3 CDD ML Descriptor Dataset Preparation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "f5436031",
   "metadata": {},
   "source": [
    "## Computational Drug Discovery - Descriptor Calculation and Dataset Preparation\n",
    "\n",
    "In this Jupyter notebook, I will be building a machine learning model using the ChEMBL bioactivity data.\n",
    "\n",
    "In **Part 3**, I will be calculating molecular descriptors that are quantitative descriptions of the compounds in the dataset. Then I will prepare this into a dataset for model building. \n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "96720fd8",
   "metadata": {},
   "source": [
    "### Download PaDEL-Descriptor"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "a43b9e48",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2023-02-20 19:01:43--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
      "Resolving github.com (github.com)... 140.82.114.3\n",
      "Connecting to github.com (github.com)|140.82.114.3|:443... connected.\n",
      "HTTP request sent, awaiting response... 302 Found\n",
      "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip [following]\n",
      "--2023-02-20 19:01:44--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.110.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 25768637 (25M) [application/zip]\n",
      "Saving to: ‘padel.zip’\n",
      "\n",
      "padel.zip           100%[===================>]  24.57M  24.9MB/s    in 1.0s    \n",
      "\n",
      "2023-02-20 19:01:45 (24.9 MB/s) - ‘padel.zip’ saved [25768637/25768637]\n",
      "\n",
      "--2023-02-20 19:01:45--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n",
      "Resolving github.com (github.com)... 140.82.114.3\n",
      "Connecting to github.com (github.com)|140.82.114.3|:443... connected.\n",
      "HTTP request sent, awaiting response... 302 Found\n",
      "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh [following]\n",
      "--2023-02-20 19:01:45--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.110.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 231 [text/plain]\n",
      "Saving to: ‘padel.sh’\n",
      "\n",
      "padel.sh            100%[===================>]     231  --.-KB/s    in 0s      \n",
      "\n",
      "2023-02-20 19:01:46 (8.16 MB/s) - ‘padel.sh’ saved [231/231]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
    "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "ad00de49",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Archive:  padel.zip\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  inflating: PaDEL-Descriptor/lib/cdk-1.4.15.jar  \n",
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      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(5).jar  \n"
     ]
    }
   ],
   "source": [
    "! unzip padel.zip"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c25c8149",
   "metadata": {},
   "source": [
    "## Load bioactivity data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "b152c62a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "6ca1e8f2",
   "metadata": {},
   "outputs": [],
   "source": [
    "df3 = pd.read_csv('data/beta_secretase_bioactivity_data_3class_pIC50.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "0f4616c4",
   "metadata": {},
   "outputs": [
    {
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       "      <th>molecule_chembl_id</th>\n",
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       "      <td>CCC(C)C[C@H](NC(=O)[C@H](CC(C)C)NC(C)=O)[C@@H]...</td>\n",
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       "      <td>8.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>6.337242</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>CHEMBL114147</td>\n",
       "      <td>CC(=O)NCC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)CC(=O)...</td>\n",
       "      <td>intermediate</td>\n",
       "      <td>737.895</td>\n",
       "      <td>1.9626</td>\n",
       "      <td>8.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.045757</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>CHEMBL419949</td>\n",
       "      <td>CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1ccccc1...</td>\n",
       "      <td>intermediate</td>\n",
       "      <td>828.020</td>\n",
       "      <td>3.5739</td>\n",
       "      <td>8.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.251812</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7229</th>\n",
       "      <td>7229</td>\n",
       "      <td>10419</td>\n",
       "      <td>CHEMBL4849016</td>\n",
       "      <td>CC[C@H](C)[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)N...</td>\n",
       "      <td>intermediate</td>\n",
       "      <td>623.861</td>\n",
       "      <td>2.3125</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.356547</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7230</th>\n",
       "      <td>7230</td>\n",
       "      <td>10420</td>\n",
       "      <td>CHEMBL4872824</td>\n",
       "      <td>CC[C@H](C)[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)N...</td>\n",
       "      <td>intermediate</td>\n",
       "      <td>637.888</td>\n",
       "      <td>2.7026</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.036212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7231</th>\n",
       "      <td>7231</td>\n",
       "      <td>10421</td>\n",
       "      <td>CHEMBL4853052</td>\n",
       "      <td>CC[C@H](C)[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)N...</td>\n",
       "      <td>inactive</td>\n",
       "      <td>651.915</td>\n",
       "      <td>3.0927</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7232</th>\n",
       "      <td>7232</td>\n",
       "      <td>10424</td>\n",
       "      <td>CHEMBL4862716</td>\n",
       "      <td>CC1=CC2Cc3nc4cc(Cl)ccc4c(NCCCCCCCCCNS(=O)(=O)c...</td>\n",
       "      <td>inactive</td>\n",
       "      <td>556.176</td>\n",
       "      <td>6.7284</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>4.966576</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7233</th>\n",
       "      <td>7233</td>\n",
       "      <td>10425</td>\n",
       "      <td>CHEMBL4859103</td>\n",
       "      <td>CC1=CC2Cc3nc4cc(Cl)ccc4c(NCCCCCCCCCNC(=O)c4cc(...</td>\n",
       "      <td>intermediate</td>\n",
       "      <td>562.154</td>\n",
       "      <td>7.8680</td>\n",
       "      <td>4.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.567031</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7234 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Unnamed: 0  Unnamed: 0.1 molecule_chembl_id  \\\n",
       "0              0             0       CHEMBL406146   \n",
       "1              1             1        CHEMBL78946   \n",
       "2              2             2       CHEMBL324109   \n",
       "3              3             3       CHEMBL114147   \n",
       "4              4             4       CHEMBL419949   \n",
       "...          ...           ...                ...   \n",
       "7229        7229         10419      CHEMBL4849016   \n",
       "7230        7230         10420      CHEMBL4872824   \n",
       "7231        7231         10421      CHEMBL4853052   \n",
       "7232        7232         10424      CHEMBL4862716   \n",
       "7233        7233         10425      CHEMBL4859103   \n",
       "\n",
       "                                       canonical_smiles         class  \\\n",
       "0     CC(C)C[C@H](NC(=O)[C@@H](NC(=O)[C@@H](N)CCC(=O...        active   \n",
       "1     CC(C)C[C@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](N...        active   \n",
       "2     CCC(C)C[C@H](NC(=O)[C@H](CC(C)C)NC(C)=O)[C@@H]...        active   \n",
       "3     CC(=O)NCC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)CC(=O)...  intermediate   \n",
       "4     CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1ccccc1...  intermediate   \n",
       "...                                                 ...           ...   \n",
       "7229  CC[C@H](C)[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)N...  intermediate   \n",
       "7230  CC[C@H](C)[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)N...  intermediate   \n",
       "7231  CC[C@H](C)[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)N...      inactive   \n",
       "7232  CC1=CC2Cc3nc4cc(Cl)ccc4c(NCCCCCCCCCNS(=O)(=O)c...      inactive   \n",
       "7233  CC1=CC2Cc3nc4cc(Cl)ccc4c(NCCCCCCCCCNC(=O)c4cc(...  intermediate   \n",
       "\n",
       "           MW    LogP  NumHDonors  NumHAcceptors     pIC50  \n",
       "0     999.085 -1.4355        13.0           13.0  6.384050  \n",
       "1     893.005 -1.7361        12.0           12.0  8.698970  \n",
       "2     751.988  2.3535         8.0            9.0  6.337242  \n",
       "3     737.895  1.9626         8.0            8.0  5.045757  \n",
       "4     828.020  3.5739         8.0            8.0  5.251812  \n",
       "...       ...     ...         ...            ...       ...  \n",
       "7229  623.861  2.3125         7.0            8.0  5.356547  \n",
       "7230  637.888  2.7026         7.0            8.0  5.036212  \n",
       "7231  651.915  3.0927         7.0            8.0  5.000000  \n",
       "7232  556.176  6.7284         3.0            5.0  4.966576  \n",
       "7233  562.154  7.8680         4.0            5.0  5.567031  \n",
       "\n",
       "[7234 rows x 10 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "eb58a271",
   "metadata": {},
   "outputs": [],
   "source": [
    "selection = ['canonical_smiles', 'molecule_chembl_id']\n",
    "df3_selection = df3[selection]\n",
    "df3_selection.to_csv('molecule.smi', sep = '\\t', index = False, header = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "d84aed2b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CC(C)C[C@H](NC(=O)[C@@H](NC(=O)[C@@H](N)CCC(=O)O)C(C)C)C(=O)N[C@@H](Cc1ccccc1)[C@@H](O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](C)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](Cc1ccccc1)C(=O)O\tCHEMBL406146\r\n",
      "CC(C)C[C@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](N)CCC(=O)O)C(C)C)[C@@H](O)C[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](Cc1ccccc1)C(=O)O\tCHEMBL78946\r\n",
      "CCC(C)C[C@H](NC(=O)[C@H](CC(C)C)NC(C)=O)[C@@H](O)CC(=O)NC(CCSC)[C@@H](O)CC(=O)N[C@H](C(=O)NCc1ccc(C(=O)O)cc1)C(C)C\tCHEMBL324109\r\n",
      "CC(=O)NCC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)CC(=O)N[C@@H](CC1CCCCC1)[C@@H](O)CC(=O)N[C@H](C(=O)NCc1ccc(C(=O)O)cc1)C(C)C\tCHEMBL114147\r\n",
      "CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1ccccc1)[C@@H](O)CC(=O)N[C@@H](CC1CCCCC1)[C@@H](O)CC(=O)N[C@H](C(=O)NCc1ccc(C(=O)O)cc1)C(C)C\tCHEMBL419949\r\n",
      "cat: stdout: Broken pipe\r\n"
     ]
    }
   ],
   "source": [
    "! cat molecule.smi | head -5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "7e8919a4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    7234\r\n"
     ]
    }
   ],
   "source": [
    "! cat molecule.smi | wc -l"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "256fed29",
   "metadata": {},
   "source": [
    "## Calculate finger print descriptors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "61501505",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "java -Xms1G -Xmx1G -Djava.awt.headless=true -jar ./PaDEL-Descriptor/PaDEL-Descriptor.jar -removesalt -standardizenitro -fingerprints -descriptortypes ./PaDEL-Descriptor/PubchemFingerprinter.xml -dir ./ -file descriptors_output.csv\r\n"
     ]
    }
   ],
   "source": [
    "! cat padel.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "9d917889",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL406146 in molecule.smi (1/7234). \n",
      "Processing CHEMBL78946 in molecule.smi (2/7234). \n",
      "Processing CHEMBL324109 in molecule.smi (3/7234). \n",
      "Processing CHEMBL114147 in molecule.smi (4/7234). \n",
      "Processing CHEMBL419949 in molecule.smi (5/7234). \n",
      "Processing CHEMBL116826 in molecule.smi (6/7234). \n",
      "Processing CHEMBL143239 in molecule.smi (7/7234). \n",
      "Processing CHEMBL332948 in molecule.smi (8/7234). \n",
      "Processing CHEMBL51386 in molecule.smi (9/7234). \n",
      "Processing CHEMBL332260 in molecule.smi (10/7234). \n",
      "Processing CHEMBL309438 in molecule.smi (18/7234). Average speed: 1.30 s/mol.\n",
      "Processing CHEMBL326488 in molecule.smi (13/7234). Average speed: 6.43 s/mol.\n",
      "Processing CHEMBL142715 in molecule.smi (12/7234). Average speed: 6.41 s/mol.\n",
      "Processing CHEMBL324122 in molecule.smi (15/7234). Average speed: 1.62 s/mol.\n",
      "Processing CHEMBL2370886 in molecule.smi (11/7234). Average speed: 6.41 s/mol.\n",
      "Processing CHEMBL114169 in molecule.smi (16/7234). Average speed: 1.62 s/mol.\n",
      "Processing CHEMBL290001 in molecule.smi (14/7234). Average speed: 3.22 s/mol.\n",
      "Processing CHEMBL143687 in molecule.smi (17/7234). Average speed: 1.30 s/mol.\n",
      "Processing CHEMBL332713 in molecule.smi (19/7234). Average speed: 0.73 s/mol.\n",
      "Processing CHEMBL82270 in molecule.smi (20/7234). Average speed: 0.66 s/mol.\n",
      "Processing CHEMBL138386 in molecule.smi (21/7234). Average speed: 0.68 s/mol.\n",
      "Processing CHEMBL432560 in molecule.smi (22/7234). Average speed: 0.69 s/mol.\n",
      "Processing CHEMBL84835 in molecule.smi (23/7234). Average speed: 0.59 s/mol.\n",
      "Processing CHEMBL316181 in molecule.smi (24/7234). Average speed: 0.59 s/mol.\n",
      "Processing CHEMBL433329 in molecule.smi (26/7234). Average speed: 0.52 s/mol.\n",
      "Processing CHEMBL84022 in molecule.smi (25/7234). Average speed: 0.52 s/mol.\n",
      "Processing CHEMBL82102 in molecule.smi (27/7234). Average speed: 0.46 s/mol.\n",
      "Processing CHEMBL84249 in molecule.smi (28/7234). Average speed: 0.46 s/mol.\n",
      "Processing CHEMBL81671 in molecule.smi (29/7234). Average speed: 0.43 s/mol.\n",
      "Processing CHEMBL312058 in molecule.smi (30/7234). Average speed: 0.39 s/mol.\n",
      "Processing CHEMBL1790644 in molecule.smi (31/7234). Average speed: 0.38 s/mol.\n",
      "Processing CHEMBL33724 in molecule.smi (32/7234). Average speed: 0.37 s/mol.\n",
      "Processing CHEMBL85378 in molecule.smi (33/7234). Average speed: 0.37 s/mol.\n",
      "Processing CHEMBL312956 in molecule.smi (34/7234). Average speed: 0.35 s/mol.\n",
      "Processing CHEMBL84834 in molecule.smi (35/7234). Average speed: 0.34 s/mol.\n",
      "Processing CHEMBL82352 in molecule.smi (36/7234). Average speed: 0.32 s/mol.\n",
      "Processing CHEMBL280244 in molecule.smi (37/7234). Average speed: 0.32 s/mol.\n",
      "Processing CHEMBL82504 in molecule.smi (38/7234). Average speed: 0.31 s/mol.\n",
      "Processing CHEMBL85379 in molecule.smi (39/7234). Average speed: 0.30 s/mol.\n",
      "Processing CHEMBL2114169 in molecule.smi (40/7234). Average speed: 0.30 s/mol.\n",
      "Processing CHEMBL81037 in molecule.smi (41/7234). Average speed: 0.28 s/mol.\n",
      "Processing CHEMBL78781 in molecule.smi (42/7234). Average speed: 0.27 s/mol.\n",
      "Processing CHEMBL81490 in molecule.smi (43/7234). Average speed: 0.27 s/mol.\n",
      "Processing CHEMBL82593 in molecule.smi (44/7234). Average speed: 0.26 s/mol.\n",
      "Processing CHEMBL78459 in molecule.smi (45/7234). Average speed: 0.26 s/mol.\n",
      "Processing CHEMBL81518 in molecule.smi (46/7234). Average speed: 0.25 s/mol.\n",
      "Processing CHEMBL309884 in molecule.smi (47/7234). Average speed: 0.25 s/mol.\n",
      "Processing CHEMBL310452 in molecule.smi (48/7234). Average speed: 0.24 s/mol.\n",
      "Processing CHEMBL311262 in molecule.smi (49/7234). Average speed: 0.24 s/mol.\n",
      "Processing CHEMBL314014 in molecule.smi (50/7234). Average speed: 0.23 s/mol.\n",
      "Processing CHEMBL1790594 in molecule.smi (51/7234). Average speed: 0.23 s/mol.\n",
      "Processing CHEMBL82607 in molecule.smi (52/7234). Average speed: 0.22 s/mol.\n",
      "Processing CHEMBL309296 in molecule.smi (53/7234). Average speed: 0.22 s/mol.\n",
      "Processing CHEMBL312277 in molecule.smi (54/7234). Average speed: 0.22 s/mol.\n",
      "Processing CHEMBL82594 in molecule.smi (55/7234). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL81218 in molecule.smi (56/7234). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL2370116 in molecule.smi (57/7234). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL2370107 in molecule.smi (58/7234). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL2370115 in molecule.smi (59/7234). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL327386 in molecule.smi (60/7234). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL2370123 in molecule.smi (61/7234). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL89118 in molecule.smi (62/7234). Average speed: 0.19 s/mol.\n",
      "Processing CHEMBL405443 in molecule.smi (63/7234). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL406089 in molecule.smi (64/7234). Average speed: 0.19 s/mol.\n",
      "Processing CHEMBL263333 in molecule.smi (65/7234). Average speed: 0.19 s/mol.\n",
      "Processing CHEMBL2370117 in molecule.smi (66/7234). Average speed: 0.19 s/mol.\n",
      "Processing CHEMBL2370095 in molecule.smi (67/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL2370094 in molecule.smi (68/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL413728 in molecule.smi (69/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL266203 in molecule.smi (70/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL426153 in molecule.smi (71/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL405808 in molecule.smi (72/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL2370121 in molecule.smi (73/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL437425 in molecule.smi (74/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL420418 in molecule.smi (75/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL90043 in molecule.smi (76/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL410405 in molecule.smi (77/7234). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL89703 in molecule.smi (78/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL327545 in molecule.smi (79/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL440612 in molecule.smi (80/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL1790741 in molecule.smi (81/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL89773 in molecule.smi (82/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL89530 in molecule.smi (83/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL2370074 in molecule.smi (84/7234). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL437918 in molecule.smi (85/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL90615 in molecule.smi (86/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL89438 in molecule.smi (87/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL2370096 in molecule.smi (88/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL411367 in molecule.smi (89/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL315706 in molecule.smi (90/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL412768 in molecule.smi (91/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL441187 in molecule.smi (92/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL265041 in molecule.smi (93/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL2370091 in molecule.smi (94/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL2370097 in molecule.smi (95/7234). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL265158 in molecule.smi (96/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL427580 in molecule.smi (97/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL2370075 in molecule.smi (98/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL52961 in molecule.smi (99/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL49711 in molecule.smi (100/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL52174 in molecule.smi (101/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL298147 in molecule.smi (102/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL51304 in molecule.smi (103/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL51003 in molecule.smi (104/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL50827 in molecule.smi (105/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL51779 in molecule.smi (106/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL52545 in molecule.smi (107/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL301944 in molecule.smi (108/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL297910 in molecule.smi (109/7234). Average speed: 0.15 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL52225 in molecule.smi (110/7234). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL300665 in molecule.smi (112/7234). Average speed: 0.14 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL200510 in molecule.smi (214/7234). Average speed: 0.10 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL380381 in molecule.smi (318/7234). Average speed: 0.08 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL393140 in molecule.smi (423/7234). Average speed: 0.08 s/mol.\n",
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     ]
    },
    {
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     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL231160 in molecule.smi (632/7234). Average speed: 0.07 s/mol.\n",
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     ]
    },
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     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL508095 in molecule.smi (841/7234). Average speed: 0.07 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL455081 in molecule.smi (945/7234). Average speed: 0.07 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL540731 in molecule.smi (1049/7234). Average speed: 0.07 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL566638 in molecule.smi (1152/7234). Average speed: 0.07 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL595066 in molecule.smi (1255/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL1093807 in molecule.smi (1358/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL1163401 in molecule.smi (1460/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL1163703 in molecule.smi (1562/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL1209165 in molecule.smi (1664/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL1257532 in molecule.smi (1766/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL1270936 in molecule.smi (1869/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL464006 in molecule.smi (1965/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL518543 in molecule.smi (1967/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL1782311 in molecule.smi (1970/7234). Average speed: 0.06 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL1504056 in molecule.smi (1971/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL1782312 in molecule.smi (1972/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL1782321 in molecule.smi (1981/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL1795871 in molecule.smi (1982/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL1909693 in molecule.smi (2073/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL1923297 in molecule.smi (2176/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL1929417 in molecule.smi (2177/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL6466 in molecule.smi (2184/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL244743 in molecule.smi (2189/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL350475 in molecule.smi (2193/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL510120 in molecule.smi (2198/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL1934195 in molecule.smi (2212/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL442813 in molecule.smi (2218/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL1631595 in molecule.smi (2224/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL1414353 in molecule.smi (2227/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL1934284 in molecule.smi (2228/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2011999 in molecule.smi (2278/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2012000 in molecule.smi (2279/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2011964 in molecule.smi (2287/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2012069 in molecule.smi (2286/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2012070 in molecule.smi (2289/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL3216554 in molecule.smi (2290/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL3216557 in molecule.smi (2292/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2011496 in molecule.smi (2293/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL3216778 in molecule.smi (2294/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL3216779 in molecule.smi (2295/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2019032 in molecule.smi (2296/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2019035 in molecule.smi (2297/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2019043 in molecule.smi (2300/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2019046 in molecule.smi (2301/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2019047 in molecule.smi (2302/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2019053 in molecule.smi (2303/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL28 in molecule.smi (2304/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2030996 in molecule.smi (2306/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2030997 in molecule.smi (2307/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2030995 in molecule.smi (2319/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL212925 in molecule.smi (2335/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2047900 in molecule.smi (2382/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2047901 in molecule.smi (2383/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2059626 in molecule.smi (2443/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2059100 in molecule.smi (2453/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2151148 in molecule.smi (2458/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2151235 in molecule.smi (2465/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2151239 in molecule.smi (2469/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2151240 in molecule.smi (2470/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2151241 in molecule.smi (2471/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2151134 in molecule.smi (2484/7234). Average speed: 0.06 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2151135 in molecule.smi (2485/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL1233206 in molecule.smi (2486/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152899 in molecule.smi (2487/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152900 in molecule.smi (2488/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2152902 in molecule.smi (2490/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2152905 in molecule.smi (2493/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152906 in molecule.smi (2494/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152907 in molecule.smi (2495/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152909 in molecule.smi (2496/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152908 in molecule.smi (2497/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152910 in molecule.smi (2498/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152911 in molecule.smi (2499/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152912 in molecule.smi (2500/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152913 in molecule.smi (2501/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2152914 in molecule.smi (2502/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2152916 in molecule.smi (2504/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2151058 in molecule.smi (2506/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2152920 in molecule.smi (2509/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2158260 in molecule.smi (2511/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2158259 in molecule.smi (2512/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2158252 in molecule.smi (2515/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2158255 in molecule.smi (2516/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2158258 in molecule.smi (2519/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL116438 in molecule.smi (2520/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2159663 in molecule.smi (2521/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2159662 in molecule.smi (2522/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2159661 in molecule.smi (2523/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2159660 in molecule.smi (2524/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2169925 in molecule.smi (2525/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2169924 in molecule.smi (2526/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2169923 in molecule.smi (2527/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2169922 in molecule.smi (2528/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172804 in molecule.smi (2529/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172803 in molecule.smi (2530/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172802 in molecule.smi (2531/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172801 in molecule.smi (2532/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172800 in molecule.smi (2533/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172799 in molecule.smi (2534/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172798 in molecule.smi (2535/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172797 in molecule.smi (2536/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172796 in molecule.smi (2537/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172795 in molecule.smi (2538/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2172793 in molecule.smi (2540/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2169947 in molecule.smi (2542/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL235825 in molecule.smi (2565/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2181884 in molecule.smi (2573/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2181914 in molecule.smi (2587/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2181913 in molecule.smi (2588/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2181984 in molecule.smi (2638/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2181998 in molecule.smi (2645/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2178147 in molecule.smi (2658/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2181988 in molecule.smi (2663/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177917 in molecule.smi (2673/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177113 in molecule.smi (2680/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177307 in molecule.smi (2690/7234). Average speed: 0.06 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2177311 in molecule.smi (2691/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177313 in molecule.smi (2692/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177341 in molecule.smi (2694/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177314 in molecule.smi (2695/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177312 in molecule.smi (2696/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177321 in molecule.smi (2697/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177329 in molecule.smi (2698/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177328 in molecule.smi (2699/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177337 in molecule.smi (2700/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177319 in molecule.smi (2701/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177315 in molecule.smi (2702/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177327 in molecule.smi (2703/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177324 in molecule.smi (2704/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2177322 in molecule.smi (2705/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177323 in molecule.smi (2709/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177333 in molecule.smi (2708/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177325 in molecule.smi (2712/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177330 in molecule.smi (2714/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177316 in molecule.smi (2718/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2177107 in molecule.smi (2725/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180015 in molecule.smi (2726/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180014 in molecule.smi (2727/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180036 in molecule.smi (2729/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180037 in molecule.smi (2728/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180035 in molecule.smi (2730/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180034 in molecule.smi (2731/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180033 in molecule.smi (2732/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180032 in molecule.smi (2733/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180031 in molecule.smi (2734/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180030 in molecule.smi (2735/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180029 in molecule.smi (2736/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2180025 in molecule.smi (2740/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2180024 in molecule.smi (2741/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2180023 in molecule.smi (2742/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2180019 in molecule.smi (2745/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2180020 in molecule.smi (2748/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2179140 in molecule.smi (2749/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL501578 in molecule.smi (2794/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2203629 in molecule.smi (2795/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL129795 in molecule.smi (2798/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL164 in molecule.smi (2799/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL150 in molecule.smi (2800/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2314778 in molecule.smi (2801/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2322207 in molecule.smi (2812/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2346802 in molecule.smi (2896/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2346801 in molecule.smi (2897/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2346799 in molecule.smi (2899/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2346797 in molecule.smi (2901/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2346796 in molecule.smi (2902/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2346794 in molecule.smi (2904/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2346791 in molecule.smi (2907/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2346789 in molecule.smi (2909/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2136098 in molecule.smi (2910/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2347190 in molecule.smi (2911/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2347189 in molecule.smi (2912/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2347188 in molecule.smi (2913/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2347187 in molecule.smi (2914/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2380805 in molecule.smi (2986/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2381575 in molecule.smi (2989/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2381576 in molecule.smi (2988/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2381574 in molecule.smi (2990/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2381682 in molecule.smi (2993/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2381676 in molecule.smi (2999/7234). Average speed: 0.06 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2381675 in molecule.smi (3000/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2381581 in molecule.smi (3001/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2381579 in molecule.smi (3003/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2381578 in molecule.smi (3004/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380439 in molecule.smi (3005/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380459 in molecule.smi (3006/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380441 in molecule.smi (3007/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380440 in molecule.smi (3008/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380457 in molecule.smi (3010/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380438 in molecule.smi (3009/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380453 in molecule.smi (3011/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380461 in molecule.smi (3012/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380443 in molecule.smi (3013/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2380458 in molecule.smi (3015/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380454 in molecule.smi (3016/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380444 in molecule.smi (3017/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380452 in molecule.smi (3018/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380447 in molecule.smi (3019/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380456 in molecule.smi (3020/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380449 in molecule.smi (3021/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2380445 in molecule.smi (3023/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380451 in molecule.smi (3024/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380455 in molecule.smi (3025/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2380450 in molecule.smi (3026/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2386726 in molecule.smi (3028/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2365642 in molecule.smi (3036/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403763 in molecule.smi (3037/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2403764 in molecule.smi (3039/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403759 in molecule.smi (3040/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403761 in molecule.smi (3041/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403771 in molecule.smi (3042/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403762 in molecule.smi (3043/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403779 in molecule.smi (3044/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2403773 in molecule.smi (3046/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403774 in molecule.smi (3047/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403778 in molecule.smi (3048/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403770 in molecule.smi (3049/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403768 in molecule.smi (3050/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403767 in molecule.smi (3051/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403772 in molecule.smi (3052/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403769 in molecule.smi (3053/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403765 in molecule.smi (3055/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403777 in molecule.smi (3054/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403776 in molecule.smi (3056/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2403766 in molecule.smi (3057/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407492 in molecule.smi (3058/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407491 in molecule.smi (3059/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407490 in molecule.smi (3060/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407489 in molecule.smi (3061/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407488 in molecule.smi (3062/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407487 in molecule.smi (3063/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407345 in molecule.smi (3064/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407344 in molecule.smi (3065/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2407342 in molecule.smi (3067/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407341 in molecule.smi (3068/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407340 in molecule.smi (3069/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407339 in molecule.smi (3070/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407338 in molecule.smi (3071/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407495 in molecule.smi (3073/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407496 in molecule.smi (3072/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407494 in molecule.smi (3074/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2407493 in molecule.smi (3075/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408785 in molecule.smi (3076/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408784 in molecule.smi (3077/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408786 in molecule.smi (3078/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408787 in molecule.smi (3079/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408754 in molecule.smi (3080/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408738 in molecule.smi (3081/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408761 in molecule.smi (3082/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408748 in molecule.smi (3083/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408745 in molecule.smi (3084/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408749 in molecule.smi (3085/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408759 in molecule.smi (3086/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408736 in molecule.smi (3087/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408763 in molecule.smi (3088/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408762 in molecule.smi (3089/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL2408765 in molecule.smi (3091/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408747 in molecule.smi (3092/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408743 in molecule.smi (3093/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408742 in molecule.smi (3094/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408740 in molecule.smi (3095/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408739 in molecule.smi (3096/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408764 in molecule.smi (3097/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408758 in molecule.smi (3098/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408744 in molecule.smi (3099/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408737 in molecule.smi (3100/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408760 in molecule.smi (3101/7234). Average speed: 0.06 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL2408741 in molecule.smi (3102/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408755 in molecule.smi (3103/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408752 in molecule.smi (3104/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408756 in molecule.smi (3105/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408753 in molecule.smi (3106/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408750 in molecule.smi (3107/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408757 in molecule.smi (3108/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425607 in molecule.smi (3110/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2408751 in molecule.smi (3109/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425606 in molecule.smi (3111/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425605 in molecule.smi (3112/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425604 in molecule.smi (3113/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425603 in molecule.smi (3114/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425602 in molecule.smi (3115/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425601 in molecule.smi (3116/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425600 in molecule.smi (3117/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425599 in molecule.smi (3118/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425598 in molecule.smi (3119/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425617 in molecule.smi (3121/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425618 in molecule.smi (3120/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425614 in molecule.smi (3122/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425613 in molecule.smi (3123/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425612 in molecule.smi (3124/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425611 in molecule.smi (3125/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425610 in molecule.smi (3126/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425609 in molecule.smi (3127/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425608 in molecule.smi (3128/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425615 in molecule.smi (3129/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2425616 in molecule.smi (3130/7234). Average speed: 0.06 s/mol.\n",
      "Processing CHEMBL2437434 in molecule.smi (3132/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3127090 in molecule.smi (3204/7234). Average speed: 0.06 s/mol.\n",
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      "Processing CHEMBL3236215 in molecule.smi (3220/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3354690 in molecule.smi (3306/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3394053 in molecule.smi (3410/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL3597549 in molecule.smi (3512/7234). Average speed: 0.06 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3680854 in molecule.smi (3616/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
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     ]
    },
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3640238 in molecule.smi (3820/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3656226 in molecule.smi (3923/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3656178 in molecule.smi (4027/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3670320 in molecule.smi (4129/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL3653409 in molecule.smi (4231/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3954417 in molecule.smi (4333/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3653715 in molecule.smi (4435/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3691369 in molecule.smi (4514/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3691371 in molecule.smi (4516/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3691374 in molecule.smi (4519/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3691377 in molecule.smi (4522/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3695727 in molecule.smi (4527/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3695736 in molecule.smi (4536/7234). Average speed: 0.05 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3695737 in molecule.smi (4537/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3695738 in molecule.smi (4538/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3639946 in molecule.smi (4544/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3695745 in molecule.smi (4546/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3695747 in molecule.smi (4548/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3695750 in molecule.smi (4551/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3654216 in molecule.smi (4556/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3261057 in molecule.smi (4568/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL3672398 in molecule.smi (4576/7234). Average speed: 0.05 s/mol.\n",
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      "Processing CHEMBL1405147 in molecule.smi (4599/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3677218 in molecule.smi (4639/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3953424 in molecule.smi (4741/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3703278 in molecule.smi (4742/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL3650830 in molecule.smi (4843/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL3899321 in molecule.smi (4946/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3673222 in molecule.smi (5048/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3683829 in molecule.smi (5150/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3688616 in molecule.smi (5253/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3688718 in molecule.smi (5356/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3688827 in molecule.smi (5457/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3939252 in molecule.smi (5663/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
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     ]
    },
    {
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     "text": [
      "Processing CHEMBL3953078 in molecule.smi (5868/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL3963446 in molecule.smi (5970/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL3908739 in molecule.smi (6174/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
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     ]
    },
    {
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     "text": [
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     ]
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      "Processing CHEMBL3911876 in molecule.smi (6566/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3987022 in molecule.smi (6567/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3920799 in molecule.smi (6568/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3890460 in molecule.smi (6569/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3918509 in molecule.smi (6570/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3941299 in molecule.smi (6571/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3902648 in molecule.smi (6572/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3939642 in molecule.smi (6573/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3908098 in molecule.smi (6574/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3944997 in molecule.smi (6575/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3917081 in molecule.smi (6576/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3953708 in molecule.smi (6577/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3929500 in molecule.smi (6578/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4112303 in molecule.smi (6579/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4112944 in molecule.smi (6580/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3650159 in molecule.smi (6581/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4112843 in molecule.smi (6582/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3907751 in molecule.smi (6583/7234). Average speed: 0.05 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL4066788 in molecule.smi (6584/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL1483796 in molecule.smi (6585/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4062641 in molecule.smi (6586/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4090604 in molecule.smi (6587/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4096411 in molecule.smi (6588/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4078371 in molecule.smi (6589/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4086961 in molecule.smi (6590/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4069747 in molecule.smi (6591/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4076855 in molecule.smi (6592/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4066837 in molecule.smi (6593/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4059546 in molecule.smi (6594/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4092459 in molecule.smi (6595/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4062101 in molecule.smi (6596/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4089395 in molecule.smi (6597/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4081363 in molecule.smi (6598/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4077530 in molecule.smi (6599/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4071843 in molecule.smi (6600/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4062635 in molecule.smi (6601/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4092083 in molecule.smi (6602/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4071284 in molecule.smi (6603/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4065393 in molecule.smi (6604/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4093064 in molecule.smi (6605/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4074001 in molecule.smi (6606/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4100768 in molecule.smi (6607/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4095483 in molecule.smi (6608/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4075051 in molecule.smi (6609/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4078427 in molecule.smi (6610/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4091480 in molecule.smi (6611/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4061944 in molecule.smi (6612/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4083698 in molecule.smi (6613/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4100140 in molecule.smi (6614/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4073296 in molecule.smi (6615/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4092406 in molecule.smi (6616/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4064708 in molecule.smi (6617/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4084653 in molecule.smi (6618/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4104527 in molecule.smi (6620/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4086633 in molecule.smi (6621/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4102593 in molecule.smi (6619/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4066885 in molecule.smi (6622/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4094377 in molecule.smi (6623/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4061602 in molecule.smi (6624/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4084170 in molecule.smi (6625/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4085715 in molecule.smi (6626/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4064148 in molecule.smi (6627/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4062728 in molecule.smi (6628/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4077211 in molecule.smi (6629/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4080380 in molecule.smi (6630/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4098403 in molecule.smi (6631/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4088234 in molecule.smi (6632/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4094980 in molecule.smi (6633/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4092875 in molecule.smi (6634/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4072118 in molecule.smi (6635/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4062699 in molecule.smi (6636/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4084381 in molecule.smi (6637/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4100832 in molecule.smi (6638/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4074071 in molecule.smi (6639/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4093123 in molecule.smi (6640/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4065448 in molecule.smi (6641/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4085364 in molecule.smi (6642/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4103296 in molecule.smi (6643/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4097477 in molecule.smi (6644/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4070299 in molecule.smi (6645/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4067413 in molecule.smi (6646/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL261063 in molecule.smi (6647/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4085945 in molecule.smi (6648/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4064412 in molecule.smi (6649/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128947 in molecule.smi (6650/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4130015 in molecule.smi (6651/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4126751 in molecule.smi (6652/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127986 in molecule.smi (6653/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127289 in molecule.smi (6654/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128727 in molecule.smi (6655/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128586 in molecule.smi (6656/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127672 in molecule.smi (6657/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127062 in molecule.smi (6658/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128447 in molecule.smi (6659/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127486 in molecule.smi (6660/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128807 in molecule.smi (6661/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127412 in molecule.smi (6662/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127550 in molecule.smi (6663/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4126598 in molecule.smi (6664/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4129873 in molecule.smi (6665/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127807 in molecule.smi (6666/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4130130 in molecule.smi (6667/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128770 in molecule.smi (6668/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4126839 in molecule.smi (6669/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128406 in molecule.smi (6670/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4129775 in molecule.smi (6671/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4129637 in molecule.smi (6672/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4126351 in molecule.smi (6673/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4126197 in molecule.smi (6674/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127572 in molecule.smi (6675/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4127426 in molecule.smi (6676/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128824 in molecule.smi (6677/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4128145 in molecule.smi (6678/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4177357 in molecule.smi (6679/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4176954 in molecule.smi (6680/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4169090 in molecule.smi (6681/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4167503 in molecule.smi (6682/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4160274 in molecule.smi (6683/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4167095 in molecule.smi (6684/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4159178 in molecule.smi (6685/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4173515 in molecule.smi (6686/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4165225 in molecule.smi (6687/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4175845 in molecule.smi (6688/7234). Average speed: 0.05 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL4161795 in molecule.smi (6689/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4169060 in molecule.smi (6690/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4165629 in molecule.smi (6691/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4170106 in molecule.smi (6692/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4162197 in molecule.smi (6693/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4159574 in molecule.smi (6694/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4167487 in molecule.smi (6695/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4174699 in molecule.smi (6696/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4164046 in molecule.smi (6697/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4171250 in molecule.smi (6698/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4160644 in molecule.smi (6699/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4167898 in molecule.smi (6700/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4175758 in molecule.smi (6701/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4173236 in molecule.smi (6702/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL222274 in molecule.smi (6703/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4166192 in molecule.smi (6704/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4166588 in molecule.smi (6705/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4174503 in molecule.smi (6706/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4170012 in molecule.smi (6707/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4159379 in molecule.smi (6708/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4168528 in molecule.smi (6709/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4217236 in molecule.smi (6710/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4212215 in molecule.smi (6711/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4208507 in molecule.smi (6712/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4218591 in molecule.smi (6713/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4206849 in molecule.smi (6714/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4206331 in molecule.smi (6715/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4211220 in molecule.smi (6716/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4204309 in molecule.smi (6717/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4204985 in molecule.smi (6718/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4204582 in molecule.smi (6719/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4218977 in molecule.smi (6720/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4205504 in molecule.smi (6721/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4211801 in molecule.smi (6722/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4218068 in molecule.smi (6723/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4208381 in molecule.smi (6724/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4208920 in molecule.smi (6725/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4202435 in molecule.smi (6727/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4204042 in molecule.smi (6726/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4215297 in molecule.smi (6728/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4204085 in molecule.smi (6729/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4202984 in molecule.smi (6730/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4208775 in molecule.smi (6731/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4207174 in molecule.smi (6732/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL1492021 in molecule.smi (6733/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3672916 in molecule.smi (6734/7234). Average speed: 0.05 s/mol.\n",
      "Feb 20, 2023 7:08:23 PM libpadeldescriptor.libPaDELDescriptorMaster hasNextJob\n",
      "SEVERE: plot_ic50.pdf\n",
      "java.io.FileNotFoundException: ./plot_ic50.pdf (No such file or directory)\n",
      "\tat java.io.FileInputStream.open0(Native Method)\n",
      "\tat java.io.FileInputStream.open(FileInputStream.java:195)\n",
      "\tat java.io.FileInputStream.<init>(FileInputStream.java:138)\n",
      "\tat libpadeldescriptor.IteratingPaDELReader.<init>(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.AddJobsToQueue(Unknown Source)\n",
      "\tat libpadeljobs.Master.DoWork(Master.java:40)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.StartCmd(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.launchCommandLine(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.main(Unknown Source)\n",
      "\n",
      "Feb 20, 2023 7:08:23 PM libpadeldescriptor.libPaDELDescriptorMaster hasNextJob\n",
      "SEVERE: mannwhitneyu_pIC50.csv\n",
      "java.io.FileNotFoundException: ./mannwhitneyu_pIC50.csv (No such file or directory)\n",
      "\tat java.io.FileInputStream.open0(Native Method)\n",
      "\tat java.io.FileInputStream.open(FileInputStream.java:195)\n",
      "\tat java.io.FileInputStream.<init>(FileInputStream.java:138)\n",
      "\tat libpadeldescriptor.IteratingPaDELReader.<init>(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.AddJobsToQueue(Unknown Source)\n",
      "\tat libpadeljobs.Master.DoWork(Master.java:40)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.StartCmd(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.launchCommandLine(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.main(Unknown Source)\n",
      "\n",
      "Feb 20, 2023 7:08:23 PM libpadeldescriptor.libPaDELDescriptorMaster hasNextJob\n",
      "SEVERE: plot_MW_vs_LogP.pdf\n",
      "java.io.FileNotFoundException: ./plot_MW_vs_LogP.pdf (No such file or directory)\n",
      "\tat java.io.FileInputStream.open0(Native Method)\n",
      "\tat java.io.FileInputStream.open(FileInputStream.java:195)\n",
      "\tat java.io.FileInputStream.<init>(FileInputStream.java:138)\n",
      "\tat libpadeldescriptor.IteratingPaDELReader.<init>(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.AddJobsToQueue(Unknown Source)\n",
      "\tat libpadeljobs.Master.DoWork(Master.java:40)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.StartCmd(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.launchCommandLine(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.main(Unknown Source)\n",
      "\n",
      "Feb 20, 2023 7:08:23 PM libpadeldescriptor.libPaDELDescriptorMaster hasNextJob\n",
      "SEVERE: mannwhitneyu_LogP.csv\n",
      "java.io.FileNotFoundException: ./mannwhitneyu_LogP.csv (No such file or directory)\n",
      "\tat java.io.FileInputStream.open0(Native Method)\n",
      "\tat java.io.FileInputStream.open(FileInputStream.java:195)\n",
      "\tat java.io.FileInputStream.<init>(FileInputStream.java:138)\n",
      "\tat libpadeldescriptor.IteratingPaDELReader.<init>(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.hasNextJob(Unknown Source)\n",
      "\tat libpadeldescriptor.libPaDELDescriptorMaster.AddJobsToQueue(Unknown Source)\n",
      "\tat libpadeljobs.Master.DoWork(Master.java:40)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.StartCmd(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.launchCommandLine(Unknown Source)\n",
      "\tat padeldescriptor.PaDELDescriptorApp.main(Unknown Source)\n",
      "\n",
      "Processing CHEMBL4212046 in molecule.smi (6736/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4205912 in molecule.smi (6735/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4203860 in molecule.smi (6737/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4215837 in molecule.smi (6738/7234). Average speed: 0.05 s/mol.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL4204163 in molecule.smi (6739/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4211913 in molecule.smi (6740/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4217023 in molecule.smi (6741/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4214785 in molecule.smi (6742/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4204215 in molecule.smi (6743/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4203347 in molecule.smi (6744/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4214603 in molecule.smi (6745/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4209354 in molecule.smi (6746/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4209994 in molecule.smi (6748/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4207711 in molecule.smi (6747/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL3301601 in molecule.smi (6749/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4217620 in molecule.smi (6750/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL4286556 in molecule.smi (6843/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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      "Processing CHEMBL4456778 in molecule.smi (6946/7234). Average speed: 0.05 s/mol.\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "Processing CHEMBL1424080 in molecule.smi (7049/7234). Average speed: 0.05 s/mol.\n",
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     ]
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      "Processing CHEMBL4855002 in molecule.smi (7208/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4857065 in molecule.smi (7209/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4859851 in molecule.smi (7210/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4852055 in molecule.smi (7211/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4876495 in molecule.smi (7212/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4874363 in molecule.smi (7213/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4851168 in molecule.smi (7214/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4879047 in molecule.smi (7215/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4848778 in molecule.smi (7216/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4867976 in molecule.smi (7217/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4846642 in molecule.smi (7218/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4857564 in molecule.smi (7220/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4850554 in molecule.smi (7219/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4874621 in molecule.smi (7222/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4859258 in molecule.smi (7221/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4865499 in molecule.smi (7223/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4848236 in molecule.smi (7224/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4877632 in molecule.smi (7225/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4873667 in molecule.smi (7226/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4866494 in molecule.smi (7227/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4858655 in molecule.smi (7228/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4864653 in molecule.smi (7229/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4872824 in molecule.smi (7231/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4849016 in molecule.smi (7230/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4853052 in molecule.smi (7232/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4862716 in molecule.smi (7233/7234). Average speed: 0.05 s/mol.\n",
      "Processing CHEMBL4859103 in molecule.smi (7234/7234). Average speed: 0.05 s/mol.\n",
      "Descriptor calculation completed in 5 mins 52.670 secs . Average speed: 0.05 s/mol.\n"
     ]
    }
   ],
   "source": [
    "! bash padel.sh"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "865b9c09",
   "metadata": {},
   "source": [
    "## Preparing the X and Y Data Matrices"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "72de5287",
   "metadata": {},
   "source": [
    "### X data matrix"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "0babe62d",
   "metadata": {},
   "outputs": [],
   "source": [
    "df3_x = pd.read_csv('data/descriptors_output.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "bcf4f777",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Name</th>\n",
       "      <th>PubchemFP0</th>\n",
       "      <th>PubchemFP1</th>\n",
       "      <th>PubchemFP2</th>\n",
       "      <th>PubchemFP3</th>\n",
       "      <th>PubchemFP4</th>\n",
       "      <th>PubchemFP5</th>\n",
       "      <th>PubchemFP6</th>\n",
       "      <th>PubchemFP7</th>\n",
       "      <th>PubchemFP8</th>\n",
       "      <th>...</th>\n",
       "      <th>PubchemFP871</th>\n",
       "      <th>PubchemFP872</th>\n",
       "      <th>PubchemFP873</th>\n",
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       "      <th>PubchemFP875</th>\n",
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       "      <th>PubchemFP878</th>\n",
       "      <th>PubchemFP879</th>\n",
       "      <th>PubchemFP880</th>\n",
       "    </tr>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL324109</td>\n",
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       "      <th>1</th>\n",
       "      <td>CHEMBL116826</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL78946</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL51386</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL114147</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>...</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <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",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>7229</th>\n",
       "      <td>CHEMBL4872824</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7230</th>\n",
       "      <td>CHEMBL4853052</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7231</th>\n",
       "      <td>CHEMBL4864653</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>7232</th>\n",
       "      <td>CHEMBL4862716</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7233</th>\n",
       "      <td>CHEMBL4859103</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "</table>\n",
       "<p>7234 rows × 882 columns</p>\n",
       "</div>"
      ],
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       "               Name  PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  \\\n",
       "0      CHEMBL324109           1           1           1           1   \n",
       "1      CHEMBL116826           1           1           1           1   \n",
       "2       CHEMBL78946           1           1           1           1   \n",
       "3       CHEMBL51386           1           1           1           1   \n",
       "4      CHEMBL114147           1           1           1           1   \n",
       "...             ...         ...         ...         ...         ...   \n",
       "7229  CHEMBL4872824           1           1           1           1   \n",
       "7230  CHEMBL4853052           1           1           1           1   \n",
       "7231  CHEMBL4864653           1           1           1           1   \n",
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       "7233  CHEMBL4859103           1           1           1           1   \n",
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       "0              0           0           0           0           0  ...   \n",
       "1              0           0           0           0           0  ...   \n",
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       "3              0           0           0           0           0  ...   \n",
       "4              0           0           0           0           0  ...   \n",
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       "7231           0           0           0           0           0  ...   \n",
       "7232           0           0           0           0           0  ...   \n",
       "7233           0           0           0           0           0  ...   \n",
       "\n",
       "      PubchemFP871  PubchemFP872  PubchemFP873  PubchemFP874  PubchemFP875  \\\n",
       "0                0             0             0             0             0   \n",
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       "2                0             0             0             0             0   \n",
       "3                0             0             0             0             0   \n",
       "4                0             0             0             0             0   \n",
       "...            ...           ...           ...           ...           ...   \n",
       "7229             0             0             0             0             0   \n",
       "7230             0             0             0             0             0   \n",
       "7231             0             0             0             0             0   \n",
       "7232             0             0             0             0             0   \n",
       "7233             0             0             0             0             0   \n",
       "\n",
       "      PubchemFP876  PubchemFP877  PubchemFP878  PubchemFP879  PubchemFP880  \n",
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       "1                0             0             0             0             0  \n",
       "2                0             0             0             0             0  \n",
       "3                0             0             0             0             0  \n",
       "4                0             0             0             0             0  \n",
       "...            ...           ...           ...           ...           ...  \n",
       "7229             0             0             0             0             0  \n",
       "7230             0             0             0             0             0  \n",
       "7231             0             0             0             0             0  \n",
       "7232             0             0             0             0             0  \n",
       "7233             0             0             0             0             0  \n",
       "\n",
       "[7234 rows x 882 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3_x"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "3dce3200",
   "metadata": {},
   "outputs": [
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7229</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7230</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7231</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7232</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7233</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7234 rows × 881 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  PubchemFP5  \\\n",
       "0              1           1           1           1           0           0   \n",
       "1              1           1           1           1           0           0   \n",
       "2              1           1           1           1           0           0   \n",
       "3              1           1           1           1           0           0   \n",
       "4              1           1           1           1           0           0   \n",
       "...          ...         ...         ...         ...         ...         ...   \n",
       "7229           1           1           1           1           0           0   \n",
       "7230           1           1           1           1           0           0   \n",
       "7231           1           1           1           1           0           0   \n",
       "7232           1           1           1           1           0           0   \n",
       "7233           1           1           1           1           0           0   \n",
       "\n",
       "      PubchemFP6  PubchemFP7  PubchemFP8  PubchemFP9  ...  PubchemFP871  \\\n",
       "0              0           0           0           1  ...             0   \n",
       "1              0           0           0           1  ...             0   \n",
       "2              0           0           0           1  ...             0   \n",
       "3              0           0           0           1  ...             0   \n",
       "4              0           0           0           1  ...             0   \n",
       "...          ...         ...         ...         ...  ...           ...   \n",
       "7229           0           0           0           1  ...             0   \n",
       "7230           0           0           0           1  ...             0   \n",
       "7231           0           0           0           1  ...             0   \n",
       "7232           0           0           0           1  ...             0   \n",
       "7233           0           0           0           1  ...             0   \n",
       "\n",
       "      PubchemFP872  PubchemFP873  PubchemFP874  PubchemFP875  PubchemFP876  \\\n",
       "0                0             0             0             0             0   \n",
       "1                0             0             0             0             0   \n",
       "2                0             0             0             0             0   \n",
       "3                0             0             0             0             0   \n",
       "4                0             0             0             0             0   \n",
       "...            ...           ...           ...           ...           ...   \n",
       "7229             0             0             0             0             0   \n",
       "7230             0             0             0             0             0   \n",
       "7231             0             0             0             0             0   \n",
       "7232             0             0             0             0             0   \n",
       "7233             0             0             0             0             0   \n",
       "\n",
       "      PubchemFP877  PubchemFP878  PubchemFP879  PubchemFP880  \n",
       "0                0             0             0             0  \n",
       "1                0             0             0             0  \n",
       "2                0             0             0             0  \n",
       "3                0             0             0             0  \n",
       "4                0             0             0             0  \n",
       "...            ...           ...           ...           ...  \n",
       "7229             0             0             0             0  \n",
       "7230             0             0             0             0  \n",
       "7231             0             0             0             0  \n",
       "7232             0             0             0             0  \n",
       "7233             0             0             0             0  \n",
       "\n",
       "[7234 rows x 881 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3_x = df3_x.drop(columns = ['Name'])\n",
    "df3_x"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "67ca1258",
   "metadata": {},
   "source": [
    "## Y variable"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b18fb1d7",
   "metadata": {},
   "source": [
    "### Convert IC50 to pIC50"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "4295cdbb",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0       6.384050\n",
       "1       8.698970\n",
       "2       6.337242\n",
       "3       5.045757\n",
       "4       5.251812\n",
       "          ...   \n",
       "7229    5.356547\n",
       "7230    5.036212\n",
       "7231    5.000000\n",
       "7232    4.966576\n",
       "7233    5.567031\n",
       "Name: pIC50, Length: 7234, dtype: float64"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3_y = df3['pIC50']\n",
    "df3_y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "91d58889",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>PubchemFP0</th>\n",
       "      <th>PubchemFP1</th>\n",
       "      <th>PubchemFP2</th>\n",
       "      <th>PubchemFP3</th>\n",
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       "      <th>PubchemFP876</th>\n",
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       "      <th>PubchemFP878</th>\n",
       "      <th>PubchemFP879</th>\n",
       "      <th>PubchemFP880</th>\n",
       "      <th>pIC50</th>\n",
       "    </tr>\n",
       "  </thead>\n",
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       "      <td>8.698970</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6.337242</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>5.045757</td>\n",
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       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>5.036212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7231</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>5.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7232</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4.966576</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7233</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>5.567031</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7234 rows × 882 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  PubchemFP5  \\\n",
       "0              1           1           1           1           0           0   \n",
       "1              1           1           1           1           0           0   \n",
       "2              1           1           1           1           0           0   \n",
       "3              1           1           1           1           0           0   \n",
       "4              1           1           1           1           0           0   \n",
       "...          ...         ...         ...         ...         ...         ...   \n",
       "7229           1           1           1           1           0           0   \n",
       "7230           1           1           1           1           0           0   \n",
       "7231           1           1           1           1           0           0   \n",
       "7232           1           1           1           1           0           0   \n",
       "7233           1           1           1           1           0           0   \n",
       "\n",
       "      PubchemFP6  PubchemFP7  PubchemFP8  PubchemFP9  ...  PubchemFP872  \\\n",
       "0              0           0           0           1  ...             0   \n",
       "1              0           0           0           1  ...             0   \n",
       "2              0           0           0           1  ...             0   \n",
       "3              0           0           0           1  ...             0   \n",
       "4              0           0           0           1  ...             0   \n",
       "...          ...         ...         ...         ...  ...           ...   \n",
       "7229           0           0           0           1  ...             0   \n",
       "7230           0           0           0           1  ...             0   \n",
       "7231           0           0           0           1  ...             0   \n",
       "7232           0           0           0           1  ...             0   \n",
       "7233           0           0           0           1  ...             0   \n",
       "\n",
       "      PubchemFP873  PubchemFP874  PubchemFP875  PubchemFP876  PubchemFP877  \\\n",
       "0                0             0             0             0             0   \n",
       "1                0             0             0             0             0   \n",
       "2                0             0             0             0             0   \n",
       "3                0             0             0             0             0   \n",
       "4                0             0             0             0             0   \n",
       "...            ...           ...           ...           ...           ...   \n",
       "7229             0             0             0             0             0   \n",
       "7230             0             0             0             0             0   \n",
       "7231             0             0             0             0             0   \n",
       "7232             0             0             0             0             0   \n",
       "7233             0             0             0             0             0   \n",
       "\n",
       "      PubchemFP878  PubchemFP879  PubchemFP880     pIC50  \n",
       "0                0             0             0  6.384050  \n",
       "1                0             0             0  8.698970  \n",
       "2                0             0             0  6.337242  \n",
       "3                0             0             0  5.045757  \n",
       "4                0             0             0  5.251812  \n",
       "...            ...           ...           ...       ...  \n",
       "7229             0             0             0  5.356547  \n",
       "7230             0             0             0  5.036212  \n",
       "7231             0             0             0  5.000000  \n",
       "7232             0             0             0  4.966576  \n",
       "7233             0             0             0  5.567031  \n",
       "\n",
       "[7234 rows x 882 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset3 = pd.concat([df3_x, df3_y], axis = 1)\n",
    "dataset3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "ce7bccb6",
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset3.to_csv('beta_secretase_bioactivity_data_3class_pIC50_pubchem_fp.csv', index = False)"
   ]
  }
 ],
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