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fixing tutorials
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@ale94mleon
ale94mleon committed Jul 30, 2022
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48 changes: 25 additions & 23 deletions docs/notebooks/how_to.ipynb
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"source": [
"# Import section\n",
"from moldrug.data import ligands, boxes, receptors\n",
"from rdkit import Chem\n",
"import tempfile, os, requests,inspect, gzip, shutil, yaml, sys\n",
"from moldrug import utils\n",
"from typing import List\n",
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"text": [
"COC(=O)C=1C=CC(=CC1)S(=O)(=O)N\n",
"{'A': {'boxcenter': [12.11, 1.84, 23.56], 'boxsize': [22.5, 22.5, 22.5]}}\n",
"/tmp/tmpnlx1gpp8 ['crem.db.gz', 'x0161.pdbqt', 'crem.db']\n"
"/tmp/tmp0n8w1rkf ['crem.db.gz', 'x0161.pdbqt', 'crem.db']\n"
]
}
],
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"data": {
"text/plain": [
"['self',\n",
" 'mol',\n",
" 'seed_mol',\n",
" 'crem_db_path',\n",
" 'costfunc',\n",
" 'grow_crem_kwargs',\n",
" 'costfunc_kwargs']"
" 'costfunc_kwargs',\n",
" 'AddHs']"
]
},
"execution_count": 4,
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" type: Local\n",
" njobs: 1\n",
" pick: 1\n",
" mol: COC(=O)C=1C=CC(=CC1)S(=O)(=O)N\n",
" AddHs: False\n",
" seed_mol: COC(=O)C=1C=CC(=CC1)S(=O)(=O)N\n",
" costfunc: Cost\n",
" costfunc_kwargs:\n",
" vina_executable: vina\n",
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" type: Local\n",
" njobs: 1\n",
" pick: 1\n",
" AddHs: False\n",
"```\n",
"\n",
"Look how this section is inside of `main` (one indentation level). `type` is the name of the class inside `moldrug.utils`; for now could be `GA` or `Local` (case insensitive). In this case we want to use the class `Local`. `njobs` and `pick` are the parameters when the class `Local` (or `GA`) is call. The rest of the parameters are just the parameters that needs `Local` for the initialization. All of them are at the same level of the previous ones. Because `costfunc_kwargs` is a dictionary; we add for its value a new indentation level:\n",
"Look how this section is inside of `main` (one indentation level). `type` is the name of the class inside `moldrug.utils`; for now could be `GA` or `Local` (case insensitive). In this case we want to use the class `Local`. `njobs`, `pick` and `AddHs` are the parameters when the class `Local` (or `GA`) is call. The rest of the parameters are just the parameters that needs `Local` for the initialization. All of them are at the same level of the previous ones. Because `costfunc_kwargs` is a dictionary; we add for its value a new indentation level:\n",
"\n",
"```yaml\n",
" costfunc_kwargs:\n",
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" \"type\": \"Local\",\n",
" \"njobs\": 1,\n",
" \"pick\": 1,\n",
" \"mol\": lig,\n",
" \"seed_mol\": lig,\n",
" \"costfunc\": \"Cost\",\n",
" \"costfunc_kwargs\": {\n",
" \"vina_executable\": \"vina\",\n",
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"text": [
"The main job is being executed.\n",
"Calculating cost function...\n",
"100%|█████████████████████████████████████████████| 2/2 [00:06<00:00, 3.35s/it]\n",
"100%|█████████████████████████████████████████████| 2/2 [00:06<00:00, 3.20s/it]\n",
"File local_pop.sdf was createad!\n",
"The main job finished!.\n"
]
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"text": [
"The main job is being executed.\n",
"Calculating cost function...\n",
"100%|█████████████████████████████████████████████| 2/2 [00:05<00:00, 2.68s/it]\n",
"100%|█████████████████████████████████████████████| 2/2 [00:05<00:00, 2.76s/it]\n",
"File local_pop.sdf was createad!\n",
"The main job finished!.\n"
]
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{
"data": {
"text/plain": [
"<moldrug.utils.Local at 0x7f389d6358b0>"
"<moldrug.utils.Local at 0x7f47ac62c940>"
]
},
"execution_count": 11,
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"data": {
"text/plain": [
"['/home/ale/GITLAB/moldrug/docs/notebooks',\n",
" '/home/ale/.vscode/extensions/ms-toolsai.jupyter-2022.6.1201981810/pythonFiles',\n",
" '/home/ale/.vscode/extensions/ms-toolsai.jupyter-2022.6.1201981810/pythonFiles/lib/python',\n",
" '/home/ale/anaconda3/envs/moldrug/lib/python39.zip',\n",
" '/home/ale/anaconda3/envs/moldrug/lib/python3.9',\n",
" '/home/ale/anaconda3/envs/moldrug/lib/python3.9/lib-dynload',\n",
" '',\n",
" '/home/ale/anaconda3/envs/moldrug/lib/python3.9/site-packages',\n",
" '/home/ale/GITLAB/moldrug',\n",
" '/tmp/tmpnlx1gpp8/custom_fitness']"
" '/tmp/tmp0n8w1rkf/custom_fitness']"
]
},
"execution_count": 14,
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"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 20/20 [00:00<00:00, 1060.01it/s]"
"100%|██████████| 20/20 [00:00<00:00, 1313.31it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Initial Population: Best individual: Individual(idx = 6, smiles = CC(C)(C)OC(=O)NO, cost = 0.14332947497346815)\n"
"Initial Population: Best individual: Individual(idx = 6, smiles = CCCCCCC=CCO, cost = 0.04045062715899039)\n"
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 20/20 [00:00<00:00, 995.33it/s]"
"100%|██████████| 20/20 [00:00<00:00, 606.98it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Generation 1: Best Individual: Individual(idx = 38, smiles = C=COCC, cost = 0.05195477634991308).\n",
"Generation 1: Best Individual: Individual(idx = 22, smiles = C#CC1(O)CCCCCCCC1, cost = 0.03751898267200682).\n",
"\n"
]
},
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"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 20/20 [00:00<00:00, 377.88it/s]"
"100%|██████████| 20/20 [00:00<00:00, 798.06it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Generation 2: Best Individual: Individual(idx = 44, smiles = CCOC(=O)N(C)N=NC, cost = 0.015742754415312588).\n",
"Generation 2: Best Individual: Individual(idx = 22, smiles = C#CC1(O)CCCCCCCC1, cost = 0.03751898267200682).\n",
"\n",
"\n",
"=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+\n",
"\n",
"The simulation finished successfully after 2 generations with a population of 20 individuals. A total number of 60 Individuals were seen during the simulation.\n",
"Initial Individual: Individual(idx = 0, smiles = CCCC(=O)OCCN, cost = 0.8568098985747594)\n",
"Final Individual: Individual(idx = 44, smiles = CCOC(=O)N(C)N=NC, cost = 0.015742754415312588)\n",
"The cost function droped in 0.8410671441594468 units.\n",
"Initial Individual: Individual(idx = 0, smiles = CCCC(=O)OCCN, cost = 0.6813211889306405)\n",
"Final Individual: Individual(idx = 22, smiles = C#CC1(O)CCCCCCCC1, cost = 0.03751898267200682)\n",
"The cost function droped in 0.6438022062586337 units.\n",
"\n",
"=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+\n",
"\n",
"'__call__' 86780.44 ms\n"
"'__call__' 92583.43 ms\n"
]
},
{
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" return Individual\n",
"\n",
"ga = utils.GA(\n",
" 'CCCC(=O)OCCN',\n",
" Chem.MolFromSmiles('CCCC(=O)OCCN'),\n",
" crem_db_path = os.path.join(tmp_path.name, 'crem.db'),\n",
" maxiter = 2,\n",
" popsize = 20,\n",
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