Drug discovery model.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "24299a8f-3272-4385-a025-790f70fdcf50",
   "metadata": {},
   "source": [
    "# Accelerated Drug Discovery Model"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8f017835-1d79-43ec-89da-a49bb35d1116",
   "metadata": {},
   "source": [
    "## Data collection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "4602adfb-671c-4f5d-b7b2-84298a04be84",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: chembl_webresource_client in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (0.10.9)\n",
      "Requirement already satisfied: urllib3 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from chembl_webresource_client) (1.26.14)\n",
      "Requirement already satisfied: requests>=2.18.4 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from chembl_webresource_client) (2.28.2)\n",
      "Requirement already satisfied: requests-cache~=1.2 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from chembl_webresource_client) (1.2.0)\n",
      "Requirement already satisfied: easydict in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from chembl_webresource_client) (1.12)\n",
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      "Requirement already satisfied: idna<4,>=2.5 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from requests>=2.18.4->chembl_webresource_client) (3.4)\n",
      "Requirement already satisfied: certifi>=2017.4.17 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from requests>=2.18.4->chembl_webresource_client) (2022.12.7)\n",
      "Requirement already satisfied: attrs>=21.2 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from requests-cache~=1.2->chembl_webresource_client) (23.1.0)\n",
      "Requirement already satisfied: cattrs>=22.2 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from requests-cache~=1.2->chembl_webresource_client) (23.2.3)\n",
      "Requirement already satisfied: platformdirs>=2.5 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from requests-cache~=1.2->chembl_webresource_client) (3.2.0)\n",
      "Requirement already satisfied: url-normalize>=1.4 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from requests-cache~=1.2->chembl_webresource_client) (1.4.3)\n",
      "Requirement already satisfied: exceptiongroup>=1.1.1 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from cattrs>=22.2->requests-cache~=1.2->chembl_webresource_client) (1.1.2)\n",
      "Requirement already satisfied: typing-extensions!=4.6.3,>=4.1.0 in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from cattrs>=22.2->requests-cache~=1.2->chembl_webresource_client) (4.5.0)\n",
      "Requirement already satisfied: six in c:\\users\\vivek singh\\appdata\\local\\programs\\python\\python310\\lib\\site-packages (from url-normalize>=1.4->requests-cache~=1.2->chembl_webresource_client) (1.16.0)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "[notice] A new release of pip is available: 23.3.2 -> 24.0\n",
      "[notice] To update, run: python.exe -m pip install --upgrade pip\n"
     ]
    }
   ],
   "source": [
    "! pip install chembl_webresource_client"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1363405d-4664-44d7-857f-098935609ca9",
   "metadata": {},
   "source": [
    "## Libraries import"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "09959822-02ac-45ad-858d-4a40c064a6ae",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from chembl_webresource_client.new_client import new_client"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8050232e-a701-426f-b8c5-b3d8a1c2a81d",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Search for Target protein "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "67b4bdc7-7eaf-4f12-a7ac-b9e882e734e4",
   "metadata": {},
   "source": [
    "### Target search for coronavirus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "7f1db529-8c22-45a3-9845-db77a17f9255",
   "metadata": {
    "tags": []
   },
   "outputs": [
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       "  <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>[]</td>\n",
       "      <td>Coronavirus</td>\n",
       "      <td>Coronavirus</td>\n",
       "      <td>17.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL613732</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>11119</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[]</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL612575</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>227859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[]</td>\n",
       "      <td>Feline coronavirus</td>\n",
       "      <td>Feline coronavirus</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL612744</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>12663</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>[]</td>\n",
       "      <td>Murine coronavirus</td>\n",
       "      <td>Murine coronavirus</td>\n",
       "      <td>14.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL5209664</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>694005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>[]</td>\n",
       "      <td>Human coronavirus 229E</td>\n",
       "      <td>Human coronavirus 229E</td>\n",
       "      <td>12.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL613837</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>11137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>[]</td>\n",
       "      <td>Human coronavirus OC43</td>\n",
       "      <td>Human coronavirus OC43</td>\n",
       "      <td>12.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL5209665</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>31631</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>[{'xref_id': 'P0C6U8', 'xref_name': None, 'xre...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>10.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3927</td>\n",
       "      <td>[{'accession': 'P0C6U8', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>227859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>[]</td>\n",
       "      <td>Middle East respiratory syndrome-related coron...</td>\n",
       "      <td>Middle East respiratory syndrome-related coron...</td>\n",
       "      <td>9.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4296578</td>\n",
       "      <td>[]</td>\n",
       "      <td>ORGANISM</td>\n",
       "      <td>1335626</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>[{'xref_id': 'P0C6X7', 'xref_name': None, 'xre...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>Replicase polyprotein 1ab</td>\n",
       "      <td>4.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL5118</td>\n",
       "      <td>[{'accession': 'P0C6X7', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>227859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>[]</td>\n",
       "      <td>Severe acute respiratory syndrome coronavirus 2</td>\n",
       "      <td>Replicase polyprotein 1ab</td>\n",
       "      <td>4.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4523582</td>\n",
       "      <td>[{'accession': 'P0DTD1', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>2697049</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      "text/plain": [
       "                                    cross_references  \\\n",
       "0                                                 []   \n",
       "1                                                 []   \n",
       "2                                                 []   \n",
       "3                                                 []   \n",
       "4                                                 []   \n",
       "5                                                 []   \n",
       "6  [{'xref_id': 'P0C6U8', 'xref_name': None, 'xre...   \n",
       "7                                                 []   \n",
       "8  [{'xref_id': 'P0C6X7', 'xref_name': None, 'xre...   \n",
       "9                                                 []   \n",
       "\n",
       "                                            organism  \\\n",
       "0                                        Coronavirus   \n",
       "1                                   SARS coronavirus   \n",
       "2                                 Feline coronavirus   \n",
       "3                                 Murine coronavirus   \n",
       "4                             Human coronavirus 229E   \n",
       "5                             Human coronavirus OC43   \n",
       "6                                   SARS coronavirus   \n",
       "7  Middle East respiratory syndrome-related coron...   \n",
       "8                                   SARS coronavirus   \n",
       "9    Severe acute respiratory syndrome coronavirus 2   \n",
       "\n",
       "                                           pref_name  score  \\\n",
       "0                                        Coronavirus   17.0   \n",
       "1                                   SARS coronavirus   14.0   \n",
       "2                                 Feline coronavirus   14.0   \n",
       "3                                 Murine coronavirus   14.0   \n",
       "4                             Human coronavirus 229E   12.0   \n",
       "5                             Human coronavirus OC43   12.0   \n",
       "6                SARS coronavirus 3C-like proteinase   10.0   \n",
       "7  Middle East respiratory syndrome-related coron...    9.0   \n",
       "8                          Replicase polyprotein 1ab    4.0   \n",
       "9                          Replicase polyprotein 1ab    4.0   \n",
       "\n",
       "   species_group_flag target_chembl_id  \\\n",
       "0               False     CHEMBL613732   \n",
       "1               False     CHEMBL612575   \n",
       "2               False     CHEMBL612744   \n",
       "3               False    CHEMBL5209664   \n",
       "4               False     CHEMBL613837   \n",
       "5               False    CHEMBL5209665   \n",
       "6               False       CHEMBL3927   \n",
       "7               False    CHEMBL4296578   \n",
       "8               False       CHEMBL5118   \n",
       "9               False    CHEMBL4523582   \n",
       "\n",
       "                                   target_components     target_type   tax_id  \n",
       "0                                                 []        ORGANISM    11119  \n",
       "1                                                 []        ORGANISM   227859  \n",
       "2                                                 []        ORGANISM    12663  \n",
       "3                                                 []        ORGANISM   694005  \n",
       "4                                                 []        ORGANISM    11137  \n",
       "5                                                 []        ORGANISM    31631  \n",
       "6  [{'accession': 'P0C6U8', 'component_descriptio...  SINGLE PROTEIN   227859  \n",
       "7                                                 []        ORGANISM  1335626  \n",
       "8  [{'accession': 'P0C6X7', 'component_descriptio...  SINGLE PROTEIN   227859  \n",
       "9  [{'accession': 'P0DTD1', 'component_descriptio...  SINGLE PROTEIN  2697049  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tg = new_client.target\n",
    "tg_query = tg.search('coronavirus')\n",
    "targets_df = pd.DataFrame.from_dict(tg_query)\n",
    "targets_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "26b01740-a547-47a9-8b37-a983f7782626",
   "metadata": {},
   "source": [
    "### Choose and get SARS coronavirus 3C-like proteinase bioactivity data (seventh entry)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "844ab464-6401-4e0d-840b-b19e15074068",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CHEMBL3927'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tg_selected = targets_df.target_chembl_id[6]\n",
    "tg_selected"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "359f99c7-e1c4-409a-9c5f-2c1ae364542c",
   "metadata": {},
   "source": [
    "##### Only the coronavirus 3C-like proteinase (CHEMBL3927) bioactivity data that are given as IC 50 values in nM (nanomolar) units will be retrieved in this case."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "eefc556d-0c30-43b9-a148-8f82468204ab",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "activity = new_client.activity\n",
    "result = activity.filter(target_chembl_id=tg_selected).filter(standard_type=\"IC50\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a96f5c87-1530-4a77-8b9b-28c5dab6db6d",
   "metadata": {
    "tags": []
   },
   "outputs": [
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       "      <td>[]</td>\n",
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       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
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       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
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       "      <td>None</td>\n",
       "      <td>7.2</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
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       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
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       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>9.4</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1481061</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL830868</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>13.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1481065</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>13.11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1481066</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>2.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 46 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  action_type activity_comment  activity_id activity_properties  \\\n",
       "0        None             None      1480935                  []   \n",
       "1        None             None      1480936                  []   \n",
       "2        None             None      1481061                  []   \n",
       "3        None             None      1481065                  []   \n",
       "4        None             None      1481066                  []   \n",
       "\n",
       "  assay_chembl_id                                  assay_description  \\\n",
       "0    CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "1    CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "2    CHEMBL830868  In vitro inhibitory concentration against SARS...   \n",
       "3    CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "4    CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "\n",
       "  assay_type assay_variant_accession assay_variant_mutation bao_endpoint  ...  \\\n",
       "0          B                    None                   None  BAO_0000190  ...   \n",
       "1          B                    None                   None  BAO_0000190  ...   \n",
       "2          B                    None                   None  BAO_0000190  ...   \n",
       "3          B                    None                   None  BAO_0000190  ...   \n",
       "4          B                    None                   None  BAO_0000190  ...   \n",
       "\n",
       "    target_organism                     target_pref_name target_tax_id  \\\n",
       "0  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "1  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "2  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "3  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "4  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "\n",
       "  text_value  toid  type units    uo_units upper_value  value  \n",
       "0       None  None  IC50    uM  UO_0000065        None    7.2  \n",
       "1       None  None  IC50    uM  UO_0000065        None    9.4  \n",
       "2       None  None  IC50    uM  UO_0000065        None   13.5  \n",
       "3       None  None  IC50    uM  UO_0000065        None  13.11  \n",
       "4       None  None  IC50    uM  UO_0000065        None    2.0  \n",
       "\n",
       "[5 rows x 46 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.DataFrame.from_dict(result)\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d77b4540-d5b9-448d-bfb7-a2741432c94a",
   "metadata": {},
   "source": [
    "#### Save the bioactivity data to a csv file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "fe88dd2a-c71d-4d2b-921b-5181eae8fb90",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "df.to_csv('data_raw.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7053960d-9b0a-4294-8877-860178f8db29",
   "metadata": {},
   "source": [
    "### Handling missing data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8debe508-70a3-4597-8a9b-0cae1cf025af",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<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>action_type</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>assay_variant_accession</th>\n",
       "      <th>assay_variant_mutation</th>\n",
       "      <th>bao_endpoint</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>None</td>\n",
       "      <td>1480935</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>7.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1480936</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>9.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1481061</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL830868</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>13.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1481065</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>13.11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1481066</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL829584</td>\n",
       "      <td>In vitro inhibitory concentration against SARS...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>2.0</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>128</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>12041507</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL2150313</td>\n",
       "      <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>10.6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>12041508</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL2150313</td>\n",
       "      <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>10.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>12041509</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL2150313</td>\n",
       "      <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>11.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>131</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>12041510</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL2150313</td>\n",
       "      <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>10.7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>132</th>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>12041511</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL2150313</td>\n",
       "      <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>...</td>\n",
       "      <td>SARS coronavirus</td>\n",
       "      <td>SARS coronavirus 3C-like proteinase</td>\n",
       "      <td>227859</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>78.9</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>133 rows × 46 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    action_type activity_comment  activity_id activity_properties  \\\n",
       "0          None             None      1480935                  []   \n",
       "1          None             None      1480936                  []   \n",
       "2          None             None      1481061                  []   \n",
       "3          None             None      1481065                  []   \n",
       "4          None             None      1481066                  []   \n",
       "..          ...              ...          ...                 ...   \n",
       "128        None             None     12041507                  []   \n",
       "129        None             None     12041508                  []   \n",
       "130        None             None     12041509                  []   \n",
       "131        None             None     12041510                  []   \n",
       "132        None             None     12041511                  []   \n",
       "\n",
       "    assay_chembl_id                                  assay_description  \\\n",
       "0      CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "1      CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "2      CHEMBL830868  In vitro inhibitory concentration against SARS...   \n",
       "3      CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "4      CHEMBL829584  In vitro inhibitory concentration against SARS...   \n",
       "..              ...                                                ...   \n",
       "128   CHEMBL2150313  Inhibition of SARS-CoV PLpro expressed in Esch...   \n",
       "129   CHEMBL2150313  Inhibition of SARS-CoV PLpro expressed in Esch...   \n",
       "130   CHEMBL2150313  Inhibition of SARS-CoV PLpro expressed in Esch...   \n",
       "131   CHEMBL2150313  Inhibition of SARS-CoV PLpro expressed in Esch...   \n",
       "132   CHEMBL2150313  Inhibition of SARS-CoV PLpro expressed in Esch...   \n",
       "\n",
       "    assay_type assay_variant_accession assay_variant_mutation bao_endpoint  \\\n",
       "0            B                    None                   None  BAO_0000190   \n",
       "1            B                    None                   None  BAO_0000190   \n",
       "2            B                    None                   None  BAO_0000190   \n",
       "3            B                    None                   None  BAO_0000190   \n",
       "4            B                    None                   None  BAO_0000190   \n",
       "..         ...                     ...                    ...          ...   \n",
       "128          B                    None                   None  BAO_0000190   \n",
       "129          B                    None                   None  BAO_0000190   \n",
       "130          B                    None                   None  BAO_0000190   \n",
       "131          B                    None                   None  BAO_0000190   \n",
       "132          B                    None                   None  BAO_0000190   \n",
       "\n",
       "     ...   target_organism                     target_pref_name target_tax_id  \\\n",
       "0    ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "1    ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "2    ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "3    ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "4    ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "..   ...               ...                                  ...           ...   \n",
       "128  ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "129  ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "130  ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "131  ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "132  ...  SARS coronavirus  SARS coronavirus 3C-like proteinase        227859   \n",
       "\n",
       "    text_value  toid  type units    uo_units upper_value  value  \n",
       "0         None  None  IC50    uM  UO_0000065        None    7.2  \n",
       "1         None  None  IC50    uM  UO_0000065        None    9.4  \n",
       "2         None  None  IC50    uM  UO_0000065        None   13.5  \n",
       "3         None  None  IC50    uM  UO_0000065        None  13.11  \n",
       "4         None  None  IC50    uM  UO_0000065        None    2.0  \n",
       "..         ...   ...   ...   ...         ...         ...    ...  \n",
       "128       None  None  IC50    uM  UO_0000065        None   10.6  \n",
       "129       None  None  IC50    uM  UO_0000065        None   10.1  \n",
       "130       None  None  IC50    uM  UO_0000065        None   11.5  \n",
       "131       None  None  IC50    uM  UO_0000065        None   10.7  \n",
       "132       None  None  IC50    uM  UO_0000065        None   78.9  \n",
       "\n",
       "[133 rows x 46 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2 = df[df.standard_value.notna()]\n",
    "df2"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "622d3d46-7774-4b66-bf69-44f97c5f523c",
   "metadata": {},
   "source": [
    "## Data Preprocessing"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9ade074c-20c5-4beb-b39a-30a15cac0ea8",
   "metadata": {},
   "source": [
    "### 3 classes classification of compounds - Active, Inactive and Intermediate"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cfd3e77a-8798-418e-904c-7f3b263cebca",
   "metadata": {},
   "source": [
    "The IC50 unit contains the bioactivity data. Compounds will be classified as **active** if their value is less than 1000 nM, and as **inactive** if it is more than 10,000 nM. We will refer to values that fall between 1,000 and 10,000 nM as  **intermediate**."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "07568c2b-48ca-46a1-b4fc-794daeb1506e",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "compound_class = []\n",
    "for i in df2.standard_value:\n",
    "  if float(i) >= 10000:\n",
    "    compound_class.append(\"inactive\")\n",
    "  elif float(i) <= 1000:\n",
    "    compound_class.append(\"active\")\n",
    "  else:\n",
    "    compound_class.append(\"intermediate\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "82049090-5fcd-4b37-ae20-6b6319b9f2c1",
   "metadata": {},
   "source": [
    "### Extracting and combining useful columns "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "54245d50-f929-40ac-9588-1828373851db",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe thead th {\n",
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       "    }\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>CHEMBL187579</td>\n",
       "      <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
       "      <td>7200.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL188487</td>\n",
       "      <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
       "      <td>9400.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL185698</td>\n",
       "      <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
       "      <td>13500.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL426082</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
       "      <td>13110.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL187717</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]</td>\n",
       "      <td>2000.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>128</th>\n",
       "      <td>CHEMBL2146517</td>\n",
       "      <td>COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...</td>\n",
       "      <td>10600.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>CHEMBL187460</td>\n",
       "      <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
       "      <td>10100.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>CHEMBL363535</td>\n",
       "      <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
       "      <td>11500.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>131</th>\n",
       "      <td>CHEMBL227075</td>\n",
       "      <td>Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1</td>\n",
       "      <td>10700.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>132</th>\n",
       "      <td>CHEMBL45830</td>\n",
       "      <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
       "      <td>78900.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>133 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    molecule_chembl_id                                   canonical_smiles  \\\n",
       "0         CHEMBL187579             Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21   \n",
       "1         CHEMBL188487             O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21   \n",
       "2         CHEMBL185698            O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21   \n",
       "3         CHEMBL426082                O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21   \n",
       "4         CHEMBL187717    O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]   \n",
       "..                 ...                                                ...   \n",
       "128      CHEMBL2146517  COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...   \n",
       "129       CHEMBL187460        C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C   \n",
       "130       CHEMBL363535             Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12   \n",
       "131       CHEMBL227075      Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1   \n",
       "132        CHEMBL45830             CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C   \n",
       "\n",
       "    standard_value  \n",
       "0           7200.0  \n",
       "1           9400.0  \n",
       "2          13500.0  \n",
       "3          13110.0  \n",
       "4           2000.0  \n",
       "..             ...  \n",
       "128        10600.0  \n",
       "129        10100.0  \n",
       "130        11500.0  \n",
       "131        10700.0  \n",
       "132        78900.0  \n",
       "\n",
       "[133 rows x 3 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "selection = ['molecule_chembl_id','canonical_smiles','standard_value']\n",
    "df3 = df2[selection]\n",
    "df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "841331a6-b1c9-4a63-9cf2-a3fd66e02345",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "      <th>compound_class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL187579</td>\n",
       "      <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
       "      <td>7200.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL188487</td>\n",
       "      <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
       "      <td>9400.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL185698</td>\n",
       "      <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
       "      <td>13500.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL426082</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
       "      <td>13110.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL187717</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]</td>\n",
       "      <td>2000.0</td>\n",
       "      <td>intermediate</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>128</th>\n",
       "      <td>CHEMBL2146517</td>\n",
       "      <td>COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...</td>\n",
       "      <td>10600.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>CHEMBL187460</td>\n",
       "      <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
       "      <td>10100.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>CHEMBL363535</td>\n",
       "      <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
       "      <td>11500.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>131</th>\n",
       "      <td>CHEMBL227075</td>\n",
       "      <td>Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1</td>\n",
       "      <td>10700.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>132</th>\n",
       "      <td>CHEMBL45830</td>\n",
       "      <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
       "      <td>78900.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>133 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    molecule_chembl_id                                   canonical_smiles  \\\n",
       "0         CHEMBL187579             Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21   \n",
       "1         CHEMBL188487             O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21   \n",
       "2         CHEMBL185698            O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21   \n",
       "3         CHEMBL426082                O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21   \n",
       "4         CHEMBL187717    O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]   \n",
       "..                 ...                                                ...   \n",
       "128      CHEMBL2146517  COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...   \n",
       "129       CHEMBL187460        C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C   \n",
       "130       CHEMBL363535             Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12   \n",
       "131       CHEMBL227075      Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1   \n",
       "132        CHEMBL45830             CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C   \n",
       "\n",
       "    standard_value compound_class  \n",
       "0           7200.0   intermediate  \n",
       "1           9400.0   intermediate  \n",
       "2          13500.0       inactive  \n",
       "3          13110.0       inactive  \n",
       "4           2000.0   intermediate  \n",
       "..             ...            ...  \n",
       "128        10600.0       inactive  \n",
       "129        10100.0       inactive  \n",
       "130        11500.0       inactive  \n",
       "131        10700.0       inactive  \n",
       "132        78900.0       inactive  \n",
       "\n",
       "[133 rows x 4 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "compound_class = pd.Series(compound_class, name='compound_class')\n",
    "df4 = pd.concat([df3, compound_class], axis=1)\n",
    "df4"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bfda31cd-2bcd-4260-8bab-b1c84e113e00",
   "metadata": {},
   "source": [
    "### Save dataframe to CSV file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "16d2d628-c374-46c5-a4c2-5a9990963f2f",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "df4.to_csv('data_preprocessed.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b427c98e-b7ec-40e9-91fc-04ea2754e08d",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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