "Lattice_1 == lattice_2 == lattice_3" 823 | ] 824 | }, 825 | { 826 | "cell_type": "code", 827 | "execution_count": 66, 828 | "id": "1032f14b", 829 | "metadata": {}, 830 | "outputs": [ 831 | { 832 | "name": "stdout", 833 | "output_type": "stream", 834 | "text": [ 835 | "1.918445 0.000000 0.854147\n", 836 | "-0.000000 3.300000 0.000000\n", 837 | "0.000000 0.000000 3.800000\n" 838 | ] 839 | } 840 | ], 841 | "source": [ 842 | "monoclinic = Lattice.monoclinic(2.1, 3.3, 3.8, 66)\n", 843 | "print(monoclinic)" 844 | ] 845 | }, 846 | { 847 | "cell_type": "code", 848 | "execution_count": 67, 849 | "id": "40c478e6", 850 | "metadata": {}, 851 | "outputs": [], 852 | "source": [ 853 | "from pymatgen import Structure" 854 | ] 855 | }, 856 | { 857 | "cell_type": "code", 858 | "execution_count": 69, 859 | "id": "9e7b4564", 860 | "metadata": {}, 861 | "outputs": [ 862 | { 863 | "name": "stdout", 864 | "output_type": "stream", 865 | "text": [ 866 | "Full Formula (Fe2)\n", 867 | "Reduced Formula: Fe\n", 868 | "abc : 2.800000 2.800000 2.800000\n", 869 | "angles: 90.000000 90.000000 90.000000\n", 870 | "Sites (2)\n", 871 | " # SP a b c\n", 872 | "--- ---- --- --- ---\n", 873 | " 0 Fe 0 0 0\n", 874 | " 1 Fe 0.5 0.5 0.5\n" 875 | ] 876 | } 877 | ], 878 | "source": [ 879 | "bcc_fe = Structure(Lattice.cubic(2.8), [\"Fe\", \"Fe\"], [[0., 0., 0.], [0.5, 0.5, 0.5]])\n", 880 | "print(bcc_fe)" 881 | ] 882 | }, 883 | { 884 | "cell_type": "code", 885 | "execution_count": 70, 886 | "id": "9876e3e4", 887 | "metadata": {}, 888 | "outputs": [ 889 | { 890 | "data": { 891 | "text/plain": [ 892 | "[PeriodicSite: Fe (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000],\n", 893 | " PeriodicSite: Fe (1.4000, 1.4000, 1.4000) [0.5000, 0.5000, 0.5000]]" 894 | ] 895 | }, 896 | "execution_count": 70, 897 | "metadata": {}, 898 | "output_type": "execute_result" 899 | } 900 | ], 901 | "source": [ 902 | "list(bcc_fe)" 903 | ] 904 | }, 905 | { 906 | "cell_type": "code", 907 | "execution_count": 71, 908 | "id": "cc1ddaff", 909 | "metadata": {}, 910 | "outputs": [], 911 | "source": [ 912 | "bcc_fe_from_cart = Structure(Lattice.cubic(2.8), [\"Fe\", \"Fe\"], [[0., 0., 0.], [1.4, 1.4, 1.4]], coords_are_cartesian=True)" 913 | ] 914 | }, 915 | { 916 | "cell_type": "code", 917 | "execution_count": 72, 918 | "id": "dd336a4b", 919 | "metadata": {}, 920 | "outputs": [ 921 | { 922 | "data": { 923 | "text/plain": [ 924 | "True" 925 | ] 926 | }, 927 | "execution_count": 72, 928 | "metadata": {}, 929 | "output_type": "execute_result" 930 | } 931 | ], 932 | "source": [ 933 | "bcc_fe == bcc_fe_from_cart" 934 | ] 935 | }, 936 | { 937 | "cell_type": "code", 938 | "execution_count": 73, 939 | "id": "f9c49b6c", 940 | "metadata": {}, 941 | "outputs": [], 942 | "source": [ 943 | "bcc_fe_from_sg = Structure.from_spacegroup(\"Im-3m\", Lattice.cubic(2.8), [\"Fe\"], [[0.0, 0.0, 0.0]])" 944 | ] 945 | }, 946 | { 947 | "cell_type": "code", 948 | "execution_count": 75, 949 | "id": "480913fe", 950 | "metadata": {}, 951 | "outputs": [ 952 | { 953 | "data": { 954 | "text/plain": [ 955 | "True" 956 | ] 957 | }, 958 | "execution_count": 75, 959 | "metadata": {}, 960 | "output_type": "execute_result" 961 | } 962 | ], 963 | "source": [ 964 | "bcc_fe == bcc_fe_from_sg" 965 | ] 966 | }, 967 | { 968 | "cell_type": "code", 969 | "execution_count": 76, 970 | "id": "9d9891ff", 971 | "metadata": {}, 972 | "outputs": [ 973 | { 974 | "data": { 975 | "text/plain": [ 976 | "21.951999999999995" 977 | ] 978 | }, 979 | "execution_count": 76, 980 | "metadata": {}, 981 | "output_type": "execute_result" 982 | } 983 | ], 984 | "source": [ 985 | "bcc_fe.volume" 986 | ] 987 | }, 988 | { 989 | "cell_type": "code", 990 | "execution_count": 78, 991 | "id": "cb9ef5c5", 992 | "metadata": {}, 993 | "outputs": [ 994 | { 995 | "data": { 996 | "text/plain": [ 997 | "\u001b[0;31mType:\u001b[0m property\n", 998 | "\u001b[0;31mString form:\u001b[0m \n", 999 | "\u001b[0;31mDocstring:\u001b[0m Returns the density in units of g/cc\n" 1000 | ] 1001 | }, 1002 | "metadata": {}, 1003 | "output_type": "display_data" 1004 | } 1005 | ], 1006 | "source": [ 1007 | "bcc_fe.density?" 1008 | ] 1009 | }, 1010 | { 1011 | "cell_type": "code", 1012 | "execution_count": 79, 1013 | "id": "e608d7aa", 1014 | "metadata": {}, 1015 | "outputs": [], 1016 | "source": [ 1017 | "nacl = Structure.from_spacegroup(\"Fm-3m\", Lattice.cubic(5.692), [\"Na+\", \"Cl-\"], [[0, 0, 0], [0.5, 0.5, 0.5]])" 1018 | ] 1019 | }, 1020 | { 1021 | "cell_type": "code", 1022 | "execution_count": 80, 1023 | "id": "4fa3d48e", 1024 | "metadata": {}, 1025 | "outputs": [ 1026 | { 1027 | "name": "stdout", 1028 | "output_type": "stream", 1029 | "text": [ 1030 | "Full Formula (Na4 Cl4)\n", 1031 | "Reduced Formula: NaCl\n", 1032 | "abc : 5.692000 5.692000 5.692000\n", 1033 | "angles: 90.000000 90.000000 90.000000\n", 1034 | "Sites (8)\n", 1035 | " # SP a b c\n", 1036 | "--- ---- --- --- ---\n", 1037 | " 0 Na+ 0 0 0\n", 1038 | " 1 Na+ 0 0.5 0.5\n", 1039 | " 2 Na+ 0.5 0 0.5\n", 1040 | " 3 Na+ 0.5 0.5 0\n", 1041 | " 4 Cl- 0.5 0.5 0.5\n", 1042 | " 5 Cl- 0.5 0 0\n", 1043 | " 6 Cl- 0 0.5 0\n", 1044 | " 7 Cl- 0 0 0.5\n" 1045 | ] 1046 | } 1047 | ], 1048 | "source": [ 1049 | "print(nacl)" 1050 | ] 1051 | }, 1052 | { 1053 | "cell_type": "code", 1054 | "execution_count": 81, 1055 | "id": "e387a9c0", 1056 | "metadata": {}, 1057 | "outputs": [ 1058 | { 1059 | "data": { 1060 | "text/plain": [ 1061 | "('Fm-3m', 225)" 1062 | ] 1063 | }, 1064 | "execution_count": 81, 1065 | "metadata": {}, 1066 | "output_type": "execute_result" 1067 | } 1068 | ], 1069 | "source": [ 1070 | "nacl.get_space_group_info()" 1071 | ] 1072 | }, 1073 | { 1074 | "cell_type": "code", 1075 | "execution_count": 82, 1076 | "id": "80ce57a6", 1077 | "metadata": {}, 1078 | "outputs": [], 1079 | "source": [ 1080 | "polonium = Structure(Lattice.cubic(3.4), [\"Po\"], [[0.0, 0.0, 0.0]])" 1081 | ] 1082 | }, 1083 | { 1084 | "cell_type": "code", 1085 | "execution_count": 83, 1086 | "id": "5e87e0ff", 1087 | "metadata": {}, 1088 | "outputs": [ 1089 | { 1090 | "name": "stdout", 1091 | "output_type": "stream", 1092 | "text": [ 1093 | "Full Formula (Po1)\n", 1094 | "Reduced Formula: Po\n", 1095 | "abc : 3.400000 3.400000 3.400000\n", 1096 | "angles: 90.000000 90.000000 90.000000\n", 1097 | "Sites (1)\n", 1098 | " # SP a b c\n", 1099 | "--- ---- --- --- ---\n", 1100 | " 0 Po 0 0 0\n" 1101 | ] 1102 | } 1103 | ], 1104 | "source": [ 1105 | "print(polonium)" 1106 | ] 1107 | }, 1108 | { 1109 | "cell_type": "code", 1110 | "execution_count": 84, 1111 | "id": "78557401", 1112 | "metadata": {}, 1113 | "outputs": [], 1114 | "source": [ 1115 | "supercell = polonium * (10, 10, 1)" 1116 | ] 1117 | }, 1118 | { 1119 | "cell_type": "code", 1120 | "execution_count": 85, 1121 | "id": "bfba370e", 1122 | "metadata": {}, 1123 | "outputs": [ 1124 | { 1125 | "name": "stdout", 1126 | "output_type": "stream", 1127 | "text": [ 1128 | "Full Formula (Po100)\n", 1129 | "Reduced Formula: Po\n", 1130 | "abc : 34.000000 34.000000 3.400000\n", 1131 | "angles: 90.000000 90.000000 90.000000\n", 1132 | "Sites (100)\n", 1133 | " # SP a b c\n", 1134 | "--- ---- --- --- ---\n", 1135 | " 0 Po 0 0 0\n", 1136 | " 1 Po 0 0.1 0\n", 1137 | " 2 Po 0 0.2 0\n", 1138 | " 3 Po 0 0.3 0\n", 1139 | " 4 Po 0 0.4 0\n", 1140 | " 5 Po 0 0.5 0\n", 1141 | " 6 Po 0 0.6 0\n", 1142 | " 7 Po 0 0.7 0\n", 1143 | " 8 Po 0 0.8 0\n", 1144 | " 9 Po 0 0.9 0\n", 1145 | " 10 Po 0.1 0 0\n", 1146 | " 11 Po 0.1 0.1 0\n", 1147 | " 12 Po 0.1 0.2 0\n", 1148 | " 13 Po 0.1 0.3 0\n", 1149 | " 14 Po 0.1 0.4 0\n", 1150 | " 15 Po 0.1 0.5 0\n", 1151 | " 16 Po 0.1 0.6 0\n", 1152 | " 17 Po 0.1 0.7 0\n", 1153 | " 18 Po 0.1 0.8 0\n", 1154 | " 19 Po 0.1 0.9 0\n", 1155 | " 20 Po 0.2 0 0\n", 1156 | " 21 Po 0.2 0.1 0\n", 1157 | " 22 Po 0.2 0.2 0\n", 1158 | " 23 Po 0.2 0.3 0\n", 1159 | " 24 Po 0.2 0.4 0\n", 1160 | " 25 Po 0.2 0.5 0\n", 1161 | " 26 Po 0.2 0.6 0\n", 1162 | " 27 Po 0.2 0.7 0\n", 1163 | " 28 Po 0.2 0.8 0\n", 1164 | " 29 Po 0.2 0.9 0\n", 1165 | " 30 Po 0.3 0 0\n", 1166 | " 31 Po 0.3 0.1 0\n", 1167 | " 32 Po 0.3 0.2 0\n", 1168 | " 33 Po 0.3 0.3 0\n", 1169 | " 34 Po 0.3 0.4 0\n", 1170 | " 35 Po 0.3 0.5 0\n", 1171 | " 36 Po 0.3 0.6 0\n", 1172 | " 37 Po 0.3 0.7 0\n", 1173 | " 38 Po 0.3 0.8 0\n", 1174 | " 39 Po 0.3 0.9 0\n", 1175 | " 40 Po 0.4 0 0\n", 1176 | " 41 Po 0.4 0.1 0\n", 1177 | " 42 Po 0.4 0.2 0\n", 1178 | " 43 Po 0.4 0.3 0\n", 1179 | " 44 Po 0.4 0.4 0\n", 1180 | " 45 Po 0.4 0.5 0\n", 1181 | " 46 Po 0.4 0.6 0\n", 1182 | " 47 Po 0.4 0.7 0\n", 1183 | " 48 Po 0.4 0.8 0\n", 1184 | " 49 Po 0.4 0.9 0\n", 1185 | " 50 Po 0.5 0 0\n", 1186 | " 51 Po 0.5 0.1 0\n", 1187 | " 52 Po 0.5 0.2 0\n", 1188 | " 53 Po 0.5 0.3 0\n", 1189 | " 54 Po 0.5 0.4 0\n", 1190 | " 55 Po 0.5 0.5 0\n", 1191 | " 56 Po 0.5 0.6 0\n", 1192 | " 57 Po 0.5 0.7 0\n", 1193 | " 58 Po 0.5 0.8 0\n", 1194 | " 59 Po 0.5 0.9 0\n", 1195 | " 60 Po 0.6 0 0\n", 1196 | " 61 Po 0.6 0.1 0\n", 1197 | " 62 Po 0.6 0.2 0\n", 1198 | " 63 Po 0.6 0.3 0\n", 1199 | " 64 Po 0.6 0.4 0\n", 1200 | " 65 Po 0.6 0.5 0\n", 1201 | " 66 Po 0.6 0.6 0\n", 1202 | " 67 Po 0.6 0.7 0\n", 1203 | " 68 Po 0.6 0.8 0\n", 1204 | " 69 Po 0.6 0.9 0\n", 1205 | " 70 Po 0.7 0 0\n", 1206 | " 71 Po 0.7 0.1 0\n", 1207 | " 72 Po 0.7 0.2 0\n", 1208 | " 73 Po 0.7 0.3 0\n", 1209 | " 74 Po 0.7 0.4 0\n", 1210 | " 75 Po 0.7 0.5 0\n", 1211 | " 76 Po 0.7 0.6 0\n", 1212 | " 77 Po 0.7 0.7 0\n", 1213 | " 78 Po 0.7 0.8 0\n", 1214 | " 79 Po 0.7 0.9 0\n", 1215 | " 80 Po 0.8 0 0\n", 1216 | " 81 Po 0.8 0.1 0\n", 1217 | " 82 Po 0.8 0.2 0\n", 1218 | " 83 Po 0.8 0.3 0\n", 1219 | " 84 Po 0.8 0.4 0\n", 1220 | " 85 Po 0.8 0.5 0\n", 1221 | " 86 Po 0.8 0.6 0\n", 1222 | " 87 Po 0.8 0.7 0\n", 1223 | " 88 Po 0.8 0.8 0\n", 1224 | " 89 Po 0.8 0.9 0\n", 1225 | " 90 Po 0.9 0 0\n", 1226 | " 91 Po 0.9 0.1 0\n", 1227 | " 92 Po 0.9 0.2 0\n", 1228 | " 93 Po 0.9 0.3 0\n", 1229 | " 94 Po 0.9 0.4 0\n", 1230 | " 95 Po 0.9 0.5 0\n", 1231 | " 96 Po 0.9 0.6 0\n", 1232 | " 97 Po 0.9 0.7 0\n", 1233 | " 98 Po 0.9 0.8 0\n", 1234 | " 99 Po 0.9 0.9 0\n" 1235 | ] 1236 | } 1237 | ], 1238 | "source": [ 1239 | "print(supercell)" 1240 | ] 1241 | }, 1242 | { 1243 | "cell_type": "code", 1244 | "execution_count": 87, 1245 | "id": "7b45a6f4", 1246 | "metadata": {}, 1247 | "outputs": [ 1248 | { 1249 | "name": "stderr", 1250 | "output_type": "stream", 1251 | "text": [ 1252 | "/home/max/.virtualenvs/aiida/lib/python3.7/site-packages/pymatgen/io/cif.py:1194: UserWarning: Issues encountered while parsing CIF: Some fractional co-ordinates rounded to ideal values to avoid issues with finite precision.\n", 1253 | " \"Issues encountered while parsing CIF: %s\" % \"\\n\".join(self.warnings)\n" 1254 | ] 1255 | } 1256 | ], 1257 | "source": [ 1258 | "batio3 = Structure.from_file(\"BaTiO3.cif\")" 1259 | ] 1260 | }, 1261 | { 1262 | "cell_type": "code", 1263 | "execution_count": 88, 1264 | "id": "7ab5e68e", 1265 | "metadata": {}, 1266 | "outputs": [ 1267 | { 1268 | "name": "stdout", 1269 | "output_type": "stream", 1270 | "text": [ 1271 | "Full Formula (Ba3 Ti3 O9)\n", 1272 | "Reduced Formula: BaTiO3\n", 1273 | "abc : 5.754672 5.754672 7.109987\n", 1274 | "angles: 90.000000 90.000000 120.000000\n", 1275 | "Sites (15)\n", 1276 | " # SP a b c\n", 1277 | "--- ---- -------- -------- --------\n", 1278 | " 0 Ba 0 0 0.002069\n", 1279 | " 1 Ba 0.666667 0.333333 0.335402\n", 1280 | " 2 Ba 0.333333 0.666667 0.668736\n", 1281 | " 3 Ti 0 0 0.51644\n", 1282 | " 4 Ti 0.666667 0.333333 0.849773\n", 1283 | " 5 Ti 0.333333 0.666667 0.183107\n", 1284 | " 6 O 0.836955 0.673911 0.647664\n", 1285 | " 7 O 0.326089 0.163045 0.647664\n", 1286 | " 8 O 0.836955 0.163045 0.647664\n", 1287 | " 9 O 0.503622 0.007244 0.980997\n", 1288 | " 10 O 0.992756 0.496378 0.980997\n", 1289 | " 11 O 0.503622 0.496378 0.980997\n", 1290 | " 12 O 0.170289 0.340577 0.31433\n", 1291 | " 13 O 0.659423 0.829711 0.31433\n", 1292 | " 14 O 0.170289 0.829711 0.31433\n" 1293 | ] 1294 | } 1295 | ], 1296 | "source": [ 1297 | "print(batio3)" 1298 | ] 1299 | }, 1300 | { 1301 | "cell_type": "code", 1302 | "execution_count": 89, 1303 | "id": "ef0e6fe7", 1304 | "metadata": {}, 1305 | "outputs": [ 1306 | { 1307 | "name": "stdout", 1308 | "output_type": "stream", 1309 | "text": [ 1310 | "('R3m', 160)\n" 1311 | ] 1312 | } 1313 | ], 1314 | "source": [ 1315 | "print(batio3.get_space_group_info())" 1316 | ] 1317 | }, 1318 | { 1319 | "cell_type": "code", 1320 | "execution_count": 91, 1321 | "id": "bf5aae07", 1322 | "metadata": {}, 1323 | "outputs": [], 1324 | "source": [ 1325 | "batio3.replace(0, \"Mg\")\n", 1326 | "supercell = batio3 * (1, 1, 4)" 1327 | ] 1328 | }, 1329 | { 1330 | "cell_type": "code", 1331 | "execution_count": 92, 1332 | "id": "1ace5b02", 1333 | "metadata": {}, 1334 | "outputs": [ 1335 | { 1336 | "name": "stdout", 1337 | "output_type": "stream", 1338 | "text": [ 1339 | "Full Formula (Ba8 Mg4 Ti12 O36)\n", 1340 | "Reduced Formula: Ba2MgTi3O9\n", 1341 | "abc : 5.754672 5.754672 28.439948\n", 1342 | "angles: 90.000000 90.000000 120.000000\n", 1343 | "Sites (60)\n", 1344 | " # SP a b c\n", 1345 | "--- ---- -------- -------- --------\n", 1346 | " 0 Mg 0 0 0.000517\n", 1347 | " 1 Mg 0 0 0.250517\n", 1348 | " 2 Mg 0 0 0.500517\n", 1349 | " 3 Mg 0 0 0.750517\n", 1350 | " 4 Ba 0.666667 0.333333 0.083851\n", 1351 | " 5 Ba 0.666667 0.333333 0.333851\n", 1352 | " 6 Ba 0.666667 0.333333 0.583851\n", 1353 | " 7 Ba 0.666667 0.333333 0.833851\n", 1354 | " 8 Ba 0.333333 0.666667 0.167184\n", 1355 | " 9 Ba 0.333333 0.666667 0.417184\n", 1356 | " 10 Ba 0.333333 0.666667 0.667184\n", 1357 | " 11 Ba 0.333333 0.666667 0.917184\n", 1358 | " 12 Ti 0 0 0.12911\n", 1359 | " 13 Ti 0 0 0.37911\n", 1360 | " 14 Ti 0 0 0.62911\n", 1361 | " 15 Ti 0 0 0.87911\n", 1362 | " 16 Ti 0.666667 0.333333 0.212443\n", 1363 | " 17 Ti 0.666667 0.333333 0.462443\n", 1364 | " 18 Ti 0.666667 0.333333 0.712443\n", 1365 | " 19 Ti 0.666667 0.333333 0.962443\n", 1366 | " 20 Ti 0.333333 0.666667 0.045777\n", 1367 | " 21 Ti 0.333333 0.666667 0.295777\n", 1368 | " 22 Ti 0.333333 0.666667 0.545777\n", 1369 | " 23 Ti 0.333333 0.666667 0.795777\n", 1370 | " 24 O 0.836955 0.673911 0.161916\n", 1371 | " 25 O 0.836955 0.673911 0.411916\n", 1372 | " 26 O 0.836955 0.673911 0.661916\n", 1373 | " 27 O 0.836955 0.673911 0.911916\n", 1374 | " 28 O 0.326089 0.163045 0.161916\n", 1375 | " 29 O 0.326089 0.163045 0.411916\n", 1376 | " 30 O 0.326089 0.163045 0.661916\n", 1377 | " 31 O 0.326089 0.163045 0.911916\n", 1378 | " 32 O 0.836955 0.163045 0.161916\n", 1379 | " 33 O 0.836955 0.163045 0.411916\n", 1380 | " 34 O 0.836955 0.163045 0.661916\n", 1381 | " 35 O 0.836955 0.163045 0.911916\n", 1382 | " 36 O 0.503622 0.007244 0.245249\n", 1383 | " 37 O 0.503622 0.007244 0.495249\n", 1384 | " 38 O 0.503622 0.007244 0.745249\n", 1385 | " 39 O 0.503622 0.007244 0.995249\n", 1386 | " 40 O 0.992756 0.496378 0.245249\n", 1387 | " 41 O 0.992756 0.496378 0.495249\n", 1388 | " 42 O 0.992756 0.496378 0.745249\n", 1389 | " 43 O 0.992756 0.496378 0.995249\n", 1390 | " 44 O 0.503622 0.496378 0.245249\n", 1391 | " 45 O 0.503622 0.496378 0.495249\n", 1392 | " 46 O 0.503622 0.496378 0.745249\n", 1393 | " 47 O 0.503622 0.496378 0.995249\n", 1394 | " 48 O 0.170289 0.340577 0.078583\n", 1395 | " 49 O 0.170289 0.340577 0.328583\n", 1396 | " 50 O 0.170289 0.340577 0.578583\n", 1397 | " 51 O 0.170289 0.340577 0.828583\n", 1398 | " 52 O 0.659423 0.829711 0.078583\n", 1399 | " 53 O 0.659423 0.829711 0.328583\n", 1400 | " 54 O 0.659423 0.829711 0.578583\n", 1401 | " 55 O 0.659423 0.829711 0.828583\n", 1402 | " 56 O 0.170289 0.829711 0.078583\n", 1403 | " 57 O 0.170289 0.829711 0.328583\n", 1404 | " 58 O 0.170289 0.829711 0.578583\n", 1405 | " 59 O 0.170289 0.829711 0.828583\n" 1406 | ] 1407 | } 1408 | ], 1409 | "source": [ 1410 | "print(supercell)" 1411 | ] 1412 | }, 1413 | { 1414 | "cell_type": "code", 1415 | "execution_count": 93, 1416 | "id": "7a0fe95a", 1417 | "metadata": {}, 1418 | "outputs": [ 1419 | { 1420 | "name": "stdout", 1421 | "output_type": "stream", 1422 | "text": [ 1423 | "('P3m1', 156)\n" 1424 | ] 1425 | } 1426 | ], 1427 | "source": [ 1428 | "print(supercell.get_space_group_info())" 1429 | ] 1430 | }, 1431 | { 1432 | "cell_type": "code", 1433 | "execution_count": 95, 1434 | "id": "62e2ff4e", 1435 | "metadata": {}, 1436 | "outputs": [], 1437 | "source": [ 1438 | "supercell_2 = batio3 * [1,1, 4]" 1439 | ] 1440 | }, 1441 | { 1442 | "cell_type": "code", 1443 | "execution_count": 96, 1444 | "id": "b47984a0", 1445 | "metadata": {}, 1446 | "outputs": [], 1447 | "source": [ 1448 | "supercell_2.replace(0, \"Mg\")" 1449 | ] 1450 | }, 1451 | { 1452 | "cell_type": "code", 1453 | "execution_count": 100, 1454 | "id": "e8e96624", 1455 | "metadata": {}, 1456 | "outputs": [ 1457 | { 1458 | "name": "stdout", 1459 | "output_type": "stream", 1460 | "text": [ 1461 | "('P3m1', 156)\n" 1462 | ] 1463 | } 1464 | ], 1465 | "source": [ 1466 | "print(supercell_2.get_space_group_info())" 1467 | ] 1468 | } 1469 | ], 1470 | "metadata": { 1471 | "kernelspec": { 1472 | "display_name": "Python 3", 1473 | "language": "python", 1474 | "name": "python3" 1475 | }, 1476 | "language_info": { 1477 | "codemirror_mode": { 1478 | "name": "ipython", 1479 | "version": 3 1480 | }, 1481 | "file_extension": ".py", 1482 | "mimetype": "text/x-python", 1483 | "name": "python", 1484 | "nbconvert_exporter": "python", 1485 | "pygments_lexer": "ipython3", 1486 | "version": "3.7.10" 1487 | } 1488 | }, 1489 | "nbformat": 4, 1490 | "nbformat_minor": 5 1491 | } 1492 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Machine-Learning-for-Materials-Science 2 | Querying databases, Organizing and Plotting Data: Query Pymatgen for properties like Young's modulus, melting temperature, and other properties. Organize data into Pandas data frames and python dictionaries and plot using Plotly Linear Regression to predict material properties: Performed linear regression using the scikit learn to package and predict Young's modulus Visualize trends in data and 'goodness of fit' of linear model Neural Network Regression to predict material properties: Used neural networks to perform non-linear, higher-order regression Visualize trends and compare the non-linear model to linear regression Neural Network Classification to predict crystal structures: Used neural networks to classify elements according to their crystal structures 3 | -------------------------------------------------------------------------------- /delaney.csv: -------------------------------------------------------------------------------- 1 | Compound ID,measured log(solubility:mol/L),ESOL predicted log(solubility:mol/L),SMILES 2 | "1,1,1,2-Tetrachloroethane",-2.18,-2.794,ClCC(Cl)(Cl)Cl 3 | "1,1,1-Trichloroethane",-2,-2.232,CC(Cl)(Cl)Cl 4 | "1,1,2,2-Tetrachloroethane",-1.74,-2.549,ClC(Cl)C(Cl)Cl 5 | "1,1,2-Trichloroethane",-1.48,-1.961,ClCC(Cl)Cl 6 | "1,1,2-Trichlorotrifluoroethane",-3.04,-3.077,FC(F)(Cl)C(F)(Cl)Cl 7 | "1,1-Dichloroethane",-1.29,-1.576,CC(Cl)Cl 8 | "1,1-Dichloroethylene",-1.64,-1.939,ClC(=C)Cl 9 | "1,1-Diethoxyethane ",-0.43,-0.899,CCOC(C)OCC 10 | "1,2,3,4-Tetrachlorobenzene",-4.57,-4.546,Clc1ccc(Cl)c(Cl)c1Cl 11 | "1,2,3,4-Tetrahydronapthalene",-4.37,-3.447,C1CCc2ccccc2C1 12 | "1,2,3,5-Tetrachlorobenzene",-4.63,-4.621,Clc1cc(Cl)c(Cl)c(Cl)c1 13 | "1,2,3-Trichlorobenzene",-4,-4.008,Clc1cccc(Cl)c1Cl 14 | "1,2,3-Trimethylbenzene ",-3.2,-3.312,Cc1cccc(C)c1C 15 | "1,2,4,5-Tetrabromobenzene",-6.98,-6.001,Brc1cc(Br)c(Br)cc1Br 16 | "1,2,4,5-Tetrachlorobenzene",-5.56,-4.621,Clc1cc(Cl)c(Cl)cc1Cl 17 | "1,2,4,5-Tetramethylbenzene",-4.59,-3.664,Cc1cc(C)c(C)cc1C 18 | "1,2,4-tribromobenzene",-4.5,-5.144,c1(Br)c(Br)cc(Br)cc1 19 | "1,2,4-Trichlorobenzene",-3.59,-4.083,Clc1ccc(Cl)c(Cl)c1 20 | "1,2,4-Trimethylbenzene",-3.31,-3.343,Cc1ccc(C)c(C)c1 21 | "1,2-Benzenediol",0.62,-1.635,Oc1ccccc1O 22 | "1,2-Dibromobenzene",-3.5,-4.172,Brc1ccccc1Br 23 | "1,2-Dibromoethane",-1.68,-2.102,BrCCBr 24 | "1,2-Dichlorobenzene",-3.05,-3.482,Clc1ccccc1Cl 25 | "1,2-Dichloroethane",-1.06,-1.374,ClCCCl 26 | "1,2-Dichloropropane",-1.6,-1.794,CC(Cl)CCl 27 | "1,2-Dichlorotetrafluoroethane",-2.74,-2.697,FC(F)(Cl)C(F)(F)Cl 28 | "1,2-Diethoxyethane ",-0.77,-0.833,CCOCCOCC 29 | "1,2-Diethylbenzene",-3.28,-3.601,CCc1ccccc1CC 30 | "1,2-Dinitrobenzene",-3.1,-2.281,O=N(=O)c1ccccc1N(=O)=O 31 | "1,2-Propylene oxide",-0.59,-0.358,CC1CO1 32 | "1,3,5-Tribromobenzene",-5.6,-5.27,Brc1cc(Br)cc(Br)c1 33 | "1,3,5-Trichlorobenzene",-4.48,-4.159,Clc1cc(Cl)cc(Cl)c1 34 | "1,3,5-Trimethylbenzene ",-3.4,-3.375,Cc1cc(C)cc(C)c1 35 | "1,3,5-Trinitrobenzene",-2.89,-2.324,O=N(=O)c1cc(cc(c1)N(=O)=O)N(=O)=O 36 | "1,3-Benzenediol",0.81,-1.59,Oc1cccc(O)c1 37 | "1,3-Butadiene",-1.87,-1.376,C=CC=C 38 | "1,3-Dibromobenzene",-3.54,-4.298,Brc1cccc(Br)c1 39 | "1,3-Dichlorobenzene",-3.04,-3.558,Clc1cccc(Cl)c1 40 | "1,3-Dichloropropane",-1.62,-1.618,ClCCCCl 41 | "1,3-diethylthiourea",-1.46,-1.028,CCNC(=S)NCC 42 | "1,3-Difluorobenzene",-2,-2.636,Fc1cccc(F)c1 43 | "1,3-Dimethylnaphthalene",-4.29,-4.147,Cc1cc(C)c2ccccc2c1 44 | "1,3-Dinitrobenzene",-2.29,-2.281,O=N(=O)c1cccc(c1)N(=O)=O 45 | "1,4-Benzenediol",-0.17,-1.59,Oc1ccc(O)cc1 46 | "1,4-Cyclohexadiene",-2.06,-1.842,C1C=CCC=C1 47 | "1,4-Dibromobenzene",-4.07,-4.298,Brc1ccc(Br)cc1 48 | "1,4-Dichlorobenzene",-3.27,-3.558,Clc1ccc(Cl)cc1 49 | "1,4-Diethylbenzene ",-3.75,-3.633,CCc1ccc(CC)cc1 50 | "1,4-Difluorobenzene",-1.97,-2.636,Fc1ccc(F)cc1 51 | "1,4-Dimethylnaphthalene ",-4.14,-4.147,Cc1ccc(C)c2ccccc12 52 | "1,4-Dinitrobenzene",-3.39,-2.281,O=N(=O)c1ccc(cc1)N(=O)=O 53 | "1,4-Pentadiene ",-2.09,-1.758,C=CCC=C 54 | "1,5-Dimethlnapthalene",-4.679,-4.147,Cc1cccc2c(C)cccc12 55 | "1,5-Hexadiene ",-2.68,-2.112,C=CCCC=C 56 | "1,7-phenantroline",-2.68,-2.994,c1cnc2c(c1)ccc3ncccc23 57 | "1,8-Cineole",-1.74,-2.579,CC12CCC(CC1)C(C)(C)O2 58 | 17a-Methyltestosterone,-3.999,-4.073,CC1(O)CCC2C3CCC4=CC(=O)CCC4(C)C3CCC21C 59 | 1-aminoacridine,-4.22,-3.542,Nc2cccc3nc1ccccc1cc23 60 | 1-Bromo-2-methylpropane,-2.43,-2.288,CC(C)CBr 61 | 1-Bromobutane,-2.37,-2.303,CCCCBr 62 | 1-Bromoheptane,-4.43,-3.366,CCCCCCCBr 63 | 1-Bromohexane,-3.81,-3.012,CCCCCCBr 64 | 1-Bromonapthalene,-4.35,-4.434,Brc1cccc2ccccc12 65 | 1-Bromooctane,-5.06,-3.721,CCCCCCCCBr 66 | 1-Bromopentane,-3.08,-2.658,CCCCCBr 67 | 1-Bromopropane,-1.73,-1.949,CCCBr 68 | 1-Butanol,0,-0.688,CCCCO 69 | 1-Butene,-1.94,-1.655,CCC=C 70 | 1-Butyne,-1.24,-1.092,CCC#C 71 | 1-Chloro-2-bromoethane,-1.32,-1.738,ClCCBr 72 | 1-Chloro-2-methylpropane,-2,-1.924,ClCC(C)C 73 | 1-Chlorobutane,-2.03,-1.94,CCCCCl 74 | 1-Chloroheptane,-4,-3.003,CCCCCCCCl 75 | 1-Chlorohexane,-3.12,-2.648,CCCCCCCl 76 | 1-Chloronapthalene,-3.93,-4.063,Clc1cccc2ccccc12 77 | 1-Chloropentane,-2.73,-2.294,CCCCCCl 78 | 1-Chloropropane,-1.47,-1.585,CCCCl 79 | 1-Decanol,-3.63,-2.814,CCCCCCCCCCO 80 | 1-Decene,-5.51,-3.781,CCCCCCCCC=C 81 | 1-Dodecanol,-4.8,-3.523,CCCCCCCCCCCCO 82 | 1-Ethylnaphthalene ,-4.17,-4.1,CCc1cccc2ccccc12 83 | 1-Heptanol,-1.81,-1.751,CCCCCCCO 84 | 1-Heptene,-3.73,-2.718,CCCCCC=C 85 | 1-Heptyne,-3.01,-2.155,CCCCCC#C 86 | 1-Hexadecanol,-7,-4.94,CCCCCCCCCCCCCCCCO 87 | 1-Hexanol,-1.24,-1.397,CCCCCCO 88 | 1-Hexene,-3.23,-2.364,CCCCC=C 89 | 1-Hexene-3-ol,-0.59,-1.199,CCCC(O)C=C 90 | 1-Hexyne ,-2.36,-1.801,CCCCC#C 91 | 1-Iodobutane,-2.96,-2.841,CCCCI 92 | 1-Iodoheptane,-4.81,-3.904,CCCCCCCI 93 | 1-Iodonapthalene,-4.55,-4.889,Ic1cccc2ccccc12 94 | 1-Iodopropane,-2.29,-2.486,CCCI 95 | 1-Methylcyclohexene ,-3.27,-2.574,CC1=CCCCC1 96 | 1-Methylfluorene,-5.22,-4.478,Cc1cccc2c1Cc3ccccc32 97 | 1-Methylnaphthalene,-3.7,-3.802,Cc1cccc2ccccc12 98 | 1-Methylphenanthrene,-5.85,-4.87,Cc1cccc2c1ccc3ccccc32 99 | 1-methyluracil,-0.807,-0.375,Cn1ccc(=O)[nH]c1=O 100 | 1-Napthol,-2.22,-3.08,Oc1cccc2ccccc12 101 | 1-Napthylamine,-1.92,-2.721,Nc1cccc2ccccc12 102 | 1-Nitronapthalene,-3.54,-3.414,O=N(=O)c1cccc2ccccc12 103 | 1-Nitropropane,-0.8,-0.816,CCCN(=O)=O 104 | 1-Nonanol,-3.01,-2.46,CCCCCCCCCO 105 | 1-Nonene ,-5.05,-3.427,CCCCCCCC=C 106 | 1-Nonyne ,-4.24,-2.864,CCCCCCCC#C 107 | 1-Octadecanol,-8.4,-5.649,CCCCCCCCCCCCCCCCCCO 108 | 1-Octanol,-2.39,-2.105,CCCCCCCCO 109 | 1-Octene ,-4.44,-3.073,CCCCCCC=C 110 | 1-Octyne ,-3.66,-2.509,CCCCCCC#C 111 | 1-Pentadecanol,-6.35,-4.586,CCCCCCCCCCCCCCCO 112 | 1-Pentanol,-0.6,-1.042,CCCCCO 113 | 1-Pentene ,-2.68,-2.01,CCCC=C 114 | 1-Pentyne,-1.64,-1.446,CCCC#C 115 | 1-Phenylethanol,-0.92,-1.919,CC(O)c1ccccc1 116 | 1-Propanol,0.62,-0.334,CCCO 117 | 1-Tetradecanol,-5.84,-4.231,CCCCCCCCCCCCCCO 118 | "2,2',3,3',4,4',5,5',6,6'-PCB",-11.6,-9.589,Clc1c(Cl)c(Cl)c(c(Cl)c1Cl)c2c(Cl)c(Cl)c(Cl)c(Cl)c2Cl 119 | "2,2',3,3',4,4',5,5'-PCB",-9.16,-8.468,Clc1cc(c(Cl)c(Cl)c1Cl)c2cc(Cl)c(Cl)c(Cl)c2Cl 120 | "2,2',3,3',4,4'-PCB",-8.01,-7.192,Clc1ccc(c(Cl)c1Cl)c2ccc(Cl)c(Cl)c2Cl 121 | "2,2',3,3',5,5',6,6'-PCB",-9.15,-8.304,Clc1cc(Cl)c(Cl)c(c1Cl)c2c(Cl)c(Cl)cc(Cl)c2Cl 122 | "2,2',3,3',5,6-PCB",-8.6,-7.185,Clc1cccc(c1Cl)c2c(Cl)c(Cl)cc(Cl)c2Cl 123 | "2,2',3,3'-PCB",-7.28,-6.079,Clc1cccc(c1Cl)c2cccc(Cl)c2Cl 124 | "2,2',3,4,4',5',6-PCB",-7.92,-7.898,Clc1ccc(c(Cl)c1)c2c(Cl)c(Cl)c(Cl)c(Cl)c2Cl 125 | "2,2',3,4,5,5',6-PCB",-8.94,-7.898,Clc1ccc(Cl)c(c1)c2c(Cl)c(Cl)c(Cl)c(Cl)c2Cl 126 | "2,2',3,4,5,5'-PCB",-7.68,-7.343,Clc1ccc(Cl)c(c1)c2cc(Cl)c(Cl)c(Cl)c2Cl 127 | "2,2',3,4,5-PCB",-7.21,-6.709,Clc1cc(Cl)c(cc1Cl)c2cccc(Cl)c2Cl 128 | "2,2',3,4,6-PCB",-7.43,-6.627,Clc1ccc(c(Cl)c1)c2c(Cl)ccc(Cl)c2Cl 129 | "2,2',3,5,5',6-PCB",-7.42,-7.261,Clc1ccc(Cl)c(c1)c2c(Cl)c(Cl)cc(Cl)c2Cl 130 | "2,2',3,5'-PCB",-6.47,-6.155,Clc1ccc(Cl)c(c1)c2cccc(Cl)c2Cl 131 | "2,2,3-Trimethylbutane",-4.36,-2.922,CC(C)C(C)(C)C 132 | "2,2',4,4',5,5'-PCB",-8.56,-7.343,Clc1cc(Cl)c(cc1Cl)c2cc(Cl)c(Cl)cc2Cl 133 | "2,2',4,4',6,6'-PCB",-8.71,-7.179,Clc1cc(Cl)c(c(Cl)c1)c2c(Cl)cc(Cl)cc2Cl 134 | "2,2',4,5'-PCB",-6.57,-6.23,Clc1ccc(c(Cl)c1)c2cc(Cl)ccc2Cl 135 | "2,2,4,6,6'-PCB",-7.32,-6.545,Clc1cc(Cl)c(c(Cl)c1)c2c(Cl)cccc2Cl 136 | "2,2,4-Trimethylpentane",-4.74,-3.276,CC(C)CC(C)(C)C 137 | "2,2,5-Trimethylhexane",-5.05,-3.631,CC(C)CCC(C)(C)C 138 | "2,2',6,6'-PCB",-7.39,-5.915,Clc1cccc(Cl)c1c2c(Cl)cccc2Cl 139 | "2,2-Dimethyl-1-butanol",-1.04,-1.365,CCC(C)(C)CO 140 | "2,2-Dimethylbutane",-3.55,-2.584,CCC(C)(C)C 141 | "2,2-Dimethylpentane",-4.36,-2.938,CCCC(C)(C)C 142 | "2,2-Dimethylpentanol",-1.52,-1.719,CCCC(C)(C)CO 143 | "2,2-Dimethylpropanol",-0.4,-1.011,CC(C)(C)CO 144 | "2,2'-PCB",-5.27,-4.984,Clc1ccccc1c2ccccc2Cl 145 | "2,3,3',4,4',5-PCB",-7.82,-7.425,Clc1ccc(cc1Cl)c2cc(Cl)c(Cl)c(Cl)c2Cl 146 | "2,3,3',4,4'6-PCB",-7.66,-7.746,Clc1ccc(c(Cl)c1Cl)c2c(Cl)cc(Cl)c(Cl)c2Cl 147 | "2,3',4,4',5-PCB",-7.39,-7.343,Clc1ccc(c(Cl)c1)c2cc(Cl)c(Cl)c(Cl)c2Cl 148 | "2,3',4,4'-PCB",-7.8,-6.709,Clc1ccc(c(Cl)c1)c2ccc(Cl)c(Cl)c2Cl 149 | "2,3,4,5,6-PCB",-7.92,-6.785,Clc2c(Cl)c(Cl)c(c1ccccc1)c(Cl)c2Cl 150 | "2,3',4',5-PCB",-7.25,-6.312,Clc1ccc(Cl)c(c1)c2ccc(Cl)c(Cl)c2 151 | "2,3,4,5-Tetrachlorophenol",-3.15,-4.335,Oc1cc(Cl)c(Cl)c(Cl)c1Cl 152 | "2,3,4,6-Tetrachlorophenol",-3.1,-4.203,Oc1c(Cl)cc(Cl)c(Cl)c1Cl 153 | "2',3,4-PCB",-6.29,-5.686,Clc1ccc(cc1)c2cccc(Cl)c2Cl 154 | "2,3,4'-PCB",-6.26,-5.686,Clc1ccc(cc1)c2cccc(Cl)c2Cl 155 | "2,3,4-Trichlorophenol",-2.67,-3.705,Oc1ccc(Cl)c(Cl)c1Cl 156 | "2,3,4-Trimethylpentane",-4.8,-3.276,CC(C)C(C)C(C)C 157 | "2,3,5,6-Tetrachlorophenol",-3.37,-4.203,Oc1c(Cl)c(Cl)cc(Cl)c1Cl 158 | "2,3',5-PCB",-6.01,-5.762,Clc1cccc(c1)c2cc(Cl)ccc2Cl 159 | "2,3,5-Trichlorophenol",-2.67,-3.78,Oc1cc(Cl)cc(Cl)c1Cl 160 | "2,3,6-Trichlorophenol",-2.64,-3.572,Oc1c(Cl)ccc(Cl)c1Cl 161 | "2,3-Dichloronitrobenzene",-3.48,-3.322,O=N(=O)c1c(Cl)c(Cl)ccc1 162 | "2,3-Dichlorophenol",-1.3,-3.144,Oc1cccc(Cl)c1Cl 163 | "2,3-Dimethyl-1,3-Butadiene",-2.4,-2.052,CC(=C)C(=C)C 164 | "2,3-Dimethylbutane",-3.65,-2.584,CC(C)C(C)C 165 | "2,3-Dimethylnaphthalene",-4.72,-4.116,Cc1cc2ccccc2cc1C 166 | "2,3-Dimethylpentane",-4.28,-2.938,CCC(C)C(C)C 167 | "2,3-Dimethylpyridine",0.38,-2.067,Cc1cccnc1C 168 | "2,4,5-PCB",-6.27,-5.762,Clc1ccc(cc1)c2cc(Cl)ccc2Cl 169 | "2,4',5-PCB",-6.25,-5.762,Clc1ccc(cc1)c2cc(Cl)ccc2Cl 170 | "2,4,5-Trichlorophenol ",-2.21,-3.78,Oc1cc(Cl)c(Cl)cc1Cl 171 | "2,4,6-PCB",-6.14,-5.604,Clc1ccc(cc1)c2c(Cl)cccc2Cl 172 | "2,4,6-Trichlorophenol",-2.34,-3.648,Oc1c(Cl)cc(Cl)cc1Cl 173 | "2,4,6-Trimethylphenol",-2.05,-2.941,Cc1cc(C)c(O)c(C)c1 174 | "2,4,6-Trinitrotoluene",-3.22,-2.606,Cc1c(cc(cc1N(=O)=O)N(=O)=O)N(=O)=O 175 | "2,4-Dichlorophenol ",-1.55,-3.22,Oc1ccc(Cl)cc1Cl 176 | "2,4-Dimethyl-2-pentanol ",-0.92,-1.647,CC(C)CC(C)(C)O 177 | "2,4-Dimethyl-3-pentanol",-1.22,-1.647,CC(C)C(O)C(C)C 178 | "2,4-Dimethyl-3-pentanone",-1.3,-1.752,CC(C)C(=O)C(C)C 179 | "2,4-Dimethylpentane",-4.26,-2.938,CC(C)CC(C)C 180 | "2,4-Dimethylphenol",-1.19,-2.621,Cc1ccc(O)c(C)c1 181 | "2,4-Dimethylpyridine",0.38,-2.098,Cc1ccnc(C)c1 182 | "2,4-Dinitrotoluene",-2.82,-2.604,Cc1ccc(cc1N(=O)=O)N(=O)=O 183 | "2,4'-PCB",-5.28,-5.142,Clc1ccc(cc1)c2ccccc2Cl 184 | "2,4-PCB",-5.25,-5.142,Clc1ccc(cc1)c2ccccc2Cl 185 | "2,6-Dichlorophenol",-1.79,-3.012,Oc1c(Cl)cccc1Cl 186 | "2,6-Dimethylnaphthalene ",-4.89,-4.147,Cc1ccc2cc(C)ccc2c1 187 | "2,6-Dimethylphenol",-1.29,-2.589,Cc1cccc(C)c1O 188 | "2,6-Dimethylpyridine",0.45,-2.098,Cc1cccc(C)n1 189 | "2,6-Dinitrotoluene",-3,-2.553,Cc1c(cccc1N(=O)=O)N(=O)=O 190 | "2,6-PCB",-5.21,-4.984,Clc1cccc(Cl)c1c2ccccc2 191 | "2,7-dimethylquinoline",-1.94,-3.342,c2c(C)cc1nc(C)ccc1c2 192 | 2-aminoanthracene,-5.17,-3.789,Nc3ccc2cc1ccccc1cc2c3 193 | 2-bromonaphthalene,-4.4,-4.434,c1c(Br)ccc2ccccc12 194 | 2-Bromonapthalene,-4.4,-4.434,Brc1ccc2ccccc2c1 195 | 2-Bromopropane,-1.59,-1.949,CC(C)Br 196 | 2-Bromotoluene,-2.23,-3.667,Cc1ccccc1Br 197 | 2-Butanone,0.52,-0.491,CCC(=O)C 198 | 2-butenal,0.32,-0.604,CC=CC=O 199 | 2-Butoxyethanol,-0.42,-0.775,CCCCOCCO 200 | 2-Chloro-2-methylbutane,-2.51,-2.278,CCC(C)(C)Cl 201 | 2-Chloroanisole,-2.46,-2.912,COc1ccccc1Cl 202 | 2-Chlorobiphenyl,-4.54,-4.528,Clc1ccccc1c2ccccc2 203 | 2-Chlorobutane,-1.96,-1.94,CCC(C)Cl 204 | 2-Chloronapthalene,-4.14,-4.063,Clc1ccc2ccccc2c1 205 | 2-Chlorophenol,-1.06,-2.553,Oc1ccccc1Cl 206 | 2-Chloropropane,-1.41,-1.585,CC(C)Cl 207 | 2-Chlorotoluene,-3.52,-3.297,Cc1ccccc1Cl 208 | 2-cyanoguanidine,-0.31,0.361,NC(N)=NC#N 209 | 2-Decanone,-3.3,-2.617,CCCCCCCCC(=O)C 210 | 2-Ethyl pyridine,0.51,-2.051,CCc1ccccn1 211 | 2-Ethyl-1-butanol,-1.17,-1.381,CCC(CC)CO 212 | 2-Ethyl-1-hexanol,-2.11,-2.089,CCCCC(CC)CO 213 | 2-Ethyl-2-hexanal,-2.46,-2.081,CCCC=C(CC)C=O 214 | 2-Ethylbutanal,-1.52,-1.523,CCC(CC)C=O 215 | 2-Ethylhexanal,-2.13,-2.232,CCCCC(CC)C=O 216 | 2-Ethylnaphthalene,-4.29,-4.1,CCc1ccc2ccccc2c1 217 | 2-Ethyltoluene,-3.21,-3.296,CCc1ccccc1C 218 | 2-Heptanol ,-1.55,-1.678,CCCCCC(C)O 219 | 2-Heptanone,-1.45,-1.554,CCCCCC(=O)C 220 | 2-Hexanol,-0.89,-1.324,CCCCC(C)O 221 | 2-Hexanone,-0.8,-1.2,CCCCC(=O)C 222 | 2-hydroxypteridine,-1.947,-1.404,Oc2ncc1nccnc1n2 223 | 2-Hydroxypyridine,1.02,-1.655,Oc1ccccn1 224 | 2-Iodopropane,-2.09,-2.486,CC(C)I 225 | 2-Isopropyltoluene,-3.76,-3.585,CC(C)c1ccccc1C 226 | 2-methoxypteridine,-1.11,-1.589,COc2ncc1nccnc1n2 227 | 2-Methy-2-Butene,-2.56,-1.994,CC=C(C)C 228 | "2-Methyl-1,3-Butadiene ",-2.03,-1.714,CC(=C)C=C 229 | 2-Methyl-1-Butene,-2.73,-1.994,CCC(=C)C 230 | 2-Methyl-1-Pentene,-3.03,-2.348,CCCC(=C)C 231 | 2-Methyl-2-heptanol,-1.72,-2.017,CCCCCC(C)(C)O 232 | 2-Methyl-2-hexanol,-1.08,-1.663,CCCCC(C)(C)O 233 | 2-Methyl-2-pentanol,-0.49,-1.308,CCCC(C)(C)O 234 | 2-Methyl-3-pentanol,-0.7,-1.308,CCC(O)C(C)C 235 | 2-Methylanthracene,-6.96,-4.87,Cc1ccc2cc3ccccc3cc2c1 236 | 2-Methylbutan-2-ol,0.15,-0.954,CCC(C)(C)O 237 | 2-Methylbutane,-3.18,-2.245,CCC(C)C 238 | 2-Methylbutanol,-0.47,-1.027,CCC(C)CO 239 | 2-Methylheptane,-5.08,-3.308,CCCCCC(C)C 240 | 2-Methylnapthalene,-3.77,-3.802,Cc1ccc2ccccc2c1 241 | 2-Methylpentane,-3.74,-2.6,CCCC(C)C 242 | 2-Methylpentanol,-1.11,-1.381,CCCC(C)CO 243 | 2-Methylphenanthrene,-5.84,-4.87,Cc1ccc2c(ccc3ccccc32)c1 244 | 2-Methylphenol,-0.62,-2.281,Cc1ccccc1O 245 | 2-Methylpropan-1-ol,0.1,-0.672,CC(C)CO 246 | 2-Methylpropane,-2.55,-1.891,CC(C)C 247 | 2-Methylpropene,-2.33,-1.573,CC(=C)C 248 | 2-methylpteridine,-0.12,-1.24,Cc2ncc1nccnc1n2 249 | 2-Methyltetrahydrofurane,0.11,-1.034,CC1CCCO1 250 | 2-Napthol,-2.28,-3.08,Oc1ccc2ccccc2c1 251 | 2-Nitropropane,-0.62,-0.743,CC(C)N(=O)=O 252 | 2-Nonanol,-2.74,-2.387,CCCCCCCC(C)O 253 | 2-Nonanone,-2.58,-2.263,CCCCCCCC(=O)C 254 | 2-Octanol,-2.09,-2.033,CCCCCCC(C)O 255 | 2-Octanone,-2.05,-1.909,CCCCCCC(=O)C 256 | 2-Pentanol,-0.29,-0.97,CCCC(C)O 257 | 2-Pentanone,-0.19,-0.846,CCCC(=O)C 258 | 2-Phenoxyethanol,-0.7,-1.761,OCCOc1ccccc1 259 | 2-Propanol,0.43,-0.261,CC(C)O 260 | 2-pyrrolidone,1.07,0.243,O=C1CCCN1 261 | 2-Undecanol,-2.94,-3.096,CCCCCCCCCC(C)O 262 | "3,3-Dimethyl-1-butanol",-0.5,-1.365,CC(C)(C)CCO 263 | "3,3-Dimethyl-2-butanol",-0.62,-1.292,CC(O)C(C)(C)C 264 | "3,3-Dimethyl-2-butanone",-0.72,-1.25,CC(=O)C(C)(C)C 265 | "3,3-Dimethylpentane",-4.23,-2.938,CCC(C)(C)CC 266 | "3,4-Dichloronitrobenzene",-3.2,-3.448,O=N(=O)c1cc(Cl)c(Cl)cc1 267 | "3,4-Dichlorophenol",-1.25,-3.352,Oc1ccc(Cl)c(Cl)c1 268 | "3,4-Dimethylphenol",-1.38,-2.621,Cc1ccc(O)cc1C 269 | "3,4-Dimethylpyridine",0.36,-2.067,Cc1ccncc1C 270 | "3,4-PCB",-6.39,-5.223,Clc1ccc(cc1Cl)c2ccccc2 271 | "3,5-Dichlorophenol",-1.34,-3.428,Oc1cc(Cl)cc(Cl)c1 272 | "3,5-Dimethylphenol",-1.4,-2.652,Cc1cc(C)cc(O)c1 273 | "3,5-Dimethylpyridine",0.38,-2.098,Cc1cncc(C)c1 274 | 3-Butanoyloxymethylphenytoin,-5.071,-3.469,O=C1N(COC(=O)CCC)C(=O)C(N1)(c2ccccc2)c3ccccc3 275 | 3-Chloroanisole,-2.78,-3.057,COc1cccc(Cl)c1 276 | 3-Chlorobiphenyl,-4.88,-4.685,c1c(Cl)cccc1c2ccccc2 277 | 3-Chlorophenol,-0.7,-2.761,Oc1cccc(Cl)c1 278 | 3-chloropropionitrile,-0.29,-0.522,ClCCC#N 279 | 3-Ethanoyloxymethylphenytoin,-4.47,-2.723,O=C1N(COC(=O)C)C(=O)C(N1)(c2ccccc2)c3ccccc3 280 | 3-Ethyl-3-pentanol,-0.85,-1.663,CCC(O)(CC)CC 281 | 3-Heptanol ,-1.47,-1.678,CCCCC(O)CC 282 | 3-Heptanoyloxymethylphenytoin,-6.301,-4.496,O=C1N(COC(=O)CCCCCC)C(=O)C(N1)(c2ccccc2)c3ccccc3 283 | 3-Hexanol,-0.8,-1.324,CCCC(O)CC 284 | 3-Hexanone,-0.83,-1.266,CCCC(=O)CC 285 | 3-Hexanoyloxymethylphenyltoin,-5.886,-4.153,O=C1N(COC(=O)CCCCC)C(=O)C(N1)(c2ccccc2)c3ccccc3 286 | 3-Hexyne,-1.99,-1.933,CCC#CCC 287 | 3-Methyl-1-Butene,-2.73,-1.994,CC(C)C=C 288 | 3-Methyl-2-butanol,-0.18,-0.954,CC(C)C(C)O 289 | 3-Methyl-2-butanone,-0.12,-0.912,CC(C)C(=O)C 290 | 3-Methyl-2-pentanol,-0.72,-1.381,CCC(C)CCO 291 | 3-Methyl-2-pentanol,-0.71,-1.308,CCC(C)CCO 292 | 3-Methyl-2-pentanone,-0.67,-1.266,CCC(C)C(=O)C 293 | 3-Methyl-3-heptanol,-1.6,-2.017,CCCCC(C)(O)CC 294 | 3-Methyl-3-hexanol,-0.98,-1.663,CCCC(C)(O)CC 295 | 3-Methyl-3-pentanol,-0.36,-1.308,CCC(C)(O)CC 296 | 3-Methylbutan-1-ol,-0.51,-1.027,CC(C)CCO 297 | 3-Methylcholanthrene,-7.92,-6.311,c1cc(C)cc2c1c3cc4cccc5CCc(c45)c3cc2 298 | 3-Methylheptane,-5.16,-3.308,CCCCC(C)CC 299 | 3-methylindole,-2.42,-2.981,Cc1c[nH]c2ccccc12 300 | 3-Methylpentane,-3.68,-2.6,CCC(C)CC 301 | 3-Methylphenol,-0.68,-2.313,Cc1cccc(O)c1 302 | 3-Octanol,-1.98,-2.033,CCCCCC(O)CC 303 | 3-Octanoyloxymethylphenytoin,-6.523,-4.84,O=C1N(COC(=O)CCCCCCC)C(=O)C(N1)(c2ccccc2)c3ccccc3 304 | 3-Pentanol,-0.24,-0.97,CCC(O)CC 305 | 3-Pentanone,-0.28,-0.912,CCC(=O)CC 306 | 3-Pentanoyloxymethylphenytoin,-4.678,-3.81,O=C1N(COC(=O)CCCC)C(=O)C(N1)(c2ccccc2)c3ccccc3 307 | 3-Propanoyloxymethylphenytoin,-4.907,-3.128,O=C1N(COC(=O)CC)C(=O)C(N1)(c2ccccc2)c3ccccc3 308 | "4,4'-PCB",-6.56,-5.299,Clc1ccc(cc1)c2ccc(Cl)cc2 309 | 4-Bromophenol,-1.09,-3.132,Oc1ccc(Br)cc1 310 | 4-Bromotoluene,-3.19,-3.667,Cc1ccc(Br)cc1 311 | 4-Chloroanisole,-2.78,-3.057,COc1ccc(Cl)cc1 312 | 4-Chlorophenol ,-0.7,-2.761,Oc1ccc(Cl)cc1 313 | 4-Chlorotoluene,-3.08,-3.297,Cc1ccc(Cl)cc1 314 | 4-Ethyltoluene,-3.11,-3.328,CCc1ccc(C)cc1 315 | 4-Heptanol,-1.4,-1.678,CCCC(O)CCC 316 | 4-Heptanone,-1.3,-1.62,CCCC(=O)CCC 317 | 4-hexylresorcinol,-2.59,-3.493,c1(O)cc(O)ccc1CCCCCC 318 | 4-hydroxypyridine,1.02,-1.655,Oc1ccncc1 319 | 4-Isopropyltoluene,-3.77,-3.617,CC(C)c1ccc(C)cc1 320 | 4-methoxypteridine,-1.11,-1.589,COc1ncnc2nccnc12 321 | 4-Methyl-2-pentanol,-0.8,-1.308,CC(C)CC(C)O 322 | 4-Methyl-2-pentanone,-0.74,-1.184,CC(C)CC(=O)C 323 | 4-Methylbiphenyl,-4.62,-4.424,Cc1ccc(cc1)c2ccccc2 324 | 4-Methylpentanol,-1.14,-1.381,CC(C)CCCO 325 | 4-methylpteridine,-0.466,-1.24,Cc1ncnc2nccnc12 326 | 4-Nitroacetanilide,-2.692,-2.219,CC(=O)Nc1ccc(cc1)N(=O)=O 327 | 4-Pentene-1-ol,-0.15,-0.791,OCCCC=C 328 | 5-(3-Methyl-2-butenyl)-5-ethylbarbital,-2.253,-2.126,O=C1NC(=O)NC(=O)C1(CC)CC=C(C)C 329 | 5-(3-Methyl-2-butenyl)-5-isoPrbarbital,-2.593,-2.465,O=C1NC(=O)NC(=O)C1(C(C)C)CC=C(C)C 330 | "5,5-Diallylbarbital",-2.077,-1.471,O=C1NC(=O)NC(=O)C1(CC=C)CC=C 331 | "5,5-Diisopropylbarbital",-2.766,-1.942,O=C1NC(=O)NC(=O)C1(C(C)C)C(C)C 332 | "5,5-Dimethylbarbituric acid",-1.742,-0.556,O=C1NC(=O)NC(=O)C1(C)C 333 | "5,6,7,8-tetrahydro-2-naphthol",-1.99,-3.086,Oc2ccc1CCCCc1c2 334 | "5,6-Dimethylchrysene",-7.01,-6.265,Cc1c(C)c2c3ccccc3ccc2c4ccccc14 335 | 5-Allyl-5-ethylbarbital,-1.614,-1.368,O=C1NC(=O)NC(=O)C1(CC)CC=C 336 | 5-Allyl-5-isopropylbarbital,-1.708,-1.706,O=C1NC(=O)NC(=O)C1(C(C)C)CC=C 337 | 5-Allyl-5-methylbarbital,-1.16,-1.013,O=C1NC(=O)NC(=O)C1(C)CC=C 338 | 5-Allyl-5-phenylbarbital,-2.369,-2.36,O=C1NC(=O)NC(=O)C1(CC=C)c1ccccc1 339 | 5-Ethyl-5-(3-methylbutyl)barbital,-2.658,-2.312,O=C1NC(=O)NC(=O)C1(CC)CCC(C)C 340 | 5-Ethyl-5-isopropylbarbituric acid,-2.148,-1.603,O=C1NC(=O)NC(=O)C1(CC)C(C)C 341 | 5-Ethyl-5-phenylbarbital,-2.322,-2.272,O=C1NC(=O)NC(=O)C1(CC)c1ccccc1 342 | 5-fluorouracil,-1.077,-0.792,Fc1c[nH]c(=O)[nH]c1=O 343 | 5-hydroxyquinoline,-2.54,-2.725,Oc1cccc2ncccc12 344 | 5-Methyl-5-ethylbarbituric acid,-1.228,-0.911,O=C1NC(=O)NC(=O)C1(C)CC 345 | 5-Methylchrysene,-6.59,-5.931,c1cccc2c3c(C)cc4ccccc4c3ccc12 346 | 5-methylcytosine,-1.458,-0.257,Nc1c(C)c[nH]c(=O)n1 347 | 5-Nonanone,-2.58,-2.329,CCCCC(=O)CCCC 348 | 6-aminochrysene,-6.2,-4.849,Nc3cc2c1ccccc1ccc2c4ccccc34 349 | 6-hydroxyquinoline,-2.16,-2.725,Oc2ccc1ncccc1c2 350 | 6-methoxypteridine,-1.139,-1.589,COc2cnc1ncncc1n2 351 | 6-Methylchrysene,-6.57,-5.931,Cc1cc2c3ccccc3ccc2c4ccccc14 352 | "7,12-Dimethylbenz(a)anthracene",-7.02,-6.297,Cc1c2ccccc2c(C)c3ccc4ccccc4c13 353 | 7-methoxypteridine,-0.91,-1.589,COc2cnc1cncnc1n2 354 | 7-methylpteridine,-0.854,-1.24,Cc2cnc1cncnc1n2 355 | 8-quinolinol,-2.42,-2.725,Oc1cccc2cccnc12 356 | "9,10-Dimethylanthracene",-6.57,-5.228,Cc1c2ccccc2c(C)c3ccccc13 357 | 9-anthrol,-4.73,-4.148,c3ccc2c(O)c1ccccc1cc2c3 358 | 9-Methylanthracene,-5.89,-4.87,Cc1c2ccccc2cc3ccccc13 359 | Abate,-6.237,-6.678,COP(=S)(OC)Oc1ccc(Sc2ccc(OP(=S)(OC)OC)cc2)cc1 360 | Acenapthene,-4.63,-3.792,C1Cc2cccc3cccc1c23 361 | Acenapthylene,-3.96,-3.682,C1=Cc2cccc3cccc1c23 362 | Acephate,0.54,-0.416,COP(=O)(NC(C)=O)SC 363 | Acetamide,1.58,0.494,CC(=O)N 364 | Acetanilide,-1.33,-1.857,CC(=O)Nc1ccccc1 365 | acetazolamide,-2.36,-0.793,CC(=O)Nc1nnc(s1)S(N)(=O)=O 366 | Acetonitrile,0.26,0.152,CC#N 367 | Acetophenone,-1.28,-2.078,CC(=O)c1ccccc1 368 | acetyl sulfisoxazole,-3.59,-2.024,CC(=O)N(S(=O)c1ccc(N)cc1)c2onc(C)c2C 369 | Acridine,-3.67,-3.846,c3ccc2nc1ccccc1cc2c3 370 | Acrolein,0.57,-0.184,C=CC=O 371 | Acrylonitrile,0.15,-0.354,C=CC#N 372 | adenine,-2.12,-1.255,Nc1ncnc2nc[nH]c12 373 | adrenosterone,-3.48,-2.99,CC34CC(=O)C1C(CCC2=CC(=O)CCC12C)C3CCC4(=O) 374 | alachlor,-3.26,-3.319,CCc1cccc(CC)c1N(COC)C(=O)CCl 375 | aldosterone,-3.85,-3.066,CC13CCC(=O)C=C1CCC4C2CCC(C(=O)CO)C2(CC(O)C34)C=O 376 | Aldrin,-6.307,-5.511,ClC1=C(Cl)C2(Cl)C3C4CC(C=C4)C3C1(Cl)C2(Cl)Cl 377 | allantoin,-1.6,0.652,NC(=O)NC1NC(=O)NC1=O 378 | allicin,-0.83,-2.045,C=CCS(=O)SCC=C 379 | allopurinol,-2.266,-0.84,O=c1[nH]cnc2[nH]ncc12 380 | alloxan,-1.25,0.436,O=C1NC(=O)C(=O)C(=O)N1 381 | alloxantin,-1.99,0.919,C1(=O)NC(=O)NC(=O)C1(O)C2(O)C(=O)NC(=O)NC2(=O) 382 | Altretamine,-3.364,-2.492,CN(C)c1nc(nc(n1)N(C)C)N(C)C 383 | Ametryn,-3.04,-3.43,CCNc1nc(NC(C)C)nc(SC)n1 384 | Amigdalin,-0.77,-0.974,OCC3OC(OCC2OC(OC(C#N)c1ccccc1)C(O)C(O)C2O)C(O)C(O)C3O 385 | Aminocarb,-2.36,-2.677,CNC(=O)Oc1ccc(N(C)C)c(C)c1 386 | aminopyrine,-0.364,-2.129,CN(C)c2c(C)n(C)n(c1ccccc1)c2=O 387 | aminothiazole,-0.36,-1.226,Nc1nccs1 388 | Amitraz,-5.47,-5.533,CN(C=Nc1ccc(C)cc1C)C=Nc2ccc(C)cc2C 389 | Amitrole,0.522,-0.674,Nc1nc[nH]n1 390 | Amobarbital,-2.468,-2.312,CCC1(CCC(C)C)C(=O)NC(=O)NC1=O 391 | ampyrone,-0.624,-1.192,Cc2c(N)c(=O)n(c1ccccc1)n2C 392 | Ancymidol,-2.596,-2.181,COc1ccc(cc1)C(O)(C2CC2)c3cncnc3 393 | Androstenedione,-3.69,-3.393,CC34CCC1C(CCC2=CC(=O)CCC12C)C3CCC4=O 394 | Androsterone,-4.402,-3.882,CC12CCC(O)CC1CCC3C2CCC4(C)C3CCC4=O 395 | Anethole,-3.13,-3.254,COc1ccc(C=CC)cc1 396 | Aniline ,-0.41,-1.632,Nc1ccccc1 397 | Anilofos,-4.432,-5.106,COP(=S)(OC)SCC(=O)N(C(C)C)c1ccc(Cl)cc1 398 | Anisole,-1.85,-2.368,COc1ccccc1 399 | Anthracene,-6.35,-4.518,c1ccc2cc3ccccc3cc2c1 400 | Anthraquinone,-5.19,-3.34,O=C1c2ccccc2C(=O)c3ccccc13 401 | Antipyrene,0.715,-1.733,Cc1cc(=O)n(c2ccccc2)n1C 402 | Apazone,-3.538,-2.9,CCCC1C(=O)N3N(C1=O)c2cc(C)ccc2N=C3N(C)C 403 | "Atovaquone(0,430mg/ml) - neutral",-5.931,-6.269,OC4=C(C1CCC(CC1)c2ccc(Cl)cc2)C(=O)c3ccccc3C4=O 404 | Atratone,-2.084,-3.185,CCNc1nc(NC(C)C)nc(OC)n1 405 | Atrazine,-3.85,-3.069,CCNc1nc(Cl)nc(NC(C)C)n1 406 | Azintamide,-1.716,-2.231,CCN(CC)C(=O)CSc1ccc(Cl)nn1 407 | Azobenzene,-4.45,-4.034,N(=Nc1ccccc1)c2ccccc2 408 | Azodrin,0.651,-0.949,CNC(=O)C=C(C)OP(=O)(OC)OC 409 | Barban,-4.37,-4.16,ClCC#CCOC(=O)Nc1cccc(Cl)c1 410 | Barbital,-2.4,-1.265,O=C1NC(=O)NC(=O)C1(CC)CC 411 | Bendroflumethiazide,-3.59,-3.741,NS(=O)(=O)c3cc2c(NC(Cc1ccccc1)NS2(=O)=O)cc3C(F)(F)F 412 | Benfluralin,-5.53,-5.205,CCCCN(CC)c1c(cc(cc1N(=O)=O)C(F)(F)F)N(=O)=O 413 | Benfuracarb,-4.71,-5.133,CCOC(=O)CCN(SN(C)C(=O)Oc1cccc2CC(C)(C)Oc21)C(C)C 414 | benodanil,-4.21,-4.245,c1c(NC(=O)c2ccccc2(I))cccc1 415 | Benomyl,-4.883,-2.902,CCCCNC(=O)n1c(NC(=O)OC)nc2ccccc12 416 | Bensulide,-4.2,-4.99,CC(C)OP(=S)(OC(C)C)SCCNS(=O)(=O)c1ccccc1 417 | Benzaldehyde,-1.19,-1.999,O=Cc1ccccc1 418 | Benzamide,-0.96,-1.501,NC(=O)c1ccccc1 419 | Benzene ,-1.64,-2.418,c1ccccc1 420 | benzhydrol,-2.55,-3.033,c1ccccc1C(O)c2ccccc2 421 | Benznidazole,-2.81,-2.321,O=C(Cn1ccnc1N(=O)=O)NCc2ccccc2 422 | Benzo(a)fluorene,-6.68,-5.189,C1c2ccccc2c3ccc4ccccc4c13 423 | Benzo(a)pyrene,-8.699,-6.007,c1ccc2c(c1)cc3ccc4cccc5ccc2c3c45 424 | Benzo(b)fluoranthene,-8.23,-6.007,c1ccc2c(c1)c3cccc4c3c2cc5ccccc54 425 | Benzo(b)fluorene,-8.04,-5.189,C1c2ccccc2c3cc4ccccc4cc13 426 | Benzo(e)pyrene,-7.8,-6.007,c1ccc2c(c1)c3cccc4ccc5cccc2c5c43 427 | Benzo(j)fluoranthene,-8,-6.007,c1ccc2c3c(ccc2c1)c4cccc5cccc3c45 428 | Benzo(k)fluoranthene,-8.49,-6.007,c1ccc2cc3c4cccc5cccc(c3cc2c1)c45 429 | Benzo[ghi]perylene,-9.018,-6.446,c1cc2ccc3ccc4ccc5cccc6c(c1)c2c3c4c56 430 | Benzocaine,-2.616,-2.383,CCOC(=O)c1ccc(N)cc1 431 | benzoin,-2.85,-3.148,OC(C(=O)c1ccccc1)c2ccccc2 432 | Benzonitrile,-1,-2.03,N#Cc1ccccc1 433 | Benzophenone,-3.12,-3.612,O=C(c1ccccc1)c2ccccc2 434 | benzothiazole,-1.5,-2.733,c2ccc1scnc1c2 435 | Benzotriazole,-0.78,-2.21,c2ccc1[nH]nnc1c2 436 | Benzoxazole,-1.16,-2.214,c2ccc1ocnc1c2 437 | Benzylchloride,-2.39,-2.887,ClCc1ccccc1 438 | Benzyltrifluoride,-2.51,-3.099,FC(F)(F)c1ccccc1 439 | benzylurea,-0.95,-1.509,NC(=O)NCc1ccccc1 440 | Betamethasone-17-valerate,-4.71,-5.062,CCCCC(=O)OC3(C(C)CC4C2CCC1=CC(=O)C=CC1(C)C2(F)C(O)CC34C)C(=O)CO 441 | Bibenzyl ,-4.62,-4.301,C(Cc1ccccc1)c2ccccc2 442 | Biphenyl,-4.345,-4.079,c1ccc(cc1)c2ccccc2 443 | biquinoline,-5.4,-4.903,c2ccc1nc(ccc1c2)c4ccc3ccccc3n4 444 | borneol,-2.32,-2.423,CC1(C)C2CCC1(C)C(O)C2 445 | Bromacil,-2.523,-3.419,CCC(C)n1c(=O)[nH]c(C)c(Br)c1=O 446 | bromadiolone,-4.445,-7.877,OC(CC(c1ccccc1)c3c(O)c2ccccc2oc3=O)c4ccc(cc4)c5ccc(Br)cc5 447 | Bromobenzene,-2.55,-3.345,Brc1ccccc1 448 | Bromochloromethane,-0.89,-1.519,ClCBr 449 | Bromodichloromethane,-1.54,-2.176,BrC(Cl)Cl 450 | Bromoethane,-1.09,-1.529,CCBr 451 | Bromomethane,-0.79,-1.109,CBr 452 | Bromophos,-6.09,-5.604,COP(=S)(OC)Oc1cc(Cl)c(Br)cc1Cl 453 | bromopropylate,-4.93,-5.833,CC(C)OC(=O)C(O)(c1ccc(Br)cc1)c2ccc(Br)cc2 454 | bromoxynil,-3.33,-3.793,Oc1c(Br)cc(C#N)cc1Br 455 | brompyrazone,-3.127,-3.005,c1ccccc1n2ncc(N)c(Br)c2(=O) 456 | bupirimate,-4.16,-3.493,CCCCc1c(C)nc(NCC)nc1OS(=O)(=O)N(C)C 457 | Butabarbital,-2.39,-1.958,O=C1NC(=O)NC(=O)C1(CC)C(C)CC 458 | butacarb,-4.24,-4.642,c1(C(C)(C)C)cc(C(C)(C)C)cc(OC(=O)NC)c1 459 | butachlor,-4.19,-4.347,CCCCOCN(C(=O)CCl)c1c(CC)cccc1CC 460 | butallylonal,-2.647,-2.766,CCC(C)C1(CC(Br)=C)C(=O)NC(=O)NC1=O 461 | Butamben,-3.082,-3.039,CCCCOC(=O)c1ccc(N)cc1 462 | Butan-2-ol,0.47,-0.616,CCC(C)O 463 | Butane,-2.57,-1.907,CCCC 464 | Butanethiol ,-2.18,-1.676,CCCCS 465 | Butethal,-1.661,-1.974,CCCCC1(CC)C(=O)NC(=O)NC1=O 466 | Buthidazole,-1.877,-2.398,CN1CC(O)N(C1=O)c2nnc(s2)C(C)(C)C 467 | Buturon,-3.9,-3.199,CC(C#C)N(C)C(=O)Nc1ccc(Cl)cc1 468 | Butyl acetate,-1.37,-1.111,CCCCOC=O 469 | Butylate,-3.68,-3.453,CCSC(=O)N(CC(C)C)CC(C)C 470 | Butylbenzene,-4.06,-3.585,CCCCc1ccccc1 471 | Butyraldehyde,-0.01,-0.749,CCCC=O 472 | Caffeine,-0.876,-1.498,Cn1cnc2n(C)c(=O)n(C)c(=O)c12 473 | Camphor,-1.96,-2.158,CC1(C)C2CCC1(C)C(=O)C2 474 | Caproaldehyde,-1.3,-1.457,CCCCCC=O 475 | captafol,-5.4,-4.365,ClC(Cl)C(Cl)(Cl)SN2C(=O)C1CC=CCC1C2=O 476 | Carbanilide,-3.15,-3.611,O=C(Nc1ccccc1)Nc2ccccc2 477 | Carbaryl,-3.224,-3.087,CNC(=O)Oc1cccc2ccccc12 478 | Carbazole,-5.27,-3.836,c1ccc2c(c1)[nH]c3ccccc32 479 | Carbetamide,-1.83,-2.29,c1c(NC(=O)OC(C)C(=O)NCC)cccc1 480 | Carbofuran,-2.8,-3.05,CNC(=O)Oc1cccc2CC(C)(C)Oc12 481 | Carbophenthion,-5.736,-5.828,CCOP(=S)(OCC)SCSc1ccc(Cl)cc1 482 | Carboxin,-3.14,-2.927,CC1=C(SCCO1)C(=O)Nc2ccccc2 483 | Carbromal,-2.68,-2.198,CCC(Br)(CC)C(=O)NC(N)=O 484 | Carvacrol,-2.08,-3.224,c1(O)c(C)ccc(C(C)C)c1 485 | Carvone,-2.06,-2.042,CC(=C)C1CC=C(C)C(=O)C1 486 | chloralose,-1.84,-1.887,OCC(O)C2OC1OC(OC1C2O)C(Cl)(Cl)Cl 487 | Chloramphenicol,-2.111,-2.613,OCC(NC(=O)C(Cl)Cl)C(O)c1ccc(cc1)N(=O)=O 488 | Chlorazine,-4.411,-3.663,CCN(CC)c1nc(Cl)nc(n1)N(CC)CC 489 | Chlorbromuron,-3.924,-3.938,CON(C)C(=O)Nc1ccc(Br)c(Cl)c1 490 | Chlorbufam,-2.617,-3.629,CC(OC(=O)Nc1cccc(Cl)c1)C#C 491 | Chlordane,-6.86,-6.039,ClC1CC2C(C1Cl)C3(Cl)C(=C(Cl)C2(Cl)C3(Cl)Cl)Cl 492 | Chlordene,-5.64,-5.152,ClC2=C(Cl)C3(Cl)C1C=CCC1C2(Cl)C3(Cl)Cl 493 | chlordimeform,-2.86,-3.164,CN(C)C=Nc1ccc(Cl)cc1C 494 | Chlorimuron-ethyl (ph 7),-4.576,-3.719,CCOC(=O)c1ccccc1S(=O)(=O)NN(C=O)c2nc(Cl)cc(OC)n2 495 | chloroacetamide,-0.02,-0.106,NC(=O)CCl 496 | Chloroacetonitrile,-0.092,-0.448,ClCC#N 497 | Chlorobenzene,-2.38,-2.975,Clc1ccccc1 498 | Chlorodibromethane,-1.9,-2.54,ClC(Br)Br 499 | Chloroethane,-1.06,-1.165,ClCC 500 | Chloroethylene,-1.75,-1.188,ClC=C 501 | Chloropham,-3.38,-3.544,CC(C)OC(=O)Nc1cccc(Cl)c1 502 | Chloropicrin,-2,-1.866,ClC(Cl)(Cl)N(=O)=O 503 | chloropropylate,-4.53,-5.093,c1ccc(Cl)cc1C(c2ccc(Cl)cc2)(O)C(=O)OC(C)C 504 | Chlorothalonil,-5.64,-3.995,c1(C#N)c(Cl)c(C#N)c(Cl)c(Cl)c(Cl)1 505 | chlorothiazide,-3.05,-1.752,NS(=O)(=O)c2cc1c(N=CNS1(=O)=O)cc2Cl 506 | Chlorotoluron,-3.46,-3.048,CN(C)C(=O)Nc1ccc(C)c(Cl)c1 507 | Chloroxuron,-4.89,-4.477,CN(C)C(=O)Nc2ccc(Oc1ccc(Cl)cc1)cc2 508 | chlorpyrifos,-5.67,-4.972,CCOP(=S)(OCC)Oc1nc(Cl)c(Cl)cc1Cl 509 | chlorquinox,-5.43,-4.438,c2(Cl)c(Cl)c(Cl)c1nccnc1c2(Cl) 510 | Chlorthalidone,-3.451,-2.564,NS(=O)(=O)c1cc(ccc1Cl)C2(O)NC(=O)c3ccccc23 511 | Chlortoluron,-3.483,-3.048,CN(C)C(=O)Nc1ccc(C)c(Cl)c1 512 | Chlorzoxazone,-2.831,-2.679,Clc2ccc1oc(=O)[nH]c1c2 513 | Cholanthrene,-7.85,-5.942,C1Cc2c3c1cccc3cc4c2ccc5ccccc54 514 | Chrysene,-8.057,-5.568,c1ccc2c(c1)ccc3c4ccccc4ccc23 515 | "cis 1,2-Dichloroethylene",-1.3,-1.561,Cl\C=C/Cl 516 | "cis-1,2-Dimethylcyclohexane",-4.3,-3.305,C/C1CCCCC1\C 517 | cis-2-Pentene,-2.54,-2.076,CC/C=C\C 518 | citral,-2.06,-2.579,CC(C)=CCCC(C)=CC(=O) 519 | Clomazone,-2.338,-3.077,CC1(C)CON(Cc2ccccc2Cl)C1=O 520 | Clonazepam,-3.499,-3.707,Clc1ccccc1C2=NCC(=O)Nc3ccc(cc23)N(=O)=O 521 | Coronene,-9.332,-6.885,c1cc2ccc3ccc4ccc5ccc6ccc1c7c2c3c4c5c67 522 | Corticosterone,-3.24,-3.454,CC12CC(O)C3C(CCC4=CC(=O)CCC34C)C2CCC1C(=O)CO 523 | Cortisone,-3.11,-2.893,CC12CC(=O)C3C(CCC4=CC(=O)CCC34C)C2CCC1(O)C(=O)CO 524 | cortisone acetate,-4.21,-3.426,CC(=O)OCC(=O)C3(O)CCC4C2CCC1=CC(=O)CCC1(C)C2C(=O)CC34C 525 | Coumachlor,-5.839,-4.554,CC(=O)CC(c1ccc(Cl)cc1)c2c(O)c3ccccc3oc2=O 526 | Coumaphos,-5.382,-5.04,CCOP(=S)(OCC)Oc2ccc1oc(=O)c(Cl)c(C)c1c2 527 | Coumatetralyl,-2.84,-5.194,O=c2c(C3CCCc4ccccc43)c(O)c1ccccc1o2 528 | Cyanazine,-3.15,-2.49,CCNc1nc(Cl)nc(NC(C)(C)C#N)n1 529 | cycloate,-3.4,-3.35,CCSC(=O)N(CC)C1CCCCC1 530 | cyclobarbital,-2.17,-2.421,CCC1(C(=O)NC(=O)NC1=O)C2=CCCCC2 531 | Cyclobutyl-5-spirobarbituric acid,-1.655,-0.527,O=C2NC(=O)C1(CCC1)C(=O)N2 532 | Cycloheptane,-3.51,-2.916,C1CCCCCC1 533 | Cycloheptanol,-0.88,-1.7,OC1CCCCCC1 534 | Cycloheptene,-3.18,-2.599,C1CCC=CCC1 535 | Cycloheptyl-5-spirobarbituric acid,-3.168,-1.844,O=C2NC(=O)C1(CCCCCC1)C(=O)N2 536 | Cyclohexane,-3.1,-2.477,C1CCCCC1 537 | Cyclohexanol ,-0.44,-1.261,OC1CCCCC1 538 | Cyclohexanone,-0.6,-0.996,O=C1CCCCC1 539 | Cyclohexene,-2.59,-2.16,C1CCC=CC1 540 | cycloheximide,-1.13,-1.532,CC1CC(C)C(=O)C(C1)C(O)CC2CC(=O)NC(=O)C2 541 | Cyclohexyl-5-spirobarbituric acid,-3.06,-1.405,O=C2NC(=O)C1(CCCCC1)C(=O)N2 542 | Cyclooctane,-4.15,-3.355,C1CCCCCCC1 543 | Cyclooctanol,-1.29,-2.14,OC1CCCCCCC1 544 | Cyclooctyl-5-spirobarbituric acid,-2.982,-2.284,O=C2NC(=O)C1(CCCCCCC1)C(=O)N2 545 | Cyclopentane ,-2.64,-2.038,C1CCCC1 546 | Cyclopentene ,-2.1,-1.72,C1CC=CC1 547 | Cyclopentyl-5-spirobarbituric acid,-2.349,-0.966,O=C2NC(=O)C1(CCCC1)C(=O)N2 548 | Cyclopropyl-5-spirobarbituric acid,-1.886,-0.088,O=C2NC(=O)C1(CC1)C(=O)N2 549 | Cycluron,-2.218,-2.629,CN(C)C(=O)NC1CCCCCCC1 550 | Cyfluthrin,-7.337,-6.84,CC1(C)C(C=C(Cl)Cl)C1C(=O)OC(C#N)c2ccc(F)c(Oc3ccccc3)c2 551 | Cyhalothrin,-8.176,-6.905,CC1(C)C(C=C(Cl)C(F)(F)F)C1C(=O)OC(C#N)c2cccc(Oc3ccccc3)c2 552 | Cypermethrin,-8.017,-6.775,CC1(C)C(C=C(Cl)Cl)C1C(=O)OC(C#N)c2cccc(Oc3ccccc3)c2 553 | cytosine,-1.155,0.051,Nc1cc[nH]c(=O)n1 554 | Danazol,-5.507,-4.557,CC23Cc1cnoc1C=C2CCC4C3CCC5(C)C4CCC5(O)C#C 555 | Dapsone,-3.094,-2.464,Nc1ccc(cc1)S(=O)(=O)c2ccc(N)cc2 556 | DDD,-7.2,-6.008,ClC(Cl)C(c1ccc(Cl)cc1)c2ccc(Cl)cc2 557 | DDE,-6.9,-6.553,ClC(Cl)=C(c1ccc(Cl)cc1)c2ccc(Cl)cc2 558 | DDT,-7.15,-6.638,Clc1ccc(cc1)C(c2ccc(Cl)cc2)C(Cl)(Cl)Cl 559 | Decalin,-5.19,-3.715,C1CCC2CCCCC2C1 560 | DEF,-5.14,-4.074,CCCCSP(=O)(SCCCC)SCCCC 561 | Deltamethrin,-8.402,-7.44,CC1(C)C(C=C(Br)Br)C1C(=O)OC(C#N)c2cccc(Oc3ccccc3)c2 562 | Deoxycorticosterone,-3.45,-3.939,CC12CCC3C(CCC4=CC(=O)CCC34C)C2CCC1C(=O)CO 563 | deoxycorticosterone acetate,-4.63,-4.472,CC(=O)OCC(=O)C3CCC4C2CCC1=CC(=O)CCC1(C)C2CCC34C 564 | Desmedipham,-4.632,-4.182,CCOC(=O)Nc2cccc(OC(=O)Nc1ccccc1)c2 565 | Dexamethasone,-3.59,-3.4,CC1CC2C3CCC4=CC(=O)C=CC4(C)C3(F)C(O)CC2(C)C1(O)C(=O)CO 566 | dexamethasone acetate,-4.9,-3.933,CC4CC3C2CCC1=CC(=O)C=CC1(C)C2(F)C(O)CC3(C)C4(O)C(=O)COC(C)=O 567 | D-fenchone,-1.85,-2.158,CC2(C)C1CCC(C)(C1)C2=O 568 | Di(2-ethylhexyl)-phthalate,-6.96,-7.117,CCCCC(CC)COC(=O)c1ccccc1C(=O)OCC(CC)CCCC 569 | Dialifor,-6.34,-5.026,CCOP(=S)(OCC)SC(CCl)N1C(=O)c2ccccc2C1=O 570 | Dialifos,-6.34,-5.026,CCOP(=S)(OCC)SC(CCl)N2C(=O)c1ccccc1C2=O 571 | Diallate,-4.286,-3.827,CC(C)N(C(C)C)C(=O)SCC(=CCl)Cl 572 | Diazepam,-3.754,-4.05,CN2C(=O)CN=C(c1ccccc1)c3cc(Cl)ccc23 573 | Diazinon,-3.64,-3.989,CCOP(=S)(OCC)Oc1cc(C)nc(n1)C(C)C 574 | Dibenzofurane,-4.6,-4.201,o1c2ccccc2c3ccccc13 575 | Dibenzothiophene,-4.38,-4.597,c1ccc2c(c1)sc3ccccc23 576 | Dibromomethane,-1.17,-1.883,BrCBr 577 | Dibutyl ether ,-1.85,-2.135,CCCCOCCCC 578 | dibutyl sebacate,-3.896,-4.726,CCCCOC(=O)CCCCCCCCC(=O)OCCCC 579 | dibutylphthalate,-4.4,-4.378,CCCCOC(=O)c1ccccc1C(=O)OCCCC 580 | Dicapthon,-4.31,-4.188,COP(=S)(OC)Oc1ccc(cc1Cl)N(=O)=O 581 | Dichloromethane,-0.63,-1.156,ClCCl 582 | Dichlorophen,-3.953,-4.924,Oc1ccc(Cl)cc1Cc2cc(Cl)ccc2O 583 | Dicofol,-5.666,-6.268,OC(c1ccc(Cl)cc1)(c2ccc(Cl)cc2)C(Cl)(Cl)Cl 584 | Dieldrin,-6.29,-4.533,ClC4=C(Cl)C5(Cl)C3C1CC(C2OC12)C3C4(Cl)C5(Cl)Cl 585 | Dienestrol,-4.95,-4.775,CC=C(C(=CC)c1ccc(O)cc1)c2ccc(O)cc2 586 | Dienochlor,-7.278,-7.848,ClC1=C(Cl)C(Cl)(C(=C1Cl)Cl)C2(Cl)C(=C(Cl)C(=C2Cl)Cl)Cl 587 | Diethyl ether ,-0.09,-0.718,CCOCC 588 | Diethyl phthalate ,-2.35,-3.016,CCOC(=O)c1ccccc1C(=O)OCC 589 | Diethyl sulfide,-1.34,-1.598,CCSCC 590 | Diethyldisulfide,-2.42,-2.364,CCSSCC 591 | diethylstilbestrol,-4.07,-5.074,CCC(=C(CC)c1ccc(O)cc1)c2ccc(O)cc2 592 | Difenoxuron,-4.16,-3.928,COc2ccc(Oc1ccc(NC(=O)N(C)C)cc1)cc2 593 | difluron,-6.02,-4.692,Fc1cccc(F)c1C(=O)NC(=O)Nc2ccc(Cl)cc2 594 | Digitoxin,-5.293,-6.114,CC1OC(CC(O)C1O)OC2C(O)CC(OC2C)OC8C(O)CC(OC7CCC3(C)C(CCC4C3CCC5(C)C(CCC45O)C6=CC(=O)OC6)C7)OC8C 595 | "Digoxin (L1=41,8mg/mL, L2=68,2mg/mL, Z=40,1mg/mL)",-4.081,-5.312,CC1OC(CC(O)C1O)OC2C(O)CC(OC2C)OC8C(O)CC(OC7CCC3(C)C(CCC4C3CC(O)C5(C)C(CCC45O)C6=CC(=O)OC6)C7)OC8C 596 | Dihexyl phthalate,-6.144,-5.758,CCCCCCOC(=O)c1ccccc1C(=O)OCCCCCC 597 | Diiodomethane,-2.34,-2.958,ICI 598 | diisooctyl phthalate,-6.637,-7.117,c1(C(=O)OCCCCCC(C)(C))c(C(=O)OCCCCCC(C)(C))cccc1 599 | Diisopropyl ether ,-1.1,-1.281,CC(C)OC(C)C 600 | Diisopropylsulfide,-2.24,-2.162,CC(C)SC(C)C 601 | Dimecron,0.523,-2.426,CCN(CC)C(=O)C(=CCOP(=O)(OC)OC)Cl 602 | Dimefuron,-4.328,-3.831,CN(C)C(=O)Nc1ccc(c(Cl)c1)n2nc(oc2=O)C(C)(C)C 603 | dimetan,-0.85,-2.304,CN(C)C(=O)OC1=CC(=O)CC(C)(C)C1 604 | dimethirimol,-2.24,-3.57,CCCCc1c(C)nc(nc1O)N(C)C 605 | Dimethoxymethane,0.48,0.092,COCOC 606 | Dimethyl phthalate,-1.66,-2.347,COC(=O)c1ccccc1C(=O)OC 607 | Dimethyl sulfide,-0.45,-0.758,CSC 608 | Dimethyldisulfide,-1.44,-1.524,CSSC 609 | Dinitramine,-5.47,-4.479,CCN(CC)c1c(cc(c(N)c1N(=O)=O)C(F)(F)F)N(=O)=O 610 | Dinoseb,-3.38,-3.715,CCC(C)c1cc(cc(N(=O)=O)c1O)N(=O)=O 611 | d-inositol,0.35,-0.887,OC1C(O)C(O)C(O)C(O)C1O 612 | Di-n-propylsulfide,-2.58,-2.307,CCCSCCC 613 | dioctyl phthalate,-5.115,-7.148,CCCCCCCCOC(=O)c1ccccc1C(=O)OCCCCCCCC 614 | Diosgenin,-7.32,-5.681,C1C(O)CCC2(C)CC3CCC4(C)C5(C)CC6OCC(C)CC6OC5CC4C3C=C21 615 | Dioxacarb,-1.57,-1.614,CNC(=O)Oc1ccccc1C2OCCO2 616 | diphenamid,-2.98,-3.147,CN(C)C(=O)C(c1ccccc1)c2ccccc2 617 | Diphenyl ether ,-3.96,-4.254,O(c1ccccc1)c2ccccc2 618 | Diphenylamine,-3.504,-3.857,N(c1ccccc1)c2ccccc2 619 | Diphenylmethane,-4.08,-4.09,C(c1ccccc1)c2ccccc2 620 | Dipropyl ether,-1.62,-1.426,CCCOCCC 621 | Disulfiram,-4.86,-3.862,CCN(CC)C(=S)SSC(=S)N(CC)CC 622 | Disulfoton,-4.23,-3.975,CCOP(=S)(OCC)SCCSCC 623 | Ditalimfos,-3.35,-3.992,CCOP(=S)(OCC)N2C(=O)c1ccccc1C2=O 624 | Diuron,-3.8,-3.301,CN(C)C(=O)Nc1ccc(Cl)c(Cl)c1 625 | d-Limonene,-4.26,-3.429,CC1=CCC(CC1)C(C)=C 626 | DNOC,-1.456,-2.818,Cc1cc(cc(N(=O)=O)c1O)N(=O)=O 627 | Dulcin,-2.17,-2.167,CCOc1ccc(NC(N)=O)cc1 628 | Dyphylline,-0.17,-0.847,Cn2c(=O)n(C)c1ncn(CC(O)CO)c1c2=O 629 | Eicosane,-8.172,-7.576,CCCCCCCCCCCCCCCCCCCC 630 | Endrin,-6.18,-4.533,ClC4=C(Cl)C5(Cl)C3C1CC(C2OC12)C3C4(Cl)C5(Cl)Cl 631 | Epiandrosterone,-4.16,-3.882,CC34CCC1C(CCC2CC(O)CCC12C)C3CCC4=O 632 | Epitostanol,-5.41,-4.545,CC45CCC2C(CCC3CC1SC1CC23C)C4CCC5O 633 | Equilenin,-5.24,-3.927,CC34CCc1c(ccc2cc(O)ccc12)C3CCC4=O 634 | Equilin,-5.282,-3.555,CC34CCC1C(=CCc2cc(O)ccc12)C3CCC4=O 635 | Eriodictyol,-3.62,-3.152,Oc2cc(O)c1C(=O)CC(Oc1c2)c3ccc(O)c(O)c3 636 | Erythritol,0.7,0.675,OCC(O)C(O)CO 637 | Estradiol,-5.03,-4.138,CC12CCC3C(CCc4cc(O)ccc34)C2CCC1O 638 | Estragole,-2.92,-3.074,c1(OC)ccc(CC=C)cc1 639 | estriol,-4.955,-3.858,CC34CCC1C(CCc2cc(O)ccc12)C3CC(O)C4O 640 | Estrone,-3.955,-3.872,CC12CCC3C(CCc4cc(O)ccc34)C2CCC1=O 641 | Ethalfluralin,-6.124,-5.063,CCN(CC(C)=C)c1c(cc(cc1N(=O)=O)C(F)(F)F)N(=O)=O 642 | Ethane,-1.36,-1.132,CC 643 | Ethanethiol,-0.6,-0.968,CCS 644 | Ethanol,1.1,0.02,CCO 645 | Ethinyl estradiol,-4.3,-4.317,CC34CCC1C(CCc2cc(O)ccc12)C3CCC4(O)C#C 646 | ethiofencarb,-2.09,-2.855,CCSCc1ccccc1OC(=O)NC 647 | Ethion,-5.54,-5.471,CCOP(=S)(OCC)SCSP(=S)(OCC)OCC 648 | Ethirimol,-3.028,-2.732,CCCCc1c(C)nc(NCC)[nH]c1=O 649 | Ethisterone,-5.66,-3.858,CC12CCC(=O)C=C1CCC3C2CCC4(C)C3CCC4(O)C#C 650 | Ethofumesate,-3.42,-3.184,CCOC2Oc1ccc(OS(C)(=O)=O)cc1C2(C)C 651 | ethofumesate,-3.42,-3.184,CCOC2Oc1ccc(OS(C)(=O)=O)cc1C2(C)C 652 | Ethoxyzolamide,-3.81,-3.085,CCOc2ccc1nc(sc1c2)S(N)(=O)=O 653 | Ethyl acetate,-0.04,-0.77,CCOC(=O)C 654 | Ethyl benzoate ,-2.32,-2.775,CCOC(=O)c1ccccc1 655 | Ethyl butyrate,-1.28,-2.254,CCCCCOC(=O)CC 656 | ethyl cinnamate,-3,-3.098,CCOC(=O)C=Cc1ccccc1 657 | Ethyl decanoate,-4.1,-3.671,CCCCCCCCCC(=O)OCC 658 | Ethyl formate,0.15,-0.402,CCOC=O 659 | Ethyl heptanoate,-2.74,-2.608,CCCCCCC(=O)OCC 660 | Ethyl hexanoate,-2.35,-2.254,CCCCCC(=O)OCC 661 | Ethyl nonanoate,-3.8,-3.316,CCCCCCCCC(=O)OCC 662 | Ethyl octanoate,-3.39,-2.962,CCCCCCCC(=O)OCC 663 | Ethyl pentanoate,-1.75,-1.899,CCCOC(=O)CCC 664 | Ethyl propionate,-0.66,-1.191,CCOC(=O)CC 665 | Ethyl propyl ether,-0.66,-1.072,CCCOCC 666 | Ethyl vinyl ether,-0.85,-0.857,CCOC=C 667 | Ethylbenzene,-2.77,-2.988,CCc1ccccc1 668 | Ethylcyclohexane,-4.25,-3.245,CCC1CCCCC1 669 | Ethylene,-0.4,-0.815,C=C 670 | Ethyl-p-aminobenzoate,-2.1,-2.383,CCOC(=O)c1ccc(N)cc1 671 | Ethyl-p-hydroxybenzoate ,-2.35,-2.761,CCOC(=O)c1ccc(O)cc1 672 | Ethyne,0.29,-0.252,C#C 673 | Etofenprox,-8.6,-6.896,CCOc1ccc(cc1)C(C)(C)COCc3cccc(Oc2ccccc2)c3 674 | Etomidate,-4.735,-3.359,CCOC(=O)c1cncn1C(C)c2ccccc2 675 | "Etoposide (148-167,25mg/ml)",-3.571,-3.292,COc1cc(cc(OC)c1O)C6C2C(COC2=O)C(OC4OC3COC(C)OC3C(O)C4O)c7cc5OCOc5cc67 676 | eucalyptol,-1.64,-2.579,CC12CCC(CC1)C(C)(C)O2 677 | Eugenol,-1.56,-2.675,COc1cc(CC=C)ccc1O 678 | Fenarimol,-4.38,-4.108,OC(c1ccc(Cl)cc1)(c2cncnc2)c3ccccc3Cl 679 | Fenfuram,-3.3,-2.885,Cc1occc1C(=O)Nc2ccccc2 680 | Fenitrothion,-4.04,-3.845,COP(=S)(OC)Oc1ccc(N(=O)=O)c(C)c1 681 | Fenothiocarb,-3.927,-3.297,CN(C)C(=O)SCCCCOc1ccccc1 682 | Fenoxycarb,-4.7,-4.662,CCOC(=O)NCCOc2ccc(Oc1ccccc1)cc2 683 | Fenpropathrin,-6.025,-6.15,CC1(C)C(C(=O)OC(C#N)c2cccc(Oc3ccccc3)c2)C1(C)C 684 | fensulfothion,-2.3,-3.283,CCOP(=S)(OCC)Oc1ccc(cc1)S(C)=O 685 | Fenthion,-4.57,-4.265,COP(=S)(OC)Oc1ccc(SC)c(C)c1 686 | Fenuron,-1.6,-1.847,CN(C)C(=O)Nc1ccccc1 687 | fluconazole,-1.8,-2.418,OC(Cn1cncn1)(Cn2cncn2)c3ccc(F)cc3F 688 | Flucythrinate,-6.876,-6.878,CC(C)C(C(=O)OC(C#N)c1cccc(Oc2ccccc2)c1)c3ccc(OC(F)F)cc3 689 | Flucytosine,-0.972,-0.132,Nc1nc(=O)[nH]cc1F 690 | Fludrocortisone,-3.43,-3.172,CC34CC(O)C1(F)C(CCC2=CC(=O)CCC12C)C3CCC4(O)C(=O)CO 691 | Flumethasone,-5.613,-3.539,CC1CC2C3CC(F)C4=CC(=O)C=CC4(C)C3(F)C(O)CC2(C)C1(O)C(=O)CO 692 | Flumetralin,-6.78,-6.584,CCN(Cc1c(F)cccc1Cl)c2c(cc(cc2N(=O)=O)C(F)(F)F)N(=O)=O 693 | Fluometuron,-3.43,-3.065,CN(C)C(=O)Nc1cccc(c1)C(F)(F)F 694 | Fluoranthene,-6,-4.957,c1ccc2c(c1)c3cccc4cccc2c34 695 | Fluorene ,-5,-4.125,C1c2ccccc2c3ccccc13 696 | Fluorobenzene,-1.8,-2.514,Fc1ccccc1 697 | Fluoromethalone,-4.099,-3.507,CC1CC2C3CCC(O)(C(=O)C)C3(C)CC(O)C2(F)C4(C)C=CC(=O)C=C14 698 | Fluorometuron,-3.32,-3.065,CN(C)C(=O)Nc1cccc(c1)C(F)(F)F 699 | Fluridone,-4.445,-4.249,Cn2cc(c1ccccc1)c(=O)c(c2)c3cccc(c3)C(F)(F)F 700 | Flurochloridone,-4.047,-4.749,FC(F)(F)c1cccc(c1)N2CC(CCl)C(Cl)C2=O 701 | Flutriafol,-3.37,-3.569,OC(Cn1cncn1)(c2ccc(F)cc2)c3ccccc3F 702 | Fluvalinate,-8.003,-8.057,CC(C)C(Nc1ccc(cc1Cl)C(F)(F)F)C(=O)OC(C#N)c2cccc(Oc3ccccc3)c2 703 | Formetanate,-2.34,-1.846,CNC(=O)Oc1cccc(N=CN(C)C)c1 704 | Formothion,-1.995,-2.087,COP(=S)(OC)SCC(=O)N(C)C=O 705 | Fructose,0.64,0.471,OCC1OC(O)(CO)C(O)C1O 706 | Furane,-0.82,-1.837,c1ccoc1 707 | Furfural,-0.1,-1.391,O=Cc1ccco1 708 | gentisin,-2.943,-1.292,c1c(O)C2C(=O)C3cc(O)ccC3OC2cc1(OC) 709 | Glafenine,-4.571,-5.052,OCC(O)COC(=O)c1ccccc1Nc2ccnc3cc(Cl)ccc23 710 | glucose,0.74,0.501,OCC1OC(O)C(O)C(O)C1O 711 | Glutethimide,-2.337,-2.591,CCC1(CCC(=O)NC1=O)c2ccccc2 712 | Glycerol,1.12,0.688,OCC(O)CO 713 | Glyceryl triacetate,-0.6,-1.285,CC(=O)OCC(COC(=O)C)OC(=O)C 714 | Griseofulvin,-3.246,-3.328,COC1=CC(=O)CC(C)C13Oc2c(Cl)c(OC)cc(OC)c2C3=O 715 | Guaiacol,-1.96,-1.941,COc1ccccc1O 716 | guanine,-3.583,-0.67,Nc2nc1[nH]cnc1c(=O)[nH]2 717 | halothane,-1.71,-2.608,FC(F)(F)C(Cl)Br 718 | hematein,-2.7,-1.795,c1cc(O)c(O)c2OCC3(O)CC4=CC(=O)C(O)=CC4=C3c21 719 | Heptachlor,-6.317,-5.26,ClC1C=CC2C1C3(Cl)C(=C(Cl)C2(Cl)C3(Cl)Cl)Cl 720 | Heptane,-4.53,-2.97,CCCCCCC 721 | "Hexachloro-1,3-butadiene",-4.92,-4.546,ClC(=C(Cl)C(=C(Cl)Cl)Cl)Cl 722 | Hexachloroethane,-3.67,-4.215,ClC(Cl)(Cl)C(Cl)(Cl)Cl 723 | hexacosane,-8.334,-9.702,CCCCCCCCCCCCCCCCCCCCCCCCCC 724 | Hexadecane,-8.4,-6.159,CCCCCCCCCCCCCCCC 725 | Hexamethylbenzene,-5.23,-4.361,Cc1c(C)c(C)c(C)c(C)c1C 726 | Hexane ,-3.84,-2.615,CCCCCC 727 | Hexestrol,-4.43,-4.854,CCC(C(CC)c1ccc(O)cc1)c2ccc(O)cc2 728 | Hexylbenzene ,-5.21,-4.22,CCCCCCc1ccccc1 729 | hydantoin,-0.4,0.603,O=C1CNC(=O)N1 730 | hydrazobenzene,-2.92,-3.492,N(Nc1ccccc1)c2ccccc2 731 | hydrobenzoin,-1.93,-2.645,c1ccccc1C(O)C(O)c2ccccc2 732 | hydrochlorothiazide,-2.63,-1.72,NS(=O)(=O)c2cc1c(NCNS1(=O)=O)cc2Cl 733 | Hydrocortisone ,-3.09,-3.159,CC12CC(O)C3C(CCC4=CC(=O)CCC34C)C2CCC1(O)C(=O)CO 734 | Hydrocortisone 21-acetate,-4.88,-3.692,CC(=O)OCC(=O)C1(O)CCC2C3CCC4=CC(=O)CCC4(C)C3C(O)CC21C 735 | hydroxychlordene,-5.46,-4.156,OC1C=CC2C1C3(Cl)C(=C(Cl)C2(Cl)C3(Cl)Cl)Cl 736 | Hydroxyprogesterone-17a,-3.817,-3.876,CC(=O)C1(O)CCC2C3CCC4=CC(=O)CCC4(C)C3CCC21C 737 | Hypoxanthine,-2.296,-0.656,O=c1[nH]cnc2nc[nH]c12 738 | Indan,-3.04,-3.057,C1Cc2ccccc2C1 739 | Indapamide,-3.586,-4.345,CC2Cc1ccccc1N2NC(=O)c3ccc(Cl)c(c3)S(N)(=O)=O 740 | indazole,-2.16,-2.34,c2ccc1[nH]ncc1c2 741 | Indole,-1.52,-2.654,c2ccc1[nH]ccc1c2 742 | indoline,-1.04,-2.195,c2ccc1NCCc1c2 743 | Inosine,-1.23,-0.834,OCC1OC(C(O)C1O)n2cnc3c(O)ncnc23 744 | Iodobenzene,-3.01,-3.8,Ic1ccccc1 745 | Iodoethane,-1.6,-2.066,CCI 746 | Iodofenphos,-6.62,-6.148,COP(=S)(OC)Oc1cc(Cl)c(I)cc1Cl 747 | Iodomethane,-1,-1.646,CI 748 | Ioxynil,-3.61,-4.615,Oc1c(I)cc(C#N)cc1I 749 | Ipazine,-3.785,-3.497,CCN(CC)c1nc(Cl)nc(NC(C)C)n1 750 | Isazofos,-3.658,-3.76,CCOP(=S)(OCC)Oc1nc(Cl)n(n1)C(C)C 751 | Isobutyl acetate,-1.21,-1.463,CC(C)COC(=O)C 752 | Isobutyl formate,-1.01,-1.095,CC(C)COC=O 753 | Isobutylbenzene,-4.12,-3.57,CC(C)Cc1ccccc1 754 | isocarbamid,-2.15,-1.508,C1N(C(=O)NCC(C)C)C(=O)NC1 755 | Isocarboxazid,-2.461,-2.251,Cc1cc(no1)C(=O)NNCc2ccccc2 756 | Isofenphos,-4.194,-4.538,CCOP(=S)(NC(C)C)Oc1ccccc1C(=O)OC(C)C 757 | isoguanine,-3.401,-1.74,Nc1nc(O)nc2nc[nH]c12 758 | Isonazid,0.009,-0.717,c1nccc(C(=O)NN)c1 759 | Isopentyl acetate,-1.92,-1.817,CC(C)CCOC(=O)C 760 | Isopentyl formate,-1.52,-1.449,CC(C)CCOC=O 761 | isophorone,-1.06,-2.015,CC1=CC(=O)CC(C)(C)C1 762 | Isoprocarb,-2.863,-2.734,CNC(=O)Oc1ccccc1C(C)C 763 | Isopropalin,-6.49,-5.306,CCCN(CCC)c1c(cc(cc1N(=O)=O)C(C)C)N(=O)=O 764 | Isopropyl acetate,-0.55,-1.191,CC(C)OC(=O)C 765 | Isopropyl formate,-0.63,-0.684,CC(C)OC=O 766 | Isopropylbenzene ,-3.27,-3.265,CC(C)c1ccccc1 767 | Isoproturon,-3.536,-2.867,CC(C)c1ccc(NC(=O)N(C)C)cc1 768 | Isoquinoline,-1.45,-2.531,c1ccc2cnccc2c1 769 | karbutilate,-2.93,-2.655,CN(C)C(=O)Nc1cccc(OC(=O)NC(C)(C)C)c1 770 | kebuzone,-3.27,-2.645,CC(=O)CCC1C(=O)N(N(C1=O)c2ccccc2)c3ccccc3 771 | Kepone,-5.259,-5.112,ClC1(C(=O)C2(Cl)C3(Cl)C14Cl)C5(Cl)C2(Cl)C3(Cl)C(Cl)(Cl)C45Cl 772 | Khellin,-3.021,-3.603,COc2c1occc1c(OC)c3c(=O)cc(C)oc23 773 | Lactose,-0.244,1.071,OCC1OC(OC2C(O)C(O)C(O)OC2CO)C(O)C(O)C1O 774 | L-arabinose,0.39,0.601,C1OC(O)C(O)C(O)C1O 775 | Lenacil,-4.594,-3.355,O=c2[nH]c1CCCc1c(=O)n2C3CCCCC3 776 | linalool,-1.99,-2.399,CC(C)=CCCC(O)(C)C=C 777 | Lindane,-4.64,-4.009,ClC1C(Cl)C(Cl)C(Cl)C(Cl)C1Cl 778 | Linuron,-3.592,-3.581,CON(C)C(=O)Nc1ccc(Cl)c(Cl)c1 779 | Lorazepam,-3.604,-3.75,OC3N=C(c1ccccc1Cl)c2cc(Cl)ccc2NC3=O 780 | Lovastatin,-6.005,-4.731,CCC(C)C(=O)OC2CC(C)C=C3C=CC(C)C(CCC1CC(O)CC(=O)O1)C23 781 | Malathion,-3.37,-3.391,CCOC(=O)CC(SP(=S)(OC)OC)C(=O)OCC 782 | Malonic acid diethylester,-0.82,-1.413,CCOC(=O)CC(=O)OCC 783 | Maltose,0.358,1.071,OCC1OC(OC2C(O)C(O)C(O)OC2CO)C(O)C(O)C1O 784 | mannitol,0.06,0.647,OCC(O)C(O)C(O)C(O)CO 785 | m-Chloroaniline,-1.37,-2.392,Nc1cccc(Cl)c1 786 | m-Chlorobromobenzene,-3.21,-3.928,Clc1cccc(Br)c1 787 | m-Chloroiodobenzene,-3.55,-4.384,Clc1cccc(I)c1 788 | m-Chloronitrobenzene ,-2.77,-2.901,Clc1cccc(c1)N(=O)=O 789 | Mebendazole,-3.88,-4.118,COC(=O)Nc2nc1ccc(cc1[nH]2)C(=O)c3ccccc3 790 | Mecarbam,-2.518,-3.738,CCOC(=O)N(C)C(=O)CSP(=S)(OCC)OCC 791 | meconin,-1.899,-0.825,c1c(OC)c(OC)C2C(=O)OCC2c1 792 | Medrogestone,-5.27,-4.593,CC(=O)C3(C)CCC4C2C=C(C)C1=CC(=O)CCC1(C)C2CCC34C 793 | Mefenacet,-4.873,-4.504,CN(C(=O)COc1nc2ccccc2s1)c3ccccc3 794 | Mefluidide,-3.24,-3.165,CC(=O)Nc1cc(NS(=O)(=O)C(F)(F)F)c(C)cc1C 795 | megestrol acetate,-5.35,-4.417,CC(=O)OC3(CCC4C2C=C(C)C1=CC(=O)CCC1(C)C2CCC34C)C(C)=O 796 | Menadione,-3.03,-2.667,CC2=CC(=O)c1ccccc1C2=O 797 | menthol,-2.53,-2.782,CC(C)C1CCC(C)CC1O 798 | Menthone,-2.35,-2.516,CC(C)C1CCC(C)CC1=O 799 | Meprobamate,-1.807,-1.376,CCCC(C)(COC(N)=O)COC(N)=O 800 | mercaptobenzothiazole,-3.18,-3.411,Sc2nc1ccccc1s2 801 | metalaxyl,-1.601,-2.87,COCC(=O)N(C(C)C(=O)OC)c1c(C)cccc1C 802 | Methane,-0.9,-0.636,C 803 | Methanol,1.57,0.441,CO 804 | Methaqualone,-2.925,-3.881,Cc1ccccc1n3c(C)nc2ccccc2c3=O 805 | metharbital,-2.23,-1.658,CCC1(CC)C(=O)NC(=O)N(C)C1=O 806 | Methazole,-2.82,-3.601,Cn2c(=O)on(c1ccc(Cl)c(Cl)c1)c2=O 807 | Methocarbamol,-0.985,-1.428,COc1ccccc1OCC(O)COC(N)=O 808 | Methoprene,-5.19,-4.795,COC(C)(C)CCCC(C)CC=CC(C)=CC(=O)OC(C)C 809 | Methoproptryne,-2.928,-3.259,COCCCNc1nc(NC(C)C)nc(SC)n1 810 | Methoxsalen,-3.664,-3.25,COc2c1occc1cc3ccc(=O)oc23 811 | Methoxychlor,-6.89,-5.538,COc1ccc(cc1)C(c2ccc(OC)cc2)C(Cl)(Cl)Cl 812 | Methyl acetate,0.46,-0.416,COC(=O)C 813 | Methyl acrylate,-0.22,-0.878,COC(=O)C=C 814 | Methyl benzoate ,-1.85,-2.462,COC(=O)c1ccccc1 815 | Methyl butyl ether ,-0.99,-1.072,CCCCOC 816 | Methyl butyrate,-0.82,-1.545,CCCOC(=O)CC 817 | Methyl decanoate,-4.69,-3.316,CCCCCCCCCC(=O)OC 818 | Methyl formate,0.58,-0.048,COC=O 819 | methyl gallate,-1.24,-1.913,COC(=O)c1cc(O)c(O)c(O)c1 820 | Methyl hexanoate,-1.87,-1.899,CCCCCC(=O)OC 821 | Methyl hydrazine,1.34,0.543,CNN 822 | methyl laurate,-4.69,-4.025,CCCCCCCCCCCC(=O)OC 823 | methyl nicotinate,-0.46,-1.621,COC(=O)c1cccnc1 824 | Methyl nonanoate,-3.38,-2.962,CCCCCCCCC(=O)OC 825 | Methyl octanoate,-3.17,-2.608,CCCCCCCC(=O)OC 826 | Methyl pentanoate,-1.36,-1.545,CCCC(=O)OCC 827 | Methyl propionate,-0.14,-0.836,CCC(=O)OC 828 | Methyl propyl ether ,-0.39,-0.718,CCCOC 829 | Methyl t-butyl ether ,-0.24,-0.984,COC(C)(C)C 830 | Methylcyclohexane ,-3.85,-2.891,CC1CCCCC1 831 | Methylcyclopentane,-3.3,-2.452,CC1CCCC1 832 | Methyldymron,-3.35,-3.863,CN(C(=O)NC(C)(C)c1ccccc1)c2ccccc2 833 | Methylparaben,-1.827,-2.441,COC(=O)c1ccc(O)cc1 834 | methyltestosterone acetate,-5.284,-4.863,CC(=O)OC3(C)CCC4C2CCC1=CC(=O)CCC1(C)C2CCC34C 835 | methylthiouracil,-2.436,-0.547,Cc1cc(=O)[nH]c(=S)[nH]1 836 | Metolachlor,-2.73,-3.431,CCc1cccc(C)c1N(C(C)COC)C(=O)CCl 837 | Metolazone,-3.78,-3.777,CC2Nc1cc(Cl)c(cc1C(=O)N2c3ccccc3C)S(N)(=O)=O 838 | Metolcarb,-1.803,-1.947,c1ccccc1(OC(=O)NC) 839 | Metoxuron,-2.564,-2.683,COc1ccc(NC(=O)N(C)C)cc1Cl 840 | Metranidazole,-1.26,-0.859,Cc1ncc(N(=O)=O)n1CCO 841 | Metribuzin,-2.253,-2.324,CSc1nnc(c(=O)n1N)C(C)(C)C 842 | Metronidazole,-1.22,-0.859,Cc1ncc(N(=O)=O)n1CCO 843 | m-Fluorobromobenzene,-2.67,-3.467,Fc1cccc(Br)c1 844 | Minoxidil,-1.989,-1.809,Nc1cc(nc(N)n1=O)N2CCCCC2 845 | Mirex,-6.8,-6.155,ClC1(C2(Cl)C3(Cl)C4(Cl)C5(Cl)C1(Cl)C3(Cl)Cl)C5(Cl)C(Cl)(Cl)C24Cl 846 | m-Methylaniline,-0.85,-1.954,Cc1cccc(N)c1 847 | m-Nitroaniline,-2.19,-1.936,Nc1cccc(c1)N(=O)=O 848 | m-Nitrophenol,-1.01,-2.318,Oc1cccc(c1)N(=O)=O 849 | m-Nitrotoluene,-2.44,-2.64,Cc1cccc(c1)N(=O)=O 850 | Monolinuron,-2.57,-2.948,CON(C)C(=O)Nc1ccc(Cl)cc1 851 | Monotropitoside,-0.742,-1.493,COC(=O)c1ccccc1OC2OC(COC3OCC(O)C(O)C3O)C(O)C(O)C2O 852 | Monuron,-2.89,-2.671,CN(C)C(=O)Nc1ccc(Cl)cc1 853 | Morin,-3.083,-2.731,Oc1ccc(c(O)c1)c3oc2cc(O)cc(O)c2c(=O)c3O 854 | m-Xylene ,-2.82,-3.035,Cc1cccc(C)c1 855 | "N,N-Diethylaniline",-3.03,-3.16,CCN(CC)c1ccccc1 856 | "N,N-Dimethylacetamide",1.11,0.123,CN(C)C(=O)C 857 | "N,N-Dimethylaniline",-1.92,-2.542,CN(C)c1ccccc1 858 | Naled,-2.28,-3.548,COP(=O)(OC)OC(Br)C(Cl)(Cl)Br 859 | Napropamide,-3.57,-4.088,CCN(CC)C(=O)C(C)Oc1cccc2ccccc12 860 | Napthacene,-8.6,-5.568,c1ccc2cc3cc4ccccc4cc3cc2c1 861 | Napthalene,-3.6,-3.468,c1ccc2ccccc2c1 862 | Neburon,-4.77,-4.157,CCCCN(C)C(=O)Nc1ccc(Cl)c(Cl)c1 863 | Nerol,-2.46,-2.603,CC(C)=CCC/C(C)=C\CO 864 | N-Ethylaniline,-1.7,-2.389,CCNc1ccccc1 865 | nevirapine,-3.19,-3.397,Cc3ccnc4N(C1CC1)c2ncccc2C(=O)Nc34 866 | Niclosamide,-4.7,-5.032,Oc1ccc(Cl)cc1C(=O)Nc2ccc(cc2Cl)N(=O)=O 867 | nicotinamide,0.61,-0.964,NC(=O)c1cccnc1 868 | nifedipine,-4.76,-4.248,COC(=O)C1=C(C)NC(=C(C1c2ccccc2N(=O)=O)C(=O)OC)C 869 | nifuroxime,-2.19,-1.843,ON=Cc1ccc(o1)N(=O)=O 870 | Nimetazepam,-3.796,-3.557,CN2C(=O)CN=C(c1ccccc1)c3cc(ccc23)N(=O)=O 871 | Niridazole,-3.22,-1.948,O=C1NCCN1c2ncc(s2)N(=O)=O 872 | Nitramine,-3.561,-4.479,CCN(CC)c1c(cc(c(N)c1N(=O)=O)C(F)(F)F)N(=O)=O 873 | Nitrapyrin,-3.76,-3.833,Clc1cccc(n1)C(Cl)(Cl)Cl 874 | Nitrazepam,-3.796,-3.473,O=C3CN=C(c1ccccc1)c2cc(ccc2N3)N(=O)=O 875 | Nitrobenzene,-1.8,-2.288,O=N(=O)c1ccccc1 876 | Nitroethane,-0.22,-0.462,CCN(=O)=O 877 | Nitrofen,-5.46,-5.361,Clc2ccc(Oc1ccc(cc1)N(=O)=O)c(Cl)c2 878 | nitrofurantoin,-3.38,-1.243,O=C2CN(N=Cc1ccc(o1)N(=O)=O)C(=O)N2 879 | nitroglycerin,-2.22,-2.029,O=N(=O)OCC(CON(=O)=O)ON(=O)=O 880 | Nitromethane,0.26,-0.042,CN(=O)=O 881 | N-Methylaniline ,-1.28,-2.097,CNc1ccccc1 882 | Nonane,-5.88,-3.678,CCCCCCCCC 883 | norbormide,-3.931,-4.238,OC(C1=CC2C5C(C1C2=C(c3ccccc3)c4ccccn4)C(=O)NC5=O)(c6ccccc6)c7ccccn7 884 | Norea,-3.171,-2.47,CN(C)C(=O)NC1CC2CC1C3CCCC23 885 | norethindrone acetate,-4.8,-4.241,CC(=O)OC3(CCC4C2CCC1=CC(=O)CCC1C2CCC34C)C#C 886 | Norethisterone,-4.57,-2.669,CC34CCC1C(CCC2=CC(=O)CCC12O)C3CCC4(O)C#C 887 | norflurazon,-4.046,-4.029,CNc2cnn(c1cccc(c1)C(F)(F)F)c(=O)c2Cl 888 | "O,P'-DDD",-6.51,-6.008,ClC(Cl)C(c1ccc(Cl)cc1)c2ccccc2Cl 889 | o-Aminophenol,-0.72,-1.465,Nc1ccccc1O 890 | o-Chloroaniline,-1.52,-2.392,Nc1ccccc1Cl 891 | o-Chlorobromobenzene,-3.19,-3.84,Clc1ccccc1Br 892 | o-Chloroiodobenzene,-3.54,-4.384,Clc1ccccc1I 893 | o-Chloronitrobenzene,-2.55,-2.775,Clc1ccccc1N(=O)=O 894 | Octane,-5.24,-3.324,CCCCCCCC 895 | O-Ethyl carbamate,0.85,-0.218,CCOC(=O)N 896 | o-Fluorobromobenzene,-2.7,-3.467,Fc1ccccc1Br 897 | o-Hydroxybenzamide,-1.82,-1.942,NC(=O)c1ccccc1O 898 | o-Methoxyphenol,-1.96,-1.941,COc1ccccc1O 899 | o-Nitroaniline,-1.96,-2.277,Nc1ccccc1N(=O)=O 900 | o-Nitroanisole,-1.96,-2.346,COc1ccccc1N(=O)=O 901 | o-Nitrophenol,-1.74,-2.318,Oc1ccccc1N(=O)=O 902 | o-Nitrotoluene,-2.33,-2.589,Cc1ccccc1N(=O)=O 903 | oryzalin,-5.16,-3.784,CCCN(CCC)c1c(cc(cc1N(=O)=O)S(N)(=O)=O)N(=O)=O 904 | osthole,-4.314,-4.076,c1cc2ccc(OC)c(CC=C(C)(C))c2oc1=O 905 | o-Toluidine,-2.21,-1.922,Cc1ccccc1N 906 | Oxadiazon,-5.696,-5.265,CC(C)Oc1cc(c(Cl)cc1Cl)n2nc(oc2=O)C(C)(C)C 907 | Oxamyl,0.106,-0.908,CNC(=O)ON=C(SC)C(=O)N(C)C 908 | Oxazepam,-3.952,-3.517,OC3N=C(c1ccccc1)c2cc(Cl)ccc2NC3=O 909 | Oxycarboxin,-2.281,-2.169,CC1=C(C(=O)Nc2ccccc2)S(=O)(=O)CCO1 910 | o-Xylene ,-2.8,-3.004,Cc1ccccc1C 911 | oxyphenbutazone,-3.73,-3.739,CCCCC1C(=O)N(N(C1=O)c2ccc(O)cc2)c3ccccc3 912 | "p,p'-Biphenyldiamine ",-2.7,-2.613,Nc1ccc(cc1)c2ccc(N)cc2 913 | "P,P'-DDD",-7.2,-6.008,ClC(Cl)C(c1ccc(Cl)cc1)c2ccc(Cl)cc2 914 | "P,P'-DDE",-6.9,-6.553,ClC(Cl)=C(c1ccc(Cl)cc1)c2ccc(Cl)cc2 915 | p-Aminophenol,-0.8,-1.231,Nc1ccc(O)cc1 916 | parabanic acid,-0.4,1.091,O=C1NC(=O)C(=O)N1 917 | Parathion,-4.66,-3.949,CCOP(=S)(OCC)Oc1ccc(cc1)N(=O)=O 918 | p-benzidine,-2.7,-2.613,Nc1ccc(cc1)c2ccc(N)cc2 919 | p-Bromoacetanilide,-3.083,-3.012,CC(=O)Nc1ccc(Br)cc1 920 | p-Bromoiodobenzene,-4.56,-4.754,Brc1ccc(I)cc1 921 | p-Chloroacetanilide,-2.843,-2.642,CC(=O)Nc1ccc(Cl)cc1 922 | p-Chloroaniline,-1.66,-2.392,Nc1ccc(Cl)cc1 923 | p-Chlorobromobenzene,-3.63,-3.928,Clc1ccc(Br)cc1 924 | p-Chloroiodobenzene,-4.03,-4.384,Clc1ccc(I)cc1 925 | p-Chloronitrobenzene,-2.92,-2.901,Clc1ccc(cc1)N(=O)=O 926 | p-Cresol,-0.73,-2.313,Cc1ccc(O)cc1 927 | Pebulate,-3.53,-3.131,CCCCN(CC)C(=O)SCCC 928 | Pencycuron,-5.915,-5.126,Clc1ccc(CN(C2CCCC2)C(=O)Nc3ccccc3)cc1 929 | Pentachlorobenzene,-5.65,-5.168,Clc1cc(Cl)c(Cl)c(Cl)c1Cl 930 | Pentachloroethane,-2.6,-3.382,ClC(Cl)C(Cl)(Cl)Cl 931 | Pentachlorophenol,-4.28,-4.835,Oc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl 932 | Pentamethylbenzene,-4,-3.993,Cc1cc(C)c(C)c(C)c1C 933 | Pentane,-3.18,-2.261,CCCCC 934 | Pentobarbital,-2.39,-2.312,O=C1NC(=O)NC(=O)C1(CC)C(C)CCC 935 | Pentyl acetate,-1.89,-1.833,CCCCCOC(=O)C 936 | Pentyl propanoate,-2.25,-1.899,CCCCC(=O)OCC 937 | Pentylbenzene,-4.64,-3.899,CCCCCc1ccccc1 938 | Pentylcyclopentane,-6.08,-3.869,CCCCCC1CCCC1 939 | Perfluidone,-3.8,-4.945,Cc1cc(ccc1NS(=O)(=O)C(F)(F)F)S(=O)(=O)c2ccccc2 940 | Permethrin,-6.291,-7.129,CC1(C)C(C=C(Cl)Cl)C1C(=O)OCc2cccc(Oc3ccccc3)c2 941 | Perylene,-8.804,-6.007,c1cc2cccc3c4cccc5cccc(c(c1)c23)c54 942 | p-Fluoroacetanilide,-1.78,-2.181,CC(=O)Nc1ccc(F)cc1 943 | Phenacetin,-2.35,-2.342,CCOc1ccc(NC(=O)C)cc1 944 | Phenanthrene,-5.26,-4.518,c1ccc2c(c1)ccc3ccccc32 945 | phenanthridine,-2.78,-3.713,c1ccc2c(c1)cnc3ccccc23 946 | Phenetole,-2.33,-2.66,CCOc1ccccc1 947 | Phenmedipham,-4.805,-4.229,COC(=O)Nc1cccc(OC(=O)Nc2cccc(C)c2)c1 948 | phenobarbital,-2.322,-2.272,CCC1(C(=O)NC(=O)NC1=O)c2ccccc2 949 | Phenol,0,-1.991,c1ccccc1O 950 | phenolphthalein,-2.9,-4.59,Oc1ccc(cc1)C2(OC(=O)c3ccccc23)c4ccc(O)cc4 951 | phenothrin,-5.24,-6.763,CC(C)=CC3C(C(=O)OCc2cccc(Oc1ccccc1)c2)C3(C)C 952 | phenylbutazone,-3.81,-4.076,CCCCC1C(=O)N(N(C1=O)c2ccccc2)c3ccccc3 953 | Phenylhydrazine,0.07,-1.866,NNc1ccccc1 954 | Phenylmethanol,-0.4,-1.699,OCc1ccccc1 955 | Phenylthiourea,-1.77,-1.701,NC(=S)Nc1ccccc1 956 | Phenytoin,-4.097,-3.057,O=C1NC(=O)C(N1)(c2ccccc2)c3ccccc3 957 | Phorate,-4.11,-3.747,CCOP(=S)(OCC)SCSCC 958 | Phosalone,-5.233,-5.024,CCOP(=S)(OCC)SCn1c(=O)oc2cc(Cl)ccc12 959 | Phoxim,-4.862,-4.557,CCOP(=S)(OCC)ON=C(C#N)c1ccccc1 960 | phthalamide,-2.932,-0.636,c1cC2C(=O)NC(=O)C2cc1 961 | phthalimide,-2.61,-1.882,O=C1NC(=O)c2ccccc12 962 | Phthalonitrile,-2.38,-1.717,N#Cc1ccccc1C#N 963 | p-Hydroxyacetanilide,-1.03,-1.495,CC(=O)Nc1ccc(O)cc1 964 | p-Hydroxybenzaldehyde ,-0.96,-2.003,Oc1ccc(C=O)cc1 965 | Picene,-7.87,-6.618,c1ccc2c(c1)ccc3c2ccc4c5ccccc5ccc43 966 | Piperine,-3.46,-3.659,O=C(C=CC=Cc2ccc1OCOc1c2)N3CCCCC3 967 | piperonal,-1.63,-2.033,O=Cc2ccc1OCOc1c2 968 | Piperophos,-4.15,-4.637,CCCOP(=S)(OCCC)SCC(=O)N1CCCCC1C 969 | Pirimicarb,-1.95,-2.34,CN(C)C(=O)Oc1nc(nc(C)c1C)N(C)C 970 | piroxicam,-4.16,-3.473,CN2C(=C(O)c1ccccc1S2(=O)=O)C(=O)Nc3ccccn3 971 | p-Methoxybenzaldehyde,-1.49,-2.252,COc1ccc(C=O)cc1 972 | p-Methylaniline ,-1.21,-1.954,Cc1ccc(N)cc1 973 | p-Nitroaniline,-2.37,-1.936,Nc1ccc(cc1)N(=O)=O 974 | p-Nitroanisole,-2.41,-2.522,COc1ccc(cc1)N(=O)=O 975 | p-Nitrophenol,-0.74,-2.318,Oc1ccc(cc1)N(=O)=O 976 | p-Nitrotoluene,-2.49,-2.64,Cc1ccc(cc1)N(=O)=O 977 | p-Phenylphenol,-3.48,-3.701,Oc1ccc(cc1)c2ccccc2 978 | Prasterone,-4.12,-3.564,CC34CCC1C(CC=C2CC(O)CCC12C)C3CCC4=O 979 | Prednisolone,-3.18,-2.974,CC12CC(O)C3C(CCC4=CC(=O)C=CC34C)C2CCC1(O)C(=O)CO 980 | prednisolone acetate,-4.37,-3.507,CC(=O)OCC(=O)C3(O)CCC4C2CCC1=CC(=O)C=CC1(C)C2C(O)CC34C 981 | pregnenolone,-4.65,-4.342,CC(=O)C3CCC4C2CC=C1CC(O)CCC1(C)C2CCC34C 982 | Primidone,-2.64,-1.897,CCC1(C(=O)NCNC1=O)c2ccccc2 983 | probarbital,-2.21,-1.603,CCC1(C(C)C)C(=O)NC(=O)NC1=O 984 | Procymidone,-4.8,-3.464,CC12CC2(C)C(=O)N(C1=O)c3cc(Cl)cc(Cl)c3 985 | Progesterone,-4.42,-4.17,CC(=O)C1CCC2C3CCC4=CC(=O)CCC4(C)C3CCC12C 986 | Prometon,-2.478,-3.448,COc1nc(NC(C)C)nc(NC(C)C)n1 987 | Prometryn,-4.1,-3.693,CSc1nc(NC(C)C)nc(NC(C)C)n1 988 | propachlor,-2.48,-3.018,CC(C)N(C(=O)CCl)c1ccccc1 989 | Propane,-1.94,-1.553,CCC 990 | Propanil,-3,-3.644,CCC(=O)Nc1ccc(Cl)c(Cl)c1 991 | Propazine,-4.43,-3.329,CC(C)Nc1nc(Cl)nc(NC(C)C)n1 992 | Propetamphos,-3.408,-2.826,CCNP(=S)(OC)OC(=CC(=O)OC(C)C)C 993 | Propiconazole,-3.493,-4.603,CCCC1COC(Cn2cncn2)(O1)c3ccc(Cl)cc3Cl 994 | Propionaldehyde,0.58,-0.394,CCC=O 995 | Propionitrile,0.28,-0.269,CCC#N 996 | Propoxur,-2.05,-2.409,CNC(=O)Oc1ccccc1OC(C)C 997 | Propyl acetate,-0.72,-1.125,CCCOC(=O)C 998 | Propyl butyrate,-1.92,-1.191,CCCC(=O)OC 999 | Propyl formate,-0.49,-0.757,CCCOC=O 1000 | Propyl propanoate,-1.34,-1.545,CCCCC(=O)OC 1001 | Propylbenzene ,-3.37,-3.281,CCCc1ccccc1 1002 | Propylcyclopentane,-4.74,-3.16,CCCC1CCCC1 1003 | Propylene,-1.08,-1.235,CC=C 1004 | Propylisopropylether,-1.34,-1.354,CCCOC(C)C 1005 | Propyne,-0.41,-0.672,CC#C 1006 | p-t-Butylphenol,-2.41,-3.192,CC(C)(C)c1ccc(O)cc1 1007 | Pteridine,0.02,-0.906,c2cnc1ncncc1n2 1008 | p-terphenyl,-7.11,-5.741,c1ccc(cc1)c2ccc(cc2)c3ccccc3 1009 | p-Toluenesulfonamide ,-1.74,-1.815,Cc1ccc(cc1)S(=O)(=O)N 1010 | p-Xylene ,-2.77,-3.035,Cc1ccc(C)cc1 1011 | pyracarbolid,-2.56,-2.83,CC1=C(CCCO1)C(=O)Nc2ccccc2 1012 | Pyrazinamide,-0.667,-0.674,NC(=O)c1cnccn1 1013 | Pyrazon,-2.878,-2.603,Nc2cnn(c1ccccc1)c(=O)c2Cl 1014 | Pyrene,-6.176,-4.957,c1cc2ccc3cccc4ccc(c1)c2c34 1015 | Pyridazine,1.1,-0.619,c1ccnnc1 1016 | Pyridine,0.76,-1.481,c1ccncc1 1017 | Pyrimidine,1.1,-0.884,c1cncnc1 1018 | Pyrolan,-2.09,-3.141,CN(C)C(=O)Oc1cc(C)nn1c2ccccc2 1019 | Quinethazone,-3.29,-2.184,CCC2NC(=O)c1cc(c(Cl)cc1N2)S(N)(=O)=O 1020 | Quinoline,-1.3,-2.663,c1ccc2ncccc2c1 1021 | Quinonamid,-5.03,-3.988,ClC(Cl)CC(=O)NC2=C(Cl)C(=O)c1ccccc1C2=O 1022 | Quintozene,-5.82,-5.098,Clc1c(Cl)c(Cl)c(N(=O)=O)c(Cl)c1Cl 1023 | Raffinose,-0.41,0.496,OCC1OC(CO)(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(O)C2O)C(O)C1O 1024 | Reposal,-2.696,-2.781,CCC1(C(=O)NC(=O)NC1=O)C2=CCC3CCC2C3 1025 | Reverse Transcriptase inhibitor 1,-2.62,-2.794,CCN2c1ncccc1N(C)C(=O)c3cccnc23 1026 | rhodanine,-1.77,-0.396,C1SC(=S)NC1(=O) 1027 | Riboflavin,-3.685,-1.865,Cc3cc2nc1c(=O)[nH]c(=O)nc1n(CC(O)C(O)C(O)CO)c2cc3C 1028 | Risocaine,-2.452,-2.709,CCCOC(=O)c1ccc(N)cc1 1029 | Ronnel,-5.72,-5.247,COP(=S)(OC)Oc1cc(Cl)c(Cl)cc1Cl 1030 | Rotenone,-4.42,-5.246,COc5cc4OCC3Oc2c1CC(Oc1ccc2C(=O)C3c4cc5OC)C(C)=C 1031 | Rovral,-4.376,-4.004,CC(C)NC(=O)N1CC(=O)N(C1=O)c2cc(Cl)cc(Cl)c2 1032 | RTI 10,-3.672,-2.771,O2c1ccccc1N(C)C(=O)c3cccnc23 1033 | RTI 11,-3.928,-3.125,O2c1ccc(N)cc1N(C)C(=O)c3cc(C)ccc23 1034 | RTI 12,-4.114,-3.446,CCN2c1nc(Cl)ccc1N(C)C(=O)c3cccnc23 1035 | RTI 13,-4.207,-4.45,CCN2c1nc(C)cc(C(F)(F)F)c1NC(=O)c3cccnc23 1036 | RTI 15,-4.554,-3.891,CCN2c1nc(C)cc(C)c1NC(=O)c3cccnc23 1037 | RTI 16,-4.634,-3.411,CCN2c1ncccc1N(C)C(=S)c3cccnc23 1038 | RTI 17,-4.706,-4.227,CCN2c1ccccc1N(C)C(=S)c3cccnc23 1039 | RTI 19,-4.749,-4.007,CCN2c1ccccc1N(C)C(=O)c3ccccc23 1040 | RTI 2,-2.86,-3.125,CCN2c1ncccc1N(CC)C(=O)c3cccnc23 1041 | RTI 20,-4.799,-3.663,C2c1ccccc1N(CCF)C(=O)c3ccccc23 1042 | RTI 22,-4.871,-4.408,CCN2c1cc(N(C)C)cc(C)c1NC(=O)c3cccnc23 1043 | RTI 23,-5.153,-4.228,CCN2c1cc(OC)cc(C)c1NC(=O)c3cccnc23 1044 | RTI 24,-5.36,-4.423,CCN2c1cc(Cl)ccc1NC(=O)c3cccnc23 1045 | RTI 3,-3.043,-3.049,O2c1cc(C)ccc1N(C)C(=O)c3cc(N)cnc23 1046 | RTI 5,-3.324,-3.471,CCN2c1ccccc1N(C)C(=O)c3cccnc23 1047 | RTI 6,-3.36,-3.335,CCN2c1nc(N(C)(CCO))ccc1NC(=O)c3cccnc23 1048 | RTI 7,-3.535,-3.663,C2c1ccccc1N(CCF)C(=O)c3ccccc23 1049 | RTI 9,-3.68,-3.784,O2c1ccccc1N(CC)C(=O)c3ccccc23 1050 | Salicin,-0.85,-0.975,OCC2OC(Oc1ccccc1CO)C(O)C(O)C2O 1051 | Salicylamide,-1.836,-1.942,NC(=O)c1ccccc1O 1052 | salicylanilide,-3.59,-3.782,c1ccccc1NC(=O)c2c(O)cccc2 1053 | Santonin,-3.09,-2.43,CC3C2CCC1(C)C=CC(=O)C(=C1C2OC3=O)C 1054 | Secobarbital,-2.356,-2.415,O=C1NC(=O)NC(=O)C1(C(C)CCC)CC=C 1055 | Siduron,-4.11,-3.779,CC1CCCCC1NC(=O)Nc2ccccc2 1056 | simazine,-4.55,-2.811,CCNc1nc(Cl)nc(NCC)n1 1057 | Simetryn,-2.676,-2.689,CSc1nc(nc(n1)N(C)C)N(C)C 1058 | Sorbitol,1.09,0.647,OCC(O)C(O)C(O)C(O)CO 1059 | "Sparsomycin (3,8mg/ml)",-1.981,-1.57,CSCS(=O)CC(CO)NC(=O)C=Cc1c(C)[nH]c(=O)[nH]c1=O 1060 | Spironolactone,-4.173,-3.842,CC(=O)SC4CC1=CC(=O)CCC1(C)C5CCC2(C)C(CCC23CCC(=O)O3)C45 1061 | stadacaine,-3.84,-5.128,CCCCOc1ccc(C(=O)OCC)c(c1)N(CC)CC 1062 | Stanolone,-4.743,-3.882,CC34CCC1C(CCC2CC(=O)CCC12C)C3CCC4O 1063 | Stirofos,-4.522,-4.32,COP(=O)(OC)OC(=CCl)c1cc(Cl)c(Cl)cc1Cl 1064 | Styrene,-2.82,-2.85,C=Cc1ccccc1 1065 | styrene oxide,-1.6,-1.826,C1OC1c2ccccc2 1066 | Succinimide,0.3,0.282,O=C1CCC(=O)N1 1067 | Sucrose,0.79,0.31,OCC2OC(OC1(CO)OC(CO)C(O)C1O)C(O)C(O)C2O 1068 | sulfaguanidine,-1.99,-0.706,NC(=N)NS(=O)(=O)c1ccc(N)cc1 1069 | Sulfallate,-3.39,-3.254,CCN(CC)C(=S)SCC(Cl)=C 1070 | Sulfanilamide,-1.34,-0.954,Nc1ccc(cc1)S(N)(=O)=O 1071 | Talbutal,-2.016,-2.06,CCC(C)C1(CC=C)C(=O)NC(=O)NC1=O 1072 | t-Butylbenzene ,-3.66,-3.554,CC(C)(C)c1ccccc1 1073 | t-Crotonaldehyde,0.32,-0.604,C/C=C/C=O 1074 | TEFLUBENZURON,-7.28,-5.462,Fc1cccc(F)c1C(=O)NC(=O)Nc2cc(Cl)c(F)c(Cl)c2F 1075 | Terbacil,-2.484,-3.033,Cc1[nH]c(=O)n(c(=O)c1Cl)C(C)(C)C 1076 | Terbufos,-4.755,-4.367,CCOP(=S)(OCC)SCSC(C)(C)C 1077 | Terbumeton,-3.239,-3.505,CCNc1nc(NC(C)(C)C)nc(OC)n1 1078 | Terbutryn,-4,-3.75,CCNc1nc(NC(C)(C)C)nc(SC)n1 1079 | Testosterone,-4.02,-3.659,CC12CCC3C(CCC4=CC(=O)CCC34C)C2CCC1O 1080 | testosterone acetate,-5.184,-4.449,CC(=O)OC3CCC4C2CCC1=CC(=O)CCC1(C)C2CCC34C 1081 | testosterone propionate,-5.37,-4.87,CCC(=O)OC3CCC4C2CCC1=CC(=O)CCC1(C)C2CCC34C 1082 | Tetrabromomethane,-3.14,-4.063,BrC(Br)(Br)Br 1083 | Tetrachloroethylene,-2.54,-3.063,ClC(=C(Cl)Cl)Cl 1084 | tetrachloroguaiacol,-4.02,-4.299,COc1c(O)c(Cl)c(Cl)c(Cl)c1Cl 1085 | Tetrachloromethane,-2.31,-2.607,ClC(Cl)(Cl)Cl 1086 | Tetradecane,-7.96,-5.45,CCCCCCCCCCCCCC 1087 | Tetrafluthrin,-7.321,-6.339,Cc1c(F)c(F)c(COC(=O)C2C(C=C(Cl)C(F)(F)F)C2(C)C)c(F)c1F 1088 | Tetrahydrofurane ,0.49,-0.62,C1CCOC1 1089 | Tetrahydropyran ,-0.03,-0.978,C1CCOCC1 1090 | tetramethylurea,0.94,-0.495,CN(C)C(=O)N(C)C 1091 | Thalidomide,-2.676,-1.944,O=C1N(C2CCC(=O)NC2=O)C(=O)c3ccccc13 1092 | theobromine,-2.523,-1.05,Cn1cnc2n(C)c(=O)[nH]c(=O)c12 1093 | Theophylline,-1.39,-1.452,Cn1c(=O)n(C)c2nc[nH]c2c1=O 1094 | Thiamphenicol,-2.154,-1.936,CS(=O)(=O)c1ccc(cc1)C(O)C(CO)NC(=O)C(Cl)Cl 1095 | thiamylal,-3.46,-3.063,CCCC(C)C1(CC=C)C(=O)NC(=S)NC1=O 1096 | thioanisole,-2.39,-2.87,c1ccccc1SC 1097 | thiofanox,-1.62,-2.7,CNC(=O)ON=C(CSC)C(C)(C)C 1098 | Thiometon,-3.091,-3.323,CCSCCSP(=S)(OC)OC 1099 | thiopental,-3.36,-2.96,CCCC(C)C1(CC)C(=O)NC(=S)NC1=O 1100 | Thiophene,-1.33,-2.232,c1ccsc1 1101 | Thiophenol ,-2.12,-2.758,Sc1ccccc1 1102 | thiouracil,-2.273,-0.992,Sc1nccc(=O)[nH]1 1103 | Thiourea,0.32,0.329,NC(=S)N 1104 | Thiram,-3.9,-2.444,CN(C)C(=S)SSC(=S)N(C)C 1105 | thymine,-1.506,-0.78,Cc1c[nH]c(=O)[nH]c1=O 1106 | Thymol,-2.22,-3.129,CC(C)c1ccc(C)cc1O 1107 | Toluene ,-2.21,-2.713,Cc1ccccc1 1108 | t-Pentylbenzene,-4.15,-3.867,CC(C)(C)Cc1ccccc1 1109 | "trans-1,4-Dimethylcyclohexane",-4.47,-3.305,C/C1CCC(\C)CC1 1110 | trans-2-Heptene ,-3.82,-2.784,CCCC/C=C/C 1111 | trans-2-Pentene ,-2.54,-2.076,CC/C=C/C 1112 | Triadimefon,-3.61,-4.132,CC(C)(C)C(=O)C(Oc1ccc(Cl)cc1)n2cncn2 1113 | Triallate,-4.88,-4.578,CC(C)N(C(C)C)C(=O)SCC(Cl)=C(Cl)Cl 1114 | Triamcinolone,-3.68,-2.734,CC34CC(O)C1(F)C(CCC2=CC(=O)C=CC12C)C3CC(O)C4(O)C(=O)CO 1115 | triamcinolone acetonide,-4.31,-3.928,CC5(C)OC4CC3C2CCC1=CC(=O)C=CC1(C)C2(F)C(O)CC3(C)C4(O5)C(=O)CO 1116 | triamcinolone diacetate,-4.13,-3.876,CC(=O)OCC(=O)C3(O)C(CC4C2CCC1=CC(=O)C=CC1(C)C2(F)C(O)CC34C)OC(C)=O 1117 | Triamterene,-2.404,-3.051,Nc3nc(N)c2nc(c1ccccc1)c(N)nc2n3 1118 | Triazolam,-4.09,-3.948,Cc3nnc4CN=C(c1ccccc1Cl)c2cc(Cl)ccc2n34 1119 | Tribromomethane,-1.91,-2.904,BrC(Br)Br 1120 | Trichlomethiazide,-2.68,-2.98,NS(=O)(=O)c2cc1c(NC(NS1(=O)=O)C(Cl)Cl)cc2Cl 1121 | Trichlorfon,-0.22,-1.866,COP(=O)(OC)C(O)C(Cl)(Cl)Cl 1122 | trichlormethiazide,-2.68,-2.98,NS(=O)(=O)c2cc1c(NC(NS1(=O)=O)C(Cl)Cl)cc2Cl 1123 | Trichloroacetonitrile,-2.168,-2.019,ClC(Cl)(Cl)C#N 1124 | Trichloroethylene,-1.96,-2.312,ClC=C(Cl)Cl 1125 | Trichloromethane,-1.17,-1.812,ClC(Cl)Cl 1126 | Trichloronate,-5.752,-5.225,CCOP(=S)(CC)Oc1cc(Cl)c(Cl)cc1Cl 1127 | Triclosan,-4.46,-5.645,Oc1cc(Cl)ccc1Oc2ccc(Cl)cc2Cl 1128 | Tricresyl phosphate,-6.01,-6.39,Cc1ccc(OP(=O)(Oc2cccc(C)c2)Oc3ccccc3C)cc1 1129 | Tricyclazole,-2.07,-2.868,Cc2cccc3sc1nncn1c23 1130 | Trietazine,-4.06,-3.233,CCNc1nc(Cl)nc(n1)N(CC)CC 1131 | Triethyl phosphate,0.43,-0.953,CCOP(=O)(OCC)OCC 1132 | Trifluralin,-5.68,-5.205,CCCN(CCC)c1c(cc(cc1N(=O)=O)C(F)(F)F)N(=O)=O 1133 | triforine,-4.19,-3.715,ClC(Cl)(Cl)C(NC=O)N1C=CN(C=C1)C(NC=O)C(Cl)(Cl)Cl 1134 | Trimazosin,-3.638,-3.958,COc2cc1c(N)nc(nc1c(OC)c2OC)N3CCN(CC3)C(=O)OCC(C)(C)O 1135 | Triphenylene,-6.726,-5.568,c1ccc2c(c1)c3ccccc3c4ccccc24 1136 | tubercidin,-1.95,-0.892,Nc1ncnc2n(ccc12)C3OC(CO)C(O)C3O 1137 | uracil,-1.488,-0.441,O=c1cc[nH]c(=O)[nH]1 1138 | Urea,0.96,0.832,NC(=O)N 1139 | uric acid,-3.93,-0.541,O=c2[nH]c(=O)c1[nH]c(=O)[nH]c1[nH]2 1140 | Valeraldehyde,-0.85,-1.103,CCCCC=O 1141 | vamidothion,1.144,-1.446,CNC(=O)C(C)SCCSP(=O)(OC)(OC) 1142 | Vinclozolin,-4.925,-4.377,CC1(OC(=O)N(C1=O)c2cc(Cl)cc(Cl)c2)C=C 1143 | Warfarin,-3.893,-3.913,CC(=O)CC(c1ccccc1)c3c(O)c2ccccc2oc3=O 1144 | Xipamide,-3.79,-3.642,Cc1cccc(C)c1NC(=O)c2cc(c(Cl)cc2O)S(N)(=O)=O 1145 | XMC,-2.581,-2.688,CNC(=O)Oc1cc(C)cc(C)c1 1146 | --------------------------------------------------------------------------------