non-specific_filter.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "6d002df7",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterCatalogEntry const> already registered; second conversion method ignored.\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "from pandas import DataFrame\n",
    "\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import Descriptors\n",
    "from rdkit.Chem.FilterCatalog import FilterCatalog, FilterCatalogParams\n",
    "\n",
    "from sklearn.preprocessing import FunctionTransformer\n",
    "\n",
    "from tqdm.auto import tqdm\n",
    "\n",
    "from scopy.ScoTox import Toxfilter\n",
    "\n",
    "from itertools import groupby"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "26ae4a41",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Количество молекул = 20323\n"
     ]
    }
   ],
   "source": [
    "molecules = [mol for mol in Chem.SDMolSupplier(\"Adenosine_20323.sdf\") if mol is not None]\n",
    "print(f'Количество молекул = {len(molecules)}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "b4a4351b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'SMILES': 'CCOC(=O)c1c(C)[nH]c(C)c1S(=O)(=O)NCC1CCN(Cc2ccccc2OC)CC1', 'Disposed': 'Rejected', 'MatchedAtoms': [((0, 1, 4, 5, 3),)], 'MatchedNames': ['pyrrole'], 'Endpoint': 'Toxicophores'}, {'SMILES': 'Cc1oc2ncn(C)c(=O)c2c1C(=O)N(Cc1ccccc1)C(C)C', 'Disposed': 'Rejected', 'MatchedAtoms': [((2, 0, 1, 5, 7),)], 'MatchedNames': ['furan'], 'Endpoint': 'Toxicophores'}, {'SMILES': 'COC(=O)c1ccccc1NC(=O)CCCn1nc(C)c2c(C)n(-c3ccccc3)nc2c1=O', 'Disposed': 'Rejected', 'MatchedAtoms': [((3, 15, 26, 31, 33, 32, 27), (12, 10, 9, 22, 29, 30, 24))], 'MatchedNames': ['masked_aniline'], 'Endpoint': 'Toxicophores'}, {'SMILES': 'CCOC(=O)c1cccc(NC(=O)CCCn2nc(C)c3c(C)n(-c4ccccc4)nc3c2=O)c1', 'Disposed': 'Rejected', 'MatchedAtoms': [((3, 12, 28, 33, 34, 32, 29), (14, 16, 15, 10, 25, 26, 27))], 'MatchedNames': ['masked_aniline'], 'Endpoint': 'Toxicophores'}, {'SMILES': 'CCOC(=O)CNC(=O)c1cc2c(=O)oc3ccccc3c2s1', 'Disposed': 'Rejected', 'MatchedAtoms': [((11, 3, 0, 1, 6, 17, 20, 21, 18, 8, 7),), ((2, 1, 0, 5, 4),)], 'MatchedNames': ['coumarines', 'thiophene'], 'Endpoint': 'Toxicophores'}, {'SMILES': 'COc1ccc(NC(=O)C(C)n2c(C)c3cnn(-c4ccccc4)c(=O)c3c2C)cc1Cl', 'Disposed': 'Rejected', 'MatchedAtoms': [((6, 15, 26, 29, 31, 30, 27), (11, 16, 14, 12, 18, 19, 23)), ((0, 1, 5, 2, 4),)], 'MatchedNames': ['masked_aniline', 'pyrrole'], 'Endpoint': 'Toxicophores'}]\n"
     ]
    }
   ],
   "source": [
    "Filter = Toxfilter(molecules, detail=True, showSMILES=True)\n",
    "filter_result = Filter.Check_Toxicophores()\n",
    "print(filter_result[0:6])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "0a1ee76d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Accepted 2361\n",
      "Rejected 17962\n"
     ]
    }
   ],
   "source": [
    "filter_result_groupby = groupby(sorted(filter_result, key=lambda x: x['Disposed']), lambda x: x['Disposed'])\n",
    "for k, g in filter_result_groupby:\n",
    "     print(k, len(list(g)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8364a8d4",
   "metadata": {},
   "outputs": [],
   "source": [
    "disposed_status = []\n",
    "for mol in filter_result:\n",
    "    disposed_status.append(mol.get('Disposed'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9c7dfb1f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "20323\n"
     ]
    }
   ],
   "source": [
    "# это ужасный велосипед, который и сейчас кажется мне сущим кошмаром, но он сработал\n",
    "\n",
    "SMILES = []\n",
    "index_list = []\n",
    "i = 0\n",
    "\n",
    "with open('Adenosine_20323.sdf', 'r', encoding='utf-8') as f:\n",
    "    for index, line in enumerate(f):\n",
    "        if \"<Smile>\" in line:\n",
    "            index_list.append(index)\n",
    "\n",
    "SMILES_index = [x+1 for x in index_list]\n",
    "\n",
    "with open('Adenosine_20323.sdf', 'r', encoding='utf-8') as f:\n",
    "    for index, line in enumerate(f):\n",
    "        if index in SMILES_index:\n",
    "            SMILES.append(line)\n",
    "\n",
    "SMILES = [s.rstrip() for s in SMILES]\n",
    "print(len(SMILES))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "94fcce7f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# создаем словарь из дескриторов структуры\n",
    "ConstDescriptors = {\"HeavyAtomCount\": Descriptors.HeavyAtomCount,\n",
    "                    \"NHOHCount\": Descriptors.NHOHCount,\n",
    "                    \"NOCount\": Descriptors.NOCount,\n",
    "                    \"NumHAcceptors\": Descriptors.NumHAcceptors,\n",
    "                    \"NumHDonors\": Descriptors.NumHDonors,\n",
    "                    \"NumHeteroatoms\": Descriptors.NumHeteroatoms,\n",
    "                    \"NumRotatableBonds\": Descriptors.NumRotatableBonds,\n",
    "                    \"NumValenceElectrons\": Descriptors.NumValenceElectrons,\n",
    "                    \"NumAromaticRings\": Descriptors.NumAromaticRings,\n",
    "                    \"NumAliphaticHeterocycles\": Descriptors.NumAliphaticHeterocycles,\n",
    "                    \"RingCount\": Descriptors.RingCount}\n",
    "\n",
    "# создаем словарь из физико-химических дескрипторов                            \n",
    "PhisChemDescriptors = {\"MW\": Descriptors.MolWt,\n",
    "                       \"LogP\": Descriptors.MolLogP,\n",
    "                       \"MR\": Descriptors.MolMR,\n",
    "                       \"TPSA\": Descriptors.TPSA}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "71e07241",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Количество дескрипторов в словаре: 15\n"
     ]
    }
   ],
   "source": [
    "# объединяем все дескрипторы в один словарь\n",
    "descriptors = {}\n",
    "descriptors.update(ConstDescriptors)\n",
    "descriptors.update(PhisChemDescriptors)\n",
    "print(f\"Количество дескрипторов в словаре: {len(descriptors)}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "19455e07",
   "metadata": {},
   "outputs": [],
   "source": [
    "# функция для генерации дескрипторов из молекул\n",
    "def mol_dsc_calc(mols): \n",
    "    return DataFrame({k: f(m) for k, f in descriptors.items()} \n",
    "             for m in mols)\n",
    "\n",
    "# оформляем sklearn трансформер для использования в конвеерном моделировании (sklearn Pipeline)\n",
    "descriptors_transformer = FunctionTransformer(mol_dsc_calc, validate=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "f1ef1d06",
   "metadata": {},
   "outputs": [],
   "source": [
    "X = descriptors_transformer.transform(molecules)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "b0a1ce0a",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>HeavyAtomCount</th>\n",
       "      <th>NHOHCount</th>\n",
       "      <th>NOCount</th>\n",
       "      <th>NumHAcceptors</th>\n",
       "      <th>NumHDonors</th>\n",
       "      <th>NumHeteroatoms</th>\n",
       "      <th>NumRotatableBonds</th>\n",
       "      <th>NumValenceElectrons</th>\n",
       "      <th>NumAromaticRings</th>\n",
       "      <th>NumAliphaticHeterocycles</th>\n",
       "      <th>RingCount</th>\n",
       "      <th>MW</th>\n",
       "      <th>LogP</th>\n",
       "      <th>MR</th>\n",
       "      <th>TPSA</th>\n",
       "      <th>smiles</th>\n",
       "      <th>disposed_status</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>32</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>6</td>\n",
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       "      <td>9</td>\n",
       "      <td>9</td>\n",
       "      <td>176</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>463.600</td>\n",
       "      <td>3.00734</td>\n",
       "      <td>122.4067</td>\n",
       "      <td>100.73</td>\n",
       "      <td>c1(c(c([nH]c1C)C)C(=O)OCC)S(NCC1CCN(Cc2c(OC)cc...</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>25</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>4</td>\n",
       "      <td>130</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>339.395</td>\n",
       "      <td>2.88572</td>\n",
       "      <td>95.4385</td>\n",
       "      <td>68.34</td>\n",
       "      <td>c12c(C(N(Cc3ccccc3)C(C)C)=O)c(oc1\\N=C/N(C2=O)C)C</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>34</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>7</td>\n",
       "      <td>174</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>459.506</td>\n",
       "      <td>3.40454</td>\n",
       "      <td>128.2442</td>\n",
       "      <td>108.11</td>\n",
       "      <td>c12c(c(n(n1)c1ccccc1)C)\\C(=N/N(C2=O)CCCC(Nc1c(...</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>35</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>180</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>473.533</td>\n",
       "      <td>3.79464</td>\n",
       "      <td>132.8612</td>\n",
       "      <td>108.11</td>\n",
       "      <td>c12c(c(n(n1)c1ccccc1)C)\\C(=N/N(C2=O)CCCC(Nc1cc...</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>23</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4</td>\n",
       "      <td>118</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>331.349</td>\n",
       "      <td>2.30060</td>\n",
       "      <td>86.8332</td>\n",
       "      <td>85.61</td>\n",
       "      <td>CCOC(CNC(C1SC2=C(C=1)C(Oc1c2cccc1)=O)=O)=O</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20318</th>\n",
       "      <td>22</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>4</td>\n",
       "      <td>112</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>316.357</td>\n",
       "      <td>4.08640</td>\n",
       "      <td>85.1422</td>\n",
       "      <td>51.22</td>\n",
       "      <td>c1cc(c(C(NC2Sc3c(N=2)ccc(c3)OCC)=O)cc1)F</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20319</th>\n",
       "      <td>24</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>3</td>\n",
       "      <td>120</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>357.416</td>\n",
       "      <td>3.09479</td>\n",
       "      <td>94.1129</td>\n",
       "      <td>79.51</td>\n",
       "      <td>c1cc2N3C(SC(=C3NC(c2cc1)=O)C(NCC1OC=CC=1)=O)=S</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20320</th>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>5</td>\n",
       "      <td>138</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>417.537</td>\n",
       "      <td>4.34999</td>\n",
       "      <td>110.1840</td>\n",
       "      <td>62.19</td>\n",
       "      <td>c1cc(c(N2c3[nH0]c([nH0](CC4OC=CC=4)c(c3SC2=S)=...</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20321</th>\n",
       "      <td>29</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>152</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>428.579</td>\n",
       "      <td>5.11890</td>\n",
       "      <td>119.2662</td>\n",
       "      <td>60.33</td>\n",
       "      <td>CCOC(C1=C(NC(=O)CSc2c[nH0](CC)c3c2cccc3)SC2=C1...</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20322</th>\n",
       "      <td>38</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>11</td>\n",
       "      <td>7</td>\n",
       "      <td>190</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>542.646</td>\n",
       "      <td>4.64890</td>\n",
       "      <td>148.2637</td>\n",
       "      <td>105.47</td>\n",
       "      <td>c1ccc([nH0]2c3[nH0]c([nH]c(c3c[nH0]2)=O)SCC(N2...</td>\n",
       "      <td>Rejected</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20323 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       HeavyAtomCount  NHOHCount  NOCount  NumHAcceptors  NumHDonors  \\\n",
       "0                  32          2        8              6           2   \n",
       "1                  25          0        6              5           0   \n",
       "2                  34          1        9              8           1   \n",
       "3                  35          1        9              8           1   \n",
       "4                  23          1        6              6           1   \n",
       "...               ...        ...      ...            ...         ...   \n",
       "20318              22          1        4              4           1   \n",
       "20319              24          2        6              6           2   \n",
       "20320              27          0        6              9           0   \n",
       "20321              29          1        5              6           1   \n",
       "20322              38          1        9              9           1   \n",
       "\n",
       "       NumHeteroatoms  NumRotatableBonds  NumValenceElectrons  \\\n",
       "0                   9                  9                  176   \n",
       "1                   6                  4                  130   \n",
       "2                   9                  7                  174   \n",
       "3                   9                  8                  180   \n",
       "4                   7                  4                  118   \n",
       "...               ...                ...                  ...   \n",
       "20318               6                  4                  112   \n",
       "20319               8                  3                  120   \n",
       "20320               9                  5                  138   \n",
       "20321               7                  7                  152   \n",
       "20322              11                  7                  190   \n",
       "\n",
       "       NumAromaticRings  NumAliphaticHeterocycles  RingCount       MW  \\\n",
       "0                     2                         1          3  463.600   \n",
       "1                     3                         0          3  339.395   \n",
       "2                     4                         0          4  459.506   \n",
       "3                     4                         0          4  473.533   \n",
       "4                     3                         0          3  331.349   \n",
       "...                 ...                       ...        ...      ...   \n",
       "20318                 3                         0          3  316.357   \n",
       "20319                 4                         0          4  357.416   \n",
       "20320                 4                         0          4  417.537   \n",
       "20321                 3                         0          4  428.579   \n",
       "20322                 5                         1          6  542.646   \n",
       "\n",
       "          LogP        MR    TPSA  \\\n",
       "0      3.00734  122.4067  100.73   \n",
       "1      2.88572   95.4385   68.34   \n",
       "2      3.40454  128.2442  108.11   \n",
       "3      3.79464  132.8612  108.11   \n",
       "4      2.30060   86.8332   85.61   \n",
       "...        ...       ...     ...   \n",
       "20318  4.08640   85.1422   51.22   \n",
       "20319  3.09479   94.1129   79.51   \n",
       "20320  4.34999  110.1840   62.19   \n",
       "20321  5.11890  119.2662   60.33   \n",
       "20322  4.64890  148.2637  105.47   \n",
       "\n",
       "                                                  smiles disposed_status  \n",
       "0      c1(c(c([nH]c1C)C)C(=O)OCC)S(NCC1CCN(Cc2c(OC)cc...        Rejected  \n",
       "1       c12c(C(N(Cc3ccccc3)C(C)C)=O)c(oc1\\N=C/N(C2=O)C)C        Rejected  \n",
       "2      c12c(c(n(n1)c1ccccc1)C)\\C(=N/N(C2=O)CCCC(Nc1c(...        Rejected  \n",
       "3      c12c(c(n(n1)c1ccccc1)C)\\C(=N/N(C2=O)CCCC(Nc1cc...        Rejected  \n",
       "4             CCOC(CNC(C1SC2=C(C=1)C(Oc1c2cccc1)=O)=O)=O        Rejected  \n",
       "...                                                  ...             ...  \n",
       "20318           c1cc(c(C(NC2Sc3c(N=2)ccc(c3)OCC)=O)cc1)F        Rejected  \n",
       "20319     c1cc2N3C(SC(=C3NC(c2cc1)=O)C(NCC1OC=CC=1)=O)=S        Rejected  \n",
       "20320  c1cc(c(N2c3[nH0]c([nH0](CC4OC=CC=4)c(c3SC2=S)=...        Rejected  \n",
       "20321  CCOC(C1=C(NC(=O)CSc2c[nH0](CC)c3c2cccc3)SC2=C1...        Rejected  \n",
       "20322  c1ccc([nH0]2c3[nH0]c([nH]c(c3c[nH0]2)=O)SCC(N2...        Rejected  \n",
       "\n",
       "[20323 rows x 17 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X['smiles'] = SMILES\n",
    "X['disposed_status'] = disposed_status\n",
    "X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "d5012ed0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Rejected    17962\n",
       "Accepted     2361\n",
       "Name: disposed_status, dtype: int64"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X['disposed_status'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "9736d5d6",
   "metadata": {},
   "outputs": [],
   "source": [
    "filtered_molecules = X.loc[(X.NumHDonors < 5) & (X.MW < 500) & (X.LogP < 5) & \n",
    "                           (X.NumHAcceptors < 10) & (X.NumRotatableBonds < 10) & (X.RingCount > 0) &\n",
    "                           (X.disposed_status == 'Accepted')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "af3cd8e6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>HeavyAtomCount</th>\n",
       "      <th>NHOHCount</th>\n",
       "      <th>NOCount</th>\n",
       "      <th>NumHAcceptors</th>\n",
       "      <th>NumHDonors</th>\n",
       "      <th>NumHeteroatoms</th>\n",
       "      <th>NumRotatableBonds</th>\n",
       "      <th>NumValenceElectrons</th>\n",
       "      <th>NumAromaticRings</th>\n",
       "      <th>NumAliphaticHeterocycles</th>\n",
       "      <th>RingCount</th>\n",
       "      <th>MW</th>\n",
       "      <th>LogP</th>\n",
       "      <th>MR</th>\n",
       "      <th>TPSA</th>\n",
       "      <th>smiles</th>\n",
       "      <th>disposed_status</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>24</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>124</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>342.830</td>\n",
       "      <td>4.92880</td>\n",
       "      <td>95.0877</td>\n",
       "      <td>63.84</td>\n",
       "      <td>CC1CCC(Nc2c3c(ON=C3c3ccc(Cl)cc3)[nH0]c[nH0]2)CC1</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>24</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>6</td>\n",
       "      <td>130</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>336.348</td>\n",
       "      <td>0.78432</td>\n",
       "      <td>84.6532</td>\n",
       "      <td>116.32</td>\n",
       "      <td>c12c(\\N=C(/N(C1=O)CC(NC(CC)C)=O)\\C)onc2C(=O)OCC</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>8</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>10</td>\n",
       "      <td>6</td>\n",
       "      <td>152</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>410.384</td>\n",
       "      <td>1.63090</td>\n",
       "      <td>103.3317</td>\n",
       "      <td>94.70</td>\n",
       "      <td>c1c(CNC(C[nH0]2c(c3c([nH0]c2)[nH0]([nH0][nH0]3...</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>84</th>\n",
       "      <td>28</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4</td>\n",
       "      <td>150</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>383.496</td>\n",
       "      <td>3.20492</td>\n",
       "      <td>106.7257</td>\n",
       "      <td>74.50</td>\n",
       "      <td>n1c(noc1c1ccc(cc1)C)CN1CCN(C(NC2CCCCC2)=O)CC1</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>85</th>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>8</td>\n",
       "      <td>144</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>369.465</td>\n",
       "      <td>4.24550</td>\n",
       "      <td>103.4957</td>\n",
       "      <td>77.25</td>\n",
       "      <td>n1c(noc1c1ccc(OCC(=O)NCC/C/2=C/CCCC2)cc1)C(C)C</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20254</th>\n",
       "      <td>22</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>4</td>\n",
       "      <td>114</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>296.378</td>\n",
       "      <td>2.34982</td>\n",
       "      <td>89.1367</td>\n",
       "      <td>58.87</td>\n",
       "      <td>Cc1cc(CNc2[nH0]c([nH0]c3c2c[nH0][nH0]3C)N(C)C)...</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20282</th>\n",
       "      <td>25</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>4</td>\n",
       "      <td>130</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>338.415</td>\n",
       "      <td>2.12042</td>\n",
       "      <td>97.8417</td>\n",
       "      <td>68.10</td>\n",
       "      <td>Cc1ccc(CNc2[nH0]c([nH0]c3c2c[nH0][nH0]3C)N2CCO...</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20283</th>\n",
       "      <td>25</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>128</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>357.797</td>\n",
       "      <td>3.25750</td>\n",
       "      <td>93.2887</td>\n",
       "      <td>77.25</td>\n",
       "      <td>n1c(onc1CNC(=O)Cc1cc(OC)ccc1)c1cc(Cl)ccc1</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20285</th>\n",
       "      <td>25</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>8</td>\n",
       "      <td>132</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>340.431</td>\n",
       "      <td>2.73222</td>\n",
       "      <td>99.7924</td>\n",
       "      <td>76.89</td>\n",
       "      <td>c1cc(CNc2c3c([nH0]([nH0]c3)C)[nH0]c([nH0]2)NCC...</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20316</th>\n",
       "      <td>28</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>148</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>379.512</td>\n",
       "      <td>2.81582</td>\n",
       "      <td>113.7537</td>\n",
       "      <td>62.11</td>\n",
       "      <td>CCCN1CCN(c2[nH0]c3c(c([nH0]2)NCc2ccc(C)cc2)c[n...</td>\n",
       "      <td>Accepted</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2138 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       HeavyAtomCount  NHOHCount  NOCount  NumHAcceptors  NumHDonors  \\\n",
       "18                 24          1        5              5           1   \n",
       "46                 24          1        9              8           1   \n",
       "56                 30          1        8              7           1   \n",
       "84                 28          1        7              5           1   \n",
       "85                 27          1        6              5           1   \n",
       "...               ...        ...      ...            ...         ...   \n",
       "20254              22          1        6              6           1   \n",
       "20282              25          1        7              7           1   \n",
       "20283              25          1        6              5           1   \n",
       "20285              25          2        7              7           2   \n",
       "20316              28          1        7              7           1   \n",
       "\n",
       "       NumHeteroatoms  NumRotatableBonds  NumValenceElectrons  \\\n",
       "18                  6                  3                  124   \n",
       "46                  9                  6                  130   \n",
       "56                 10                  6                  152   \n",
       "84                  7                  4                  150   \n",
       "85                  6                  8                  144   \n",
       "...               ...                ...                  ...   \n",
       "20254               6                  4                  114   \n",
       "20282               7                  4                  130   \n",
       "20283               7                  6                  128   \n",
       "20285               7                  8                  132   \n",
       "20316               7                  6                  148   \n",
       "\n",
       "       NumAromaticRings  NumAliphaticHeterocycles  RingCount       MW  \\\n",
       "18                    3                         0          4  342.830   \n",
       "46                    2                         0          2  336.348   \n",
       "56                    4                         0          4  410.384   \n",
       "84                    2                         1          4  383.496   \n",
       "85                    2                         0          3  369.465   \n",
       "...                 ...                       ...        ...      ...   \n",
       "20254                 3                         0          3  296.378   \n",
       "20282                 3                         1          4  338.415   \n",
       "20283                 3                         0          3  357.797   \n",
       "20285                 3                         0          3  340.431   \n",
       "20316                 3                         1          4  379.512   \n",
       "\n",
       "          LogP        MR    TPSA  \\\n",
       "18     4.92880   95.0877   63.84   \n",
       "46     0.78432   84.6532  116.32   \n",
       "56     1.63090  103.3317   94.70   \n",
       "84     3.20492  106.7257   74.50   \n",
       "85     4.24550  103.4957   77.25   \n",
       "...        ...       ...     ...   \n",
       "20254  2.34982   89.1367   58.87   \n",
       "20282  2.12042   97.8417   68.10   \n",
       "20283  3.25750   93.2887   77.25   \n",
       "20285  2.73222   99.7924   76.89   \n",
       "20316  2.81582  113.7537   62.11   \n",
       "\n",
       "                                                  smiles disposed_status  \n",
       "18      CC1CCC(Nc2c3c(ON=C3c3ccc(Cl)cc3)[nH0]c[nH0]2)CC1        Accepted  \n",
       "46       c12c(\\N=C(/N(C1=O)CC(NC(CC)C)=O)\\C)onc2C(=O)OCC        Accepted  \n",
       "56     c1c(CNC(C[nH0]2c(c3c([nH0]c2)[nH0]([nH0][nH0]3...        Accepted  \n",
       "84         n1c(noc1c1ccc(cc1)C)CN1CCN(C(NC2CCCCC2)=O)CC1        Accepted  \n",
       "85        n1c(noc1c1ccc(OCC(=O)NCC/C/2=C/CCCC2)cc1)C(C)C        Accepted  \n",
       "...                                                  ...             ...  \n",
       "20254  Cc1cc(CNc2[nH0]c([nH0]c3c2c[nH0][nH0]3C)N(C)C)...        Accepted  \n",
       "20282  Cc1ccc(CNc2[nH0]c([nH0]c3c2c[nH0][nH0]3C)N2CCO...        Accepted  \n",
       "20283          n1c(onc1CNC(=O)Cc1cc(OC)ccc1)c1cc(Cl)ccc1        Accepted  \n",
       "20285  c1cc(CNc2c3c([nH0]([nH0]c3)C)[nH0]c([nH0]2)NCC...        Accepted  \n",
       "20316  CCCN1CCN(c2[nH0]c3c(c([nH0]2)NCc2ccc(C)cc2)c[n...        Accepted  \n",
       "\n",
       "[2138 rows x 17 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_molecules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "8b90145c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2138\n"
     ]
    }
   ],
   "source": [
    "smiles_list = filtered_molecules['smiles'].tolist()\n",
    "print(len(smiles_list))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "3f42fc6c",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('accepted_smiles.txt', 'w', encoding='utf-8') as f:\n",
    "    for item in smiles_list:    \n",
    "        f.write(\"%s\\n\" % item)"
   ]
  }
 ],
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