Part1_QSAR_Drug_Discovery.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Drug Discovery using Quantitative structure-activity relationship (QSAR)\n",
    "## Project Outline\n",
    "1.) Data Collection and Cleanup from ChEMBL Database\n",
    "\n",
    "2.) Descriptor Calculation and Exploratory Data Analysis\n",
    "\n",
    "3.) Calculating \"Molecular Descriptors\" (quantitative dewcription of compounds in dataset)\n",
    "\n",
    "4.) Model Building and Evaluation (Regression model with Random Forest)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Part 1: Data Collection and Cleanup"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### ChEMBL Database\n",
    "ChEMBL Database is compilation of bioactive molecules with drugike properties"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: chembl_webresource_client in /opt/anaconda3/lib/python3.8/site-packages (0.10.2)\n",
      "Requirement already satisfied: requests>=2.18.4 in /opt/anaconda3/lib/python3.8/site-packages (from chembl_webresource_client) (2.24.0)\n",
      "Requirement already satisfied: requests-cache>=0.4.7 in /opt/anaconda3/lib/python3.8/site-packages (from chembl_webresource_client) (0.5.2)\n",
      "Requirement already satisfied: easydict in /opt/anaconda3/lib/python3.8/site-packages (from chembl_webresource_client) (1.9)\n",
      "Requirement already satisfied: urllib3 in /opt/anaconda3/lib/python3.8/site-packages (from chembl_webresource_client) (1.25.9)\n",
      "Requirement already satisfied: chardet<4,>=3.0.2 in /opt/anaconda3/lib/python3.8/site-packages (from requests>=2.18.4->chembl_webresource_client) (3.0.4)\n",
      "Requirement already satisfied: idna<3,>=2.5 in /opt/anaconda3/lib/python3.8/site-packages (from requests>=2.18.4->chembl_webresource_client) (2.10)\n",
      "Requirement already satisfied: certifi>=2017.4.17 in /opt/anaconda3/lib/python3.8/site-packages (from requests>=2.18.4->chembl_webresource_client) (2020.6.20)\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "pip install chembl_webresource_client"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Library Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from chembl_webresource_client.new_client import new_client"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Target Protein Search"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cross_references</th>\n",
       "      <th>organism</th>\n",
       "      <th>pref_name</th>\n",
       "      <th>score</th>\n",
       "      <th>species_group_flag</th>\n",
       "      <th>target_chembl_id</th>\n",
       "      <th>target_components</th>\n",
       "      <th>target_type</th>\n",
       "      <th>tax_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[{'xref_id': 'P22303', 'xref_name': None, 'xre...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>27.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL220</td>\n",
       "      <td>[{'accession': 'P22303', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Cholinesterases; ACHE &amp; BCHE</td>\n",
       "      <td>27.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2095233</td>\n",
       "      <td>[{'accession': 'P06276', 'component_descriptio...</td>\n",
       "      <td>SELECTIVITY GROUP</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[]</td>\n",
       "      <td>Drosophila melanogaster</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>17.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2242744</td>\n",
       "      <td>[{'accession': 'P07140', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7227</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>[]</td>\n",
       "      <td>Nephotettix cincticeps</td>\n",
       "      <td>Ace-orthologous acetylcholinesterase</td>\n",
       "      <td>17.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2366514</td>\n",
       "      <td>[{'accession': 'Q9NJH6', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>94400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>[{'xref_id': 'P04058', 'xref_name': None, 'xre...</td>\n",
       "      <td>Torpedo californica</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4780</td>\n",
       "      <td>[{'accession': 'P04058', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7787</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>[{'xref_id': 'P21836', 'xref_name': None, 'xre...</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3198</td>\n",
       "      <td>[{'accession': 'P21836', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>10090</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>[{'xref_id': 'P37136', 'xref_name': None, 'xre...</td>\n",
       "      <td>Rattus norvegicus</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3199</td>\n",
       "      <td>[{'accession': 'P37136', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>10116</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>[{'xref_id': 'O42275', 'xref_name': None, 'xre...</td>\n",
       "      <td>Electrophorus electricus</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4078</td>\n",
       "      <td>[{'accession': 'O42275', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>8005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>[{'xref_id': 'P23795', 'xref_name': None, 'xre...</td>\n",
       "      <td>Bos taurus</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4768</td>\n",
       "      <td>[{'accession': 'P23795', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>9913</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>[]</td>\n",
       "      <td>Anopheles gambiae</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2046266</td>\n",
       "      <td>[{'accession': 'Q869C3', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7165</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>[]</td>\n",
       "      <td>Leptinotarsa decemlineata</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2366490</td>\n",
       "      <td>[{'accession': 'Q27677', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7539</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>[]</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3227914</td>\n",
       "      <td>[{'accession': 'P36196', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>9031</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>[]</td>\n",
       "      <td>Danio rerio</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3308995</td>\n",
       "      <td>[{'accession': 'Q9DDE3', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7955</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>[]</td>\n",
       "      <td>Aedes aegypti</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>15.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4295607</td>\n",
       "      <td>[{'accession': 'Q6A2E2', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>[{'xref_id': 'Q95P20', 'xref_name': None, 'xre...</td>\n",
       "      <td>Musca domestica</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL5752</td>\n",
       "      <td>[{'accession': 'Q95P20', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7370</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>[]</td>\n",
       "      <td>Plutella xylostella</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2242729</td>\n",
       "      <td>[{'accession': 'Q8MZM0', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>51655</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>[]</td>\n",
       "      <td>Musca domestica</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2242743</td>\n",
       "      <td>[{'accession': 'Q7YWJ9', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>7370</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>[]</td>\n",
       "      <td>Pediculus humanus capitis</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2362988</td>\n",
       "      <td>[{'accession': 'A2PZ98', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>121226</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>[]</td>\n",
       "      <td>Spodoptera litura</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2366422</td>\n",
       "      <td>[{'accession': 'C5IU80', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>69820</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>[]</td>\n",
       "      <td>Laodelphax striatella</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2366446</td>\n",
       "      <td>[{'accession': 'K4JQ36', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>195883</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>[]</td>\n",
       "      <td>Schizaphis graminum</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2366511</td>\n",
       "      <td>[{'accession': 'Q9BMJ1', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>13262</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>[]</td>\n",
       "      <td>Caenorhabditis elegans</td>\n",
       "      <td>Acetylcholinesterase 1</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3341583</td>\n",
       "      <td>[{'accession': 'P38433', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>6239</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>[]</td>\n",
       "      <td>Rattus norvegicus</td>\n",
       "      <td>Acetylcholinesterase and butyrylcholinesterase...</td>\n",
       "      <td>13.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2111475</td>\n",
       "      <td>[{'accession': 'P37136', 'component_descriptio...</td>\n",
       "      <td>SELECTIVITY GROUP</td>\n",
       "      <td>10116</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cross_references  \\\n",
       "0   [{'xref_id': 'P22303', 'xref_name': None, 'xre...   \n",
       "1                                                  []   \n",
       "2                                                  []   \n",
       "3                                                  []   \n",
       "4   [{'xref_id': 'P04058', 'xref_name': None, 'xre...   \n",
       "5   [{'xref_id': 'P21836', 'xref_name': None, 'xre...   \n",
       "6   [{'xref_id': 'P37136', 'xref_name': None, 'xre...   \n",
       "7   [{'xref_id': 'O42275', 'xref_name': None, 'xre...   \n",
       "8   [{'xref_id': 'P23795', 'xref_name': None, 'xre...   \n",
       "9                                                  []   \n",
       "10                                                 []   \n",
       "11                                                 []   \n",
       "12                                                 []   \n",
       "13                                                 []   \n",
       "14  [{'xref_id': 'Q95P20', 'xref_name': None, 'xre...   \n",
       "15                                                 []   \n",
       "16                                                 []   \n",
       "17                                                 []   \n",
       "18                                                 []   \n",
       "19                                                 []   \n",
       "20                                                 []   \n",
       "21                                                 []   \n",
       "22                                                 []   \n",
       "\n",
       "                     organism  \\\n",
       "0                Homo sapiens   \n",
       "1                Homo sapiens   \n",
       "2     Drosophila melanogaster   \n",
       "3      Nephotettix cincticeps   \n",
       "4         Torpedo californica   \n",
       "5                Mus musculus   \n",
       "6           Rattus norvegicus   \n",
       "7    Electrophorus electricus   \n",
       "8                  Bos taurus   \n",
       "9           Anopheles gambiae   \n",
       "10  Leptinotarsa decemlineata   \n",
       "11              Gallus gallus   \n",
       "12                Danio rerio   \n",
       "13              Aedes aegypti   \n",
       "14            Musca domestica   \n",
       "15        Plutella xylostella   \n",
       "16            Musca domestica   \n",
       "17  Pediculus humanus capitis   \n",
       "18          Spodoptera litura   \n",
       "19      Laodelphax striatella   \n",
       "20        Schizaphis graminum   \n",
       "21     Caenorhabditis elegans   \n",
       "22          Rattus norvegicus   \n",
       "\n",
       "                                            pref_name  score  \\\n",
       "0                                Acetylcholinesterase   27.0   \n",
       "1                        Cholinesterases; ACHE & BCHE   27.0   \n",
       "2                                Acetylcholinesterase   17.0   \n",
       "3                Ace-orthologous acetylcholinesterase   17.0   \n",
       "4                                Acetylcholinesterase   15.0   \n",
       "5                                Acetylcholinesterase   15.0   \n",
       "6                                Acetylcholinesterase   15.0   \n",
       "7                                Acetylcholinesterase   15.0   \n",
       "8                                Acetylcholinesterase   15.0   \n",
       "9                                Acetylcholinesterase   15.0   \n",
       "10                               Acetylcholinesterase   15.0   \n",
       "11                               Acetylcholinesterase   15.0   \n",
       "12                               Acetylcholinesterase   15.0   \n",
       "13                               Acetylcholinesterase   15.0   \n",
       "14                               Acetylcholinesterase   14.0   \n",
       "15                               Acetylcholinesterase   14.0   \n",
       "16                               Acetylcholinesterase   14.0   \n",
       "17                               Acetylcholinesterase   14.0   \n",
       "18                               Acetylcholinesterase   14.0   \n",
       "19                               Acetylcholinesterase   14.0   \n",
       "20                               Acetylcholinesterase   14.0   \n",
       "21                             Acetylcholinesterase 1   14.0   \n",
       "22  Acetylcholinesterase and butyrylcholinesterase...   13.0   \n",
       "\n",
       "    species_group_flag target_chembl_id  \\\n",
       "0                False        CHEMBL220   \n",
       "1                False    CHEMBL2095233   \n",
       "2                False    CHEMBL2242744   \n",
       "3                False    CHEMBL2366514   \n",
       "4                False       CHEMBL4780   \n",
       "5                False       CHEMBL3198   \n",
       "6                False       CHEMBL3199   \n",
       "7                False       CHEMBL4078   \n",
       "8                False       CHEMBL4768   \n",
       "9                False    CHEMBL2046266   \n",
       "10               False    CHEMBL2366490   \n",
       "11               False    CHEMBL3227914   \n",
       "12               False    CHEMBL3308995   \n",
       "13               False    CHEMBL4295607   \n",
       "14               False       CHEMBL5752   \n",
       "15               False    CHEMBL2242729   \n",
       "16               False    CHEMBL2242743   \n",
       "17               False    CHEMBL2362988   \n",
       "18               False    CHEMBL2366422   \n",
       "19               False    CHEMBL2366446   \n",
       "20               False    CHEMBL2366511   \n",
       "21               False    CHEMBL3341583   \n",
       "22               False    CHEMBL2111475   \n",
       "\n",
       "                                    target_components        target_type  \\\n",
       "0   [{'accession': 'P22303', 'component_descriptio...     SINGLE PROTEIN   \n",
       "1   [{'accession': 'P06276', 'component_descriptio...  SELECTIVITY GROUP   \n",
       "2   [{'accession': 'P07140', 'component_descriptio...     SINGLE PROTEIN   \n",
       "3   [{'accession': 'Q9NJH6', 'component_descriptio...     SINGLE PROTEIN   \n",
       "4   [{'accession': 'P04058', 'component_descriptio...     SINGLE PROTEIN   \n",
       "5   [{'accession': 'P21836', 'component_descriptio...     SINGLE PROTEIN   \n",
       "6   [{'accession': 'P37136', 'component_descriptio...     SINGLE PROTEIN   \n",
       "7   [{'accession': 'O42275', 'component_descriptio...     SINGLE PROTEIN   \n",
       "8   [{'accession': 'P23795', 'component_descriptio...     SINGLE PROTEIN   \n",
       "9   [{'accession': 'Q869C3', 'component_descriptio...     SINGLE PROTEIN   \n",
       "10  [{'accession': 'Q27677', 'component_descriptio...     SINGLE PROTEIN   \n",
       "11  [{'accession': 'P36196', 'component_descriptio...     SINGLE PROTEIN   \n",
       "12  [{'accession': 'Q9DDE3', 'component_descriptio...     SINGLE PROTEIN   \n",
       "13  [{'accession': 'Q6A2E2', 'component_descriptio...     SINGLE PROTEIN   \n",
       "14  [{'accession': 'Q95P20', 'component_descriptio...     SINGLE PROTEIN   \n",
       "15  [{'accession': 'Q8MZM0', 'component_descriptio...     SINGLE PROTEIN   \n",
       "16  [{'accession': 'Q7YWJ9', 'component_descriptio...     SINGLE PROTEIN   \n",
       "17  [{'accession': 'A2PZ98', 'component_descriptio...     SINGLE PROTEIN   \n",
       "18  [{'accession': 'C5IU80', 'component_descriptio...     SINGLE PROTEIN   \n",
       "19  [{'accession': 'K4JQ36', 'component_descriptio...     SINGLE PROTEIN   \n",
       "20  [{'accession': 'Q9BMJ1', 'component_descriptio...     SINGLE PROTEIN   \n",
       "21  [{'accession': 'P38433', 'component_descriptio...     SINGLE PROTEIN   \n",
       "22  [{'accession': 'P37136', 'component_descriptio...  SELECTIVITY GROUP   \n",
       "\n",
       "    tax_id  \n",
       "0     9606  \n",
       "1     9606  \n",
       "2     7227  \n",
       "3    94400  \n",
       "4     7787  \n",
       "5    10090  \n",
       "6    10116  \n",
       "7     8005  \n",
       "8     9913  \n",
       "9     7165  \n",
       "10    7539  \n",
       "11    9031  \n",
       "12    7955  \n",
       "13    7159  \n",
       "14    7370  \n",
       "15   51655  \n",
       "16    7370  \n",
       "17  121226  \n",
       "18   69820  \n",
       "19  195883  \n",
       "20   13262  \n",
       "21    6239  \n",
       "22   10116  "
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Target search acetylcholineesterase\n",
    "target = new_client.target\n",
    "target_query = target.search('acetylcholinesterase')\n",
    "targets = pd.DataFrame.from_dict(target_query)\n",
    "targets"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Select and extract bioactivity data for Human Acetlycholinesterase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CHEMBL220'"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Selecting the human acetlycholinesterase\n",
    "selected_target = targets.target_chembl_id[0]\n",
    "selected_target"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>bao_label</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>33969</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.75</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>37563</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>37565</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>50.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>38902</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>41170</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.8</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>7021</th>\n",
       "      <td>None</td>\n",
       "      <td>18798886</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3.81</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7022</th>\n",
       "      <td>None</td>\n",
       "      <td>18798887</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3.46</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7023</th>\n",
       "      <td>None</td>\n",
       "      <td>18798888</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7024</th>\n",
       "      <td>None</td>\n",
       "      <td>18798889</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(/C=C/c1ccccc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7025</th>\n",
       "      <td>None</td>\n",
       "      <td>18798890</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(/C=C/c1ccc(O)cc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.51</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7026 rows × 43 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     activity_comment  activity_id activity_properties assay_chembl_id  \\\n",
       "0                None        33969                  []    CHEMBL643384   \n",
       "1                None        37563                  []    CHEMBL643384   \n",
       "2                None        37565                  []    CHEMBL643384   \n",
       "3                None        38902                  []    CHEMBL643384   \n",
       "4                None        41170                  []    CHEMBL643384   \n",
       "...               ...          ...                 ...             ...   \n",
       "7021             None     18798886                  []   CHEMBL4274263   \n",
       "7022             None     18798887                  []   CHEMBL4274263   \n",
       "7023             None     18798888                  []   CHEMBL4274263   \n",
       "7024             None     18798889                  []   CHEMBL4274263   \n",
       "7025             None     18798890                  []   CHEMBL4274263   \n",
       "\n",
       "                                      assay_description assay_type  \\\n",
       "0     Inhibitory concentration against acetylcholine...          B   \n",
       "1     Inhibitory concentration against acetylcholine...          B   \n",
       "2     Inhibitory concentration against acetylcholine...          B   \n",
       "3     Inhibitory concentration against acetylcholine...          B   \n",
       "4     Inhibitory concentration against acetylcholine...          B   \n",
       "...                                                 ...        ...   \n",
       "7021  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7022  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7023  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7024  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7025  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "\n",
       "     bao_endpoint   bao_format              bao_label  \\\n",
       "0     BAO_0000190  BAO_0000357  single protein format   \n",
       "1     BAO_0000190  BAO_0000357  single protein format   \n",
       "2     BAO_0000190  BAO_0000357  single protein format   \n",
       "3     BAO_0000190  BAO_0000357  single protein format   \n",
       "4     BAO_0000190  BAO_0000357  single protein format   \n",
       "...           ...          ...                    ...   \n",
       "7021  BAO_0000190  BAO_0000357  single protein format   \n",
       "7022  BAO_0000190  BAO_0000357  single protein format   \n",
       "7023  BAO_0000190  BAO_0000357  single protein format   \n",
       "7024  BAO_0000190  BAO_0000357  single protein format   \n",
       "7025  BAO_0000190  BAO_0000357  single protein format   \n",
       "\n",
       "                                       canonical_smiles  ... target_organism  \\\n",
       "0                 CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1  ...    Homo sapiens   \n",
       "1            O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1  ...    Homo sapiens   \n",
       "2     CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1  ...    Homo sapiens   \n",
       "3         O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F  ...    Homo sapiens   \n",
       "4             CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C  ...    Homo sapiens   \n",
       "...                                                 ...  ...             ...   \n",
       "7021  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...  ...    Homo sapiens   \n",
       "7022  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...  ...    Homo sapiens   \n",
       "7023  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...  ...    Homo sapiens   \n",
       "7024           O=C(/C=C/c1ccccc1)NCCC1CCN(Cc2ccccc2)CC1  ...    Homo sapiens   \n",
       "7025        O=C(/C=C/c1ccc(O)cc1)NCCC1CCN(Cc2ccccc2)CC1  ...    Homo sapiens   \n",
       "\n",
       "          target_pref_name target_tax_id text_value  toid  type units  \\\n",
       "0     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "1     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "2     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "3     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "4     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "...                    ...           ...        ...   ...   ...   ...   \n",
       "7021  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7022  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7023  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7024  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7025  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "\n",
       "        uo_units upper_value value  \n",
       "0     UO_0000065        None  0.75  \n",
       "1     UO_0000065        None   0.1  \n",
       "2     UO_0000065        None  50.0  \n",
       "3     UO_0000065        None   0.3  \n",
       "4     UO_0000065        None   0.8  \n",
       "...          ...         ...   ...  \n",
       "7021  UO_0000065        None  3.81  \n",
       "7022  UO_0000065        None  3.46  \n",
       "7023  UO_0000065        None  2.78  \n",
       "7024  UO_0000065        None  0.45  \n",
       "7025  UO_0000065        None  2.51  \n",
       "\n",
       "[7026 rows x 43 columns]"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Bioactivity data for target protein reported as pChEMBL values as IC50 nM\n",
    "#Making sure we dont have a mixture of bioactivity units\n",
    "activity = new_client.activity\n",
    "res = activity.filter(target_chembl_id=selected_target).filter(standard_type = \"IC50\")\n",
    "df = pd.DataFrame.from_dict(res)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Save data to csv\n",
    "df.to_csv(\"acetylcholinesterase_bioactivity_data_raw.csv\", index = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Handling Missing Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "<ipython-input-32-f8e906c5503c>:3: UserWarning: Boolean Series key will be reindexed to match DataFrame index.\n",
      "  df2 = df2[df.canonical_smiles.notna()]\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>bao_label</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>33969</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.75</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>37563</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>37565</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>50.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>38902</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>41170</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.8</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>7021</th>\n",
       "      <td>None</td>\n",
       "      <td>18798886</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3.81</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7022</th>\n",
       "      <td>None</td>\n",
       "      <td>18798887</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3.46</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7023</th>\n",
       "      <td>None</td>\n",
       "      <td>18798888</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7024</th>\n",
       "      <td>None</td>\n",
       "      <td>18798889</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(/C=C/c1ccccc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7025</th>\n",
       "      <td>None</td>\n",
       "      <td>18798890</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(/C=C/c1ccc(O)cc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.51</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5835 rows × 43 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     activity_comment  activity_id activity_properties assay_chembl_id  \\\n",
       "0                None        33969                  []    CHEMBL643384   \n",
       "1                None        37563                  []    CHEMBL643384   \n",
       "2                None        37565                  []    CHEMBL643384   \n",
       "3                None        38902                  []    CHEMBL643384   \n",
       "4                None        41170                  []    CHEMBL643384   \n",
       "...               ...          ...                 ...             ...   \n",
       "7021             None     18798886                  []   CHEMBL4274263   \n",
       "7022             None     18798887                  []   CHEMBL4274263   \n",
       "7023             None     18798888                  []   CHEMBL4274263   \n",
       "7024             None     18798889                  []   CHEMBL4274263   \n",
       "7025             None     18798890                  []   CHEMBL4274263   \n",
       "\n",
       "                                      assay_description assay_type  \\\n",
       "0     Inhibitory concentration against acetylcholine...          B   \n",
       "1     Inhibitory concentration against acetylcholine...          B   \n",
       "2     Inhibitory concentration against acetylcholine...          B   \n",
       "3     Inhibitory concentration against acetylcholine...          B   \n",
       "4     Inhibitory concentration against acetylcholine...          B   \n",
       "...                                                 ...        ...   \n",
       "7021  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7022  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7023  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7024  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7025  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "\n",
       "     bao_endpoint   bao_format              bao_label  \\\n",
       "0     BAO_0000190  BAO_0000357  single protein format   \n",
       "1     BAO_0000190  BAO_0000357  single protein format   \n",
       "2     BAO_0000190  BAO_0000357  single protein format   \n",
       "3     BAO_0000190  BAO_0000357  single protein format   \n",
       "4     BAO_0000190  BAO_0000357  single protein format   \n",
       "...           ...          ...                    ...   \n",
       "7021  BAO_0000190  BAO_0000357  single protein format   \n",
       "7022  BAO_0000190  BAO_0000357  single protein format   \n",
       "7023  BAO_0000190  BAO_0000357  single protein format   \n",
       "7024  BAO_0000190  BAO_0000357  single protein format   \n",
       "7025  BAO_0000190  BAO_0000357  single protein format   \n",
       "\n",
       "                                       canonical_smiles  ... target_organism  \\\n",
       "0                 CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1  ...    Homo sapiens   \n",
       "1            O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1  ...    Homo sapiens   \n",
       "2     CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1  ...    Homo sapiens   \n",
       "3         O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F  ...    Homo sapiens   \n",
       "4             CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C  ...    Homo sapiens   \n",
       "...                                                 ...  ...             ...   \n",
       "7021  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...  ...    Homo sapiens   \n",
       "7022  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...  ...    Homo sapiens   \n",
       "7023  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...  ...    Homo sapiens   \n",
       "7024           O=C(/C=C/c1ccccc1)NCCC1CCN(Cc2ccccc2)CC1  ...    Homo sapiens   \n",
       "7025        O=C(/C=C/c1ccc(O)cc1)NCCC1CCN(Cc2ccccc2)CC1  ...    Homo sapiens   \n",
       "\n",
       "          target_pref_name target_tax_id text_value  toid  type units  \\\n",
       "0     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "1     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "2     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "3     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "4     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "...                    ...           ...        ...   ...   ...   ...   \n",
       "7021  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7022  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7023  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7024  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7025  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "\n",
       "        uo_units upper_value value  \n",
       "0     UO_0000065        None  0.75  \n",
       "1     UO_0000065        None   0.1  \n",
       "2     UO_0000065        None  50.0  \n",
       "3     UO_0000065        None   0.3  \n",
       "4     UO_0000065        None   0.8  \n",
       "...          ...         ...   ...  \n",
       "7021  UO_0000065        None  3.81  \n",
       "7022  UO_0000065        None  3.46  \n",
       "7023  UO_0000065        None  2.78  \n",
       "7024  UO_0000065        None  0.45  \n",
       "7025  UO_0000065        None  2.51  \n",
       "\n",
       "[5835 rows x 43 columns]"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Dropping columns with missing standard_value and canonical_smiles\n",
    "#standard value represents the potency of the drug (concentration of drug; lower is better)\n",
    "#Canonical refers to the bonding structure of molecule and SMILES is a linear text format\n",
    "df2 = df[df.standard_value.notna()]\n",
    "df2 = df2[df.canonical_smiles.notna()]\n",
    "df2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>bao_label</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>33969</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.75</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>37563</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>37565</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>50.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>38902</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>41170</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL643384</td>\n",
       "      <td>Inhibitory concentration against acetylcholine...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.8</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>7019</th>\n",
       "      <td>None</td>\n",
       "      <td>18798884</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7020</th>\n",
       "      <td>None</td>\n",
       "      <td>18798885</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.54</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7021</th>\n",
       "      <td>None</td>\n",
       "      <td>18798886</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3.81</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7022</th>\n",
       "      <td>None</td>\n",
       "      <td>18798887</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3.46</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7023</th>\n",
       "      <td>None</td>\n",
       "      <td>18798888</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4274263</td>\n",
       "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>single protein format</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Acetylcholinesterase</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>2.78</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4695 rows × 43 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     activity_comment  activity_id activity_properties assay_chembl_id  \\\n",
       "0                None        33969                  []    CHEMBL643384   \n",
       "1                None        37563                  []    CHEMBL643384   \n",
       "2                None        37565                  []    CHEMBL643384   \n",
       "3                None        38902                  []    CHEMBL643384   \n",
       "4                None        41170                  []    CHEMBL643384   \n",
       "...               ...          ...                 ...             ...   \n",
       "7019             None     18798884                  []   CHEMBL4274263   \n",
       "7020             None     18798885                  []   CHEMBL4274263   \n",
       "7021             None     18798886                  []   CHEMBL4274263   \n",
       "7022             None     18798887                  []   CHEMBL4274263   \n",
       "7023             None     18798888                  []   CHEMBL4274263   \n",
       "\n",
       "                                      assay_description assay_type  \\\n",
       "0     Inhibitory concentration against acetylcholine...          B   \n",
       "1     Inhibitory concentration against acetylcholine...          B   \n",
       "2     Inhibitory concentration against acetylcholine...          B   \n",
       "3     Inhibitory concentration against acetylcholine...          B   \n",
       "4     Inhibitory concentration against acetylcholine...          B   \n",
       "...                                                 ...        ...   \n",
       "7019  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7020  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7021  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7022  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "7023  Inhibition of human erythrocyte AChE using ace...          B   \n",
       "\n",
       "     bao_endpoint   bao_format              bao_label  \\\n",
       "0     BAO_0000190  BAO_0000357  single protein format   \n",
       "1     BAO_0000190  BAO_0000357  single protein format   \n",
       "2     BAO_0000190  BAO_0000357  single protein format   \n",
       "3     BAO_0000190  BAO_0000357  single protein format   \n",
       "4     BAO_0000190  BAO_0000357  single protein format   \n",
       "...           ...          ...                    ...   \n",
       "7019  BAO_0000190  BAO_0000357  single protein format   \n",
       "7020  BAO_0000190  BAO_0000357  single protein format   \n",
       "7021  BAO_0000190  BAO_0000357  single protein format   \n",
       "7022  BAO_0000190  BAO_0000357  single protein format   \n",
       "7023  BAO_0000190  BAO_0000357  single protein format   \n",
       "\n",
       "                                       canonical_smiles  ... target_organism  \\\n",
       "0                 CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1  ...    Homo sapiens   \n",
       "1            O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1  ...    Homo sapiens   \n",
       "2     CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1  ...    Homo sapiens   \n",
       "3         O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F  ...    Homo sapiens   \n",
       "4             CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C  ...    Homo sapiens   \n",
       "...                                                 ...  ...             ...   \n",
       "7019  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...  ...    Homo sapiens   \n",
       "7020  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...  ...    Homo sapiens   \n",
       "7021  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...  ...    Homo sapiens   \n",
       "7022  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...  ...    Homo sapiens   \n",
       "7023  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...  ...    Homo sapiens   \n",
       "\n",
       "          target_pref_name target_tax_id text_value  toid  type units  \\\n",
       "0     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "1     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "2     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "3     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "4     Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "...                    ...           ...        ...   ...   ...   ...   \n",
       "7019  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7020  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7021  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7022  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "7023  Acetylcholinesterase          9606       None  None  IC50    uM   \n",
       "\n",
       "        uo_units upper_value value  \n",
       "0     UO_0000065        None  0.75  \n",
       "1     UO_0000065        None   0.1  \n",
       "2     UO_0000065        None  50.0  \n",
       "3     UO_0000065        None   0.3  \n",
       "4     UO_0000065        None   0.8  \n",
       "...          ...         ...   ...  \n",
       "7019  UO_0000065        None  2.44  \n",
       "7020  UO_0000065        None  2.54  \n",
       "7021  UO_0000065        None  3.81  \n",
       "7022  UO_0000065        None  3.46  \n",
       "7023  UO_0000065        None  2.78  \n",
       "\n",
       "[4695 rows x 43 columns]"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df2.canonical_smiles.unique())\n",
    "df2_nr = df2.drop_duplicates(['canonical_smiles'])\n",
    "df2_nr"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Pre-processing of Bioactivity Data\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL133897</td>\n",
       "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
       "      <td>750.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL336398</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
       "      <td>100.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL131588</td>\n",
       "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
       "      <td>50000.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL130628</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
       "      <td>300.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL130478</td>\n",
       "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
       "      <td>800.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7019</th>\n",
       "      <td>CHEMBL4293155</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
       "      <td>2440.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7020</th>\n",
       "      <td>CHEMBL4282558</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
       "      <td>2540.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7021</th>\n",
       "      <td>CHEMBL4281727</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
       "      <td>3810.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7022</th>\n",
       "      <td>CHEMBL4292349</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
       "      <td>3460.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7023</th>\n",
       "      <td>CHEMBL4278260</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
       "      <td>2780.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4695 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     molecule_chembl_id                                   canonical_smiles  \\\n",
       "0          CHEMBL133897              CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1   \n",
       "1          CHEMBL336398         O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1   \n",
       "2          CHEMBL131588  CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1   \n",
       "3          CHEMBL130628      O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F   \n",
       "4          CHEMBL130478          CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C   \n",
       "...                 ...                                                ...   \n",
       "7019      CHEMBL4293155  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...   \n",
       "7020      CHEMBL4282558  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...   \n",
       "7021      CHEMBL4281727  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...   \n",
       "7022      CHEMBL4292349  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...   \n",
       "7023      CHEMBL4278260  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...   \n",
       "\n",
       "     standard_value  \n",
       "0             750.0  \n",
       "1             100.0  \n",
       "2           50000.0  \n",
       "3             300.0  \n",
       "4             800.0  \n",
       "...             ...  \n",
       "7019         2440.0  \n",
       "7020         2540.0  \n",
       "7021         3810.0  \n",
       "7022         3460.0  \n",
       "7023         2780.0  \n",
       "\n",
       "[4695 rows x 3 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Combining 3 columns (molecule_chmebl_id, canonical_smiles, standard_value) and bioactivity_class into DF\n",
    "selection = ['molecule_chembl_id', 'canonical_smiles', 'standard_value']\n",
    "df3 = df2_nr[selection]\n",
    "df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Saving dataframe to csv\n",
    "df3.to_csv('acetylcholinesterase_bioactivity_data_preprocessed.csv', index = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Labelling compounds as active, inactive, or intermediate\n",
    "Bioacitvity measured in IC50 units. \n",
    "Active: IC50 < 1,000 nM\n",
    "Intermediate: 1,000 nM < IC50 < 10,000 nM\n",
    "Inactive: IC50 > 10,000 nM "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL133897</td>\n",
       "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
       "      <td>750.0</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL336398</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
       "      <td>100.0</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL131588</td>\n",
       "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
       "      <td>50000.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL130628</td>\n",
       "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
       "      <td>300.0</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL130478</td>\n",
       "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
       "      <td>800.0</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4690</th>\n",
       "      <td>CHEMBL4293155</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
       "      <td>2440.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4691</th>\n",
       "      <td>CHEMBL4282558</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
       "      <td>2540.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4692</th>\n",
       "      <td>CHEMBL4281727</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
       "      <td>3810.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4693</th>\n",
       "      <td>CHEMBL4292349</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
       "      <td>3460.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4694</th>\n",
       "      <td>CHEMBL4278260</td>\n",
       "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
       "      <td>2780.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4695 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     molecule_chembl_id                                   canonical_smiles  \\\n",
       "0          CHEMBL133897              CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1   \n",
       "1          CHEMBL336398         O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1   \n",
       "2          CHEMBL131588  CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1   \n",
       "3          CHEMBL130628      O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F   \n",
       "4          CHEMBL130478          CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C   \n",
       "...                 ...                                                ...   \n",
       "4690      CHEMBL4293155  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...   \n",
       "4691      CHEMBL4282558  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...   \n",
       "4692      CHEMBL4281727  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...   \n",
       "4693      CHEMBL4292349  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...   \n",
       "4694      CHEMBL4278260  CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...   \n",
       "\n",
       "      standard_value         class  \n",
       "0              750.0        active  \n",
       "1              100.0        active  \n",
       "2            50000.0      inactive  \n",
       "3              300.0        active  \n",
       "4              800.0        active  \n",
       "...              ...           ...  \n",
       "4690          2440.0  intermediate  \n",
       "4691          2540.0  intermediate  \n",
       "4692          3810.0  intermediate  \n",
       "4693          3460.0  intermediate  \n",
       "4694          2780.0  intermediate  \n",
       "\n",
       "[4695 rows x 4 columns]"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Implementing the 3 Class Labelling \n",
    "df4 = pd.read_csv('acetylcholinesterase_bioactivity_data_preprocessed.csv')\n",
    "\n",
    "bioactivity_threshold = []\n",
    "for i in df4.standard_value:\n",
    "    if float(i) >= 10000:\n",
    "        bioactivity_threshold.append(\"inactive\")\n",
    "    elif float(i) <= 1000:\n",
    "        bioactivity_threshold.append(\"active\")\n",
    "    else:\n",
    "        bioactivity_threshold.append(\"intermediate\")\n",
    "        \n",
    "bioactivity_class = pd.Series(bioactivity_threshold, name = 'class')\n",
    "df5 = pd.concat([df4, bioactivity_class], axis = 1)\n",
    "df5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "df5.to_csv('acetylcholinesterase_bioactivity_data_curated.csv', index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "updating: acetylcholinesterase_bioactivity_data_curated.csv (deflated 82%)\n",
      "updating: acetylcholinesterase_bioactivity_data_preprocessed.csv (deflated 81%)\n",
      "updating: acetylcholinesterase_bioactivity_data_raw.csv (deflated 90%)\n"
     ]
    }
   ],
   "source": [
    "!zip acetylcholinesetrase.zip *.csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 9576\n",
      "-rw-r--r--  1 nitheshperumal  staff   102557 Nov  6 10:08 Part1_QSAR_Drug_Discovery.ipynb\n",
      "-rw-r--r--  1 nitheshperumal  staff    17814 Nov  6 10:08 Part2_QSAR_Drug_Discovery.ipynb\n",
      "-rw-r--r--  1 nitheshperumal  staff   475825 Nov  6 10:11 acetylcholinesetrase.zip\n",
      "-rw-r--r--  1 nitheshperumal  staff   385924 Nov  6 10:11 acetylcholinesterase_bioactivity_data_curated.csv\n",
      "-rw-r--r--  1 nitheshperumal  staff   342989 Nov  6 10:11 acetylcholinesterase_bioactivity_data_preprocessed.csv\n",
      "-rw-r--r--  1 nitheshperumal  staff  3562870 Nov  6 10:10 acetylcholinesterase_bioactivity_data_raw.csv\n"
     ]
    }
   ],
   "source": [
    "ls -l"
   ]
  }
 ],
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