part_1_drug_discovery.ipynb

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  "metadata": {
    "colab": {
      "name": "part-1-drug-discovery.ipynb",
      "provenance": [],
      "authorship_tag": "ABX9TyNmnGP+xQCtdnbSojDYc3sp",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/ammiellewb/druglikeness/blob/main/part_1_drug_discovery.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "-TNGQ9fT3M9b",
        "outputId": "bb8d252e-4008-4053-ab89-ac8d30e45d5c"
      },
      "source": [
        "# downloading package to retrieve data from the ChEMBL database\n",
        "! pip install chembl_webresource_client"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting chembl_webresource_client\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/2e/48/0db29040c92726fcc6f99a5bc89e0ea8cf5a9d84753ebaaf53108792da2a/chembl-webresource-client-0.10.2.tar.gz (51kB)\n",
            "\r\u001b[K     |██████▍                         | 10kB 15.2MB/s eta 0:00:01\r\u001b[K     |████████████▊                   | 20kB 20.6MB/s eta 0:00:01\r\u001b[K     |███████████████████             | 30kB 20.5MB/s eta 0:00:01\r\u001b[K     |█████████████████████████▍      | 40kB 16.7MB/s eta 0:00:01\r\u001b[K     |███████████████████████████████▊| 51kB 15.1MB/s eta 0:00:01\r\u001b[K     |████████████████████████████████| 61kB 4.5MB/s \n",
            "\u001b[?25hRequirement already satisfied: urllib3 in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (1.24.3)\n",
            "Requirement already satisfied: requests>=2.18.4 in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (2.23.0)\n",
            "Collecting requests-cache>=0.4.7\n",
            "  Downloading https://files.pythonhosted.org/packages/7f/55/9b1c40eb83c16d8fc79c5f6c2ffade04208b080670fbfc35e0a5effb5a92/requests_cache-0.5.2-py2.py3-none-any.whl\n",
            "Requirement already satisfied: easydict in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (1.9)\n",
            "Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests>=2.18.4->chembl_webresource_client) (3.0.4)\n",
            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests>=2.18.4->chembl_webresource_client) (2020.12.5)\n",
            "Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests>=2.18.4->chembl_webresource_client) (2.10)\n",
            "Building wheels for collected packages: chembl-webresource-client\n",
            "  Building wheel for chembl-webresource-client (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for chembl-webresource-client: filename=chembl_webresource_client-0.10.2-cp37-none-any.whl size=55661 sha256=ab394169cdd5a3f4b8a4243b25dd764441b9ba83f4a413ef91ab4aea29731c3f\n",
            "  Stored in directory: /root/.cache/pip/wheels/e6/96/19/3f042bfda7c669bfe24c8278477f57b0fbbf3e488b4c09e3a8\n",
            "Successfully built chembl-webresource-client\n",
            "Installing collected packages: requests-cache, chembl-webresource-client\n",
            "Successfully installed chembl-webresource-client-0.10.2 requests-cache-0.5.2\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "iqSth_v_3WBe"
      },
      "source": [
        "# importing needed libraries\n",
        "import pandas as pd\n",
        "from chembl_webresource_client.new_client import new_client"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "id": "Nt1C0TeA3WKF",
        "outputId": "1b79819f-a066-4c46-c1a7-c8bcb14cb577"
      },
      "source": [
        "# searching for coronavirus\n",
        "target = new_client.target\n",
        "target_query = target.search(\"acetylcholinesterase\")\n",
        "targets = pd.DataFrame.from_dict(target_query)\n",
        "targets"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
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              "</style>\n",
              "<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>[{'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>4</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>5</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>6</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>7</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>8</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>9</th>\n",
              "      <td>[]</td>\n",
              "      <td>Bemisia tabaci</td>\n",
              "      <td>AChE2</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2366409</td>\n",
              "      <td>[{'accession': 'B3SST5', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7038</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>Nephotettix cincticeps</td>\n",
              "      <td>Ace-orthologous acetylcholinesterase</td>\n",
              "      <td>15.0</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>12</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>13</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>14</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>15</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>16</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>17</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>18</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>19</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>20</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>21</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>22</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>23</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  ...  tax_id\n",
              "0   [{'xref_id': 'P22303', 'xref_name': None, 'xre...  ...    9606\n",
              "1                                                  []  ...    9606\n",
              "2                                                  []  ...    7227\n",
              "3   [{'xref_id': 'P04058', 'xref_name': None, 'xre...  ...    7787\n",
              "4   [{'xref_id': 'P21836', 'xref_name': None, 'xre...  ...   10090\n",
              "5   [{'xref_id': 'P37136', 'xref_name': None, 'xre...  ...   10116\n",
              "6   [{'xref_id': 'O42275', 'xref_name': None, 'xre...  ...    8005\n",
              "7   [{'xref_id': 'P23795', 'xref_name': None, 'xre...  ...    9913\n",
              "8                                                  []  ...    7165\n",
              "9                                                  []  ...    7038\n",
              "10                                                 []  ...    7539\n",
              "11                                                 []  ...   94400\n",
              "12                                                 []  ...    9031\n",
              "13                                                 []  ...    7955\n",
              "14                                                 []  ...    7159\n",
              "15  [{'xref_id': 'Q95P20', 'xref_name': None, 'xre...  ...    7370\n",
              "16                                                 []  ...   51655\n",
              "17                                                 []  ...    7370\n",
              "18                                                 []  ...  121226\n",
              "19                                                 []  ...   69820\n",
              "20                                                 []  ...  195883\n",
              "21                                                 []  ...   13262\n",
              "22                                                 []  ...    6239\n",
              "23                                                 []  ...   10116\n",
              "\n",
              "[24 rows x 9 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 3
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "id": "biaM70D93WOj",
        "outputId": "16ba4a3b-865f-46d3-baeb-74ee571ad010"
      },
      "source": [
        "# looking for \"SINGLE PROTEIN\" only in target_type\n",
        "# selecting bioactivity data for SARS coronavirus 3C-like proteinase\n",
        "selected_target = targets.target_chembl_id[0]\n",
        "\n",
        "# printing unique identification of target\n",
        "selected_target"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'CHEMBL220'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 4
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "6UMXFdV03WRn"
      },
      "source": [
        "activity = new_client.activity\n",
        "\n",
        "# only selecting IC50 molecules\n",
        "res = activity.filter(target_chembl_id=selected_target).filter(standard_type=\"IC50\")"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "I3pHVbjn3WWk",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 779
        },
        "outputId": "8889e224-b953-4157-ce23-31dc38a72fff"
      },
      "source": [
        "df = pd.DataFrame.from_dict(res)\n",
        "df"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>assay_variant_accession</th>\n",
              "      <th>assay_variant_mutation</th>\n",
              "      <th>bao_endpoint</th>\n",
              "      <th>bao_format</th>\n",
              "      <th>bao_label</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>data_validity_comment</th>\n",
              "      <th>data_validity_description</th>\n",
              "      <th>document_chembl_id</th>\n",
              "      <th>document_journal</th>\n",
              "      <th>document_year</th>\n",
              "      <th>ligand_efficiency</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>molecule_pref_name</th>\n",
              "      <th>parent_molecule_chembl_id</th>\n",
              "      <th>pchembl_value</th>\n",
              "      <th>potential_duplicate</th>\n",
              "      <th>qudt_units</th>\n",
              "      <th>record_id</th>\n",
              "      <th>relation</th>\n",
              "      <th>src_id</th>\n",
              "      <th>standard_flag</th>\n",
              "      <th>standard_relation</th>\n",
              "      <th>standard_text_value</th>\n",
              "      <th>standard_type</th>\n",
              "      <th>standard_units</th>\n",
              "      <th>standard_upper_value</th>\n",
              "      <th>standard_value</th>\n",
              "      <th>target_chembl_id</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '19.61', 'le': '0.36', 'lle': '3.32', ...</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>6.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252547</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>750.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '18.57', 'le': '0.38', 'lle': '2.45', ...</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>7.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252533</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>100.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252530</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '16.11', 'le': '0.34', 'lle': '1.81', ...</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>6.52</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252534</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>300.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '17.60', 'le': '0.36', 'lle': '3.00', ...</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>6.10</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252552</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>800.0</td>\n",
              "      <td>CHEMBL220</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",
              "      <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",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7474</th>\n",
              "      <td>None</td>\n",
              "      <td>19468459</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C(F)(F)F)CC3...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>{'bei': '9.32', 'le': '0.18', 'lle': '-2.84', ...</td>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>5.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255436</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>7570.0</td>\n",
              "      <td>CHEMBL220</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>7.57</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7475</th>\n",
              "      <td>None</td>\n",
              "      <td>19468460</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C)CC3)sc2-c2...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255435</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>CHEMBL220</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7476</th>\n",
              "      <td>None</td>\n",
              "      <td>19487200</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>C/C=C1\\[C@H]2C=C(C)C[C@]1(N)c1ccc(=O)[nH]c1C2</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '22.15', 'le': '0.41', 'lle': '3.37', ...</td>\n",
              "      <td>CHEMBL395280</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL395280</td>\n",
              "      <td>5.37</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258965</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>4300.0</td>\n",
              "      <td>CHEMBL220</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>4.3</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7477</th>\n",
              "      <td>None</td>\n",
              "      <td>19487204</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(O)c2c(c1)C1=C(c3c(O)c(O)cc(C)c3-c3cc(OC...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '8.34', 'le': '0.16', 'lle': '0.75', '...</td>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>4.81</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258961</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>15500.0</td>\n",
              "      <td>CHEMBL220</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>15.5</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7478</th>\n",
              "      <td>None</td>\n",
              "      <td>19487205</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(O)c(C(C)=O)c(-c2c(C)cc(O)c3oc4c(O)cc(C)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '7.46', 'le': '0.14', 'lle': '-2.11', ...</td>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>4.17</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258960</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>68300.0</td>\n",
              "      <td>CHEMBL220</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>68.3</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>7479 rows × 45 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value value\n",
              "0                None        33969  ...        None  0.75\n",
              "1                None        37563  ...        None   0.1\n",
              "2                None        37565  ...        None  50.0\n",
              "3                None        38902  ...        None   0.3\n",
              "4                None        41170  ...        None   0.8\n",
              "...               ...          ...  ...         ...   ...\n",
              "7474             None     19468459  ...        None  7.57\n",
              "7475             None     19468460  ...        None  10.0\n",
              "7476             None     19487200  ...        None   4.3\n",
              "7477             None     19487204  ...        None  15.5\n",
              "7478             None     19487205  ...        None  68.3\n",
              "\n",
              "[7479 rows x 45 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 7
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "OEYNlbG33WZg"
      },
      "source": [
        "# saving the dataframe to csv file\n",
        "df.to_csv(\"acetylcholinesterase_01_bioactivity_data_raw.csv\", index=False)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "s_M4DXjSTrN1",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 813
        },
        "outputId": "46010d7f-6952-49aa-d41e-a46ad52d1f89"
      },
      "source": [
        "# dropping compounds with missing values\n",
        "df2 = df[df.standard_value.notna()]\n",
        "df2 = df2[df.canonical_smiles.notna()]\n",
        "df2"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/usr/local/lib/python3.7/dist-packages/ipykernel_launcher.py:3: UserWarning: Boolean Series key will be reindexed to match DataFrame index.\n",
            "  This is separate from the ipykernel package so we can avoid doing imports until\n"
          ],
          "name": "stderr"
        },
        {
          "output_type": "execute_result",
          "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>assay_variant_accession</th>\n",
              "      <th>assay_variant_mutation</th>\n",
              "      <th>bao_endpoint</th>\n",
              "      <th>bao_format</th>\n",
              "      <th>bao_label</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>data_validity_comment</th>\n",
              "      <th>data_validity_description</th>\n",
              "      <th>document_chembl_id</th>\n",
              "      <th>document_journal</th>\n",
              "      <th>document_year</th>\n",
              "      <th>ligand_efficiency</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>molecule_pref_name</th>\n",
              "      <th>parent_molecule_chembl_id</th>\n",
              "      <th>pchembl_value</th>\n",
              "      <th>potential_duplicate</th>\n",
              "      <th>qudt_units</th>\n",
              "      <th>record_id</th>\n",
              "      <th>relation</th>\n",
              "      <th>src_id</th>\n",
              "      <th>standard_flag</th>\n",
              "      <th>standard_relation</th>\n",
              "      <th>standard_text_value</th>\n",
              "      <th>standard_type</th>\n",
              "      <th>standard_units</th>\n",
              "      <th>standard_upper_value</th>\n",
              "      <th>standard_value</th>\n",
              "      <th>target_chembl_id</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '19.61', 'le': '0.36', 'lle': '3.32', ...</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>6.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252547</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>750.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '18.57', 'le': '0.38', 'lle': '2.45', ...</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>7.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252533</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>100.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252530</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '16.11', 'le': '0.34', 'lle': '1.81', ...</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>6.52</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252534</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>300.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '17.60', 'le': '0.36', 'lle': '3.00', ...</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>6.10</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252552</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>800.0</td>\n",
              "      <td>CHEMBL220</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",
              "      <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",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7474</th>\n",
              "      <td>None</td>\n",
              "      <td>19468459</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C(F)(F)F)CC3...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>{'bei': '9.32', 'le': '0.18', 'lle': '-2.84', ...</td>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>5.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255436</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>7570.0</td>\n",
              "      <td>CHEMBL220</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>7.57</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7475</th>\n",
              "      <td>None</td>\n",
              "      <td>19468460</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C)CC3)sc2-c2...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255435</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>CHEMBL220</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7476</th>\n",
              "      <td>None</td>\n",
              "      <td>19487200</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>C/C=C1\\[C@H]2C=C(C)C[C@]1(N)c1ccc(=O)[nH]c1C2</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '22.15', 'le': '0.41', 'lle': '3.37', ...</td>\n",
              "      <td>CHEMBL395280</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL395280</td>\n",
              "      <td>5.37</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258965</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>4300.0</td>\n",
              "      <td>CHEMBL220</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>4.3</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7477</th>\n",
              "      <td>None</td>\n",
              "      <td>19487204</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(O)c2c(c1)C1=C(c3c(O)c(O)cc(C)c3-c3cc(OC...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '8.34', 'le': '0.16', 'lle': '0.75', '...</td>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>4.81</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258961</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>15500.0</td>\n",
              "      <td>CHEMBL220</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>15.5</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7478</th>\n",
              "      <td>None</td>\n",
              "      <td>19487205</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(O)c(C(C)=O)c(-c2c(C)cc(O)c3oc4c(O)cc(C)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '7.46', 'le': '0.14', 'lle': '-2.11', ...</td>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>4.17</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258960</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>68300.0</td>\n",
              "      <td>CHEMBL220</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>68.3</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>6270 rows × 45 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value value\n",
              "0                None        33969  ...        None  0.75\n",
              "1                None        37563  ...        None   0.1\n",
              "2                None        37565  ...        None  50.0\n",
              "3                None        38902  ...        None   0.3\n",
              "4                None        41170  ...        None   0.8\n",
              "...               ...          ...  ...         ...   ...\n",
              "7474             None     19468459  ...        None  7.57\n",
              "7475             None     19468460  ...        None  10.0\n",
              "7476             None     19487200  ...        None   4.3\n",
              "7477             None     19487204  ...        None  15.5\n",
              "7478             None     19487205  ...        None  68.3\n",
              "\n",
              "[6270 rows x 45 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 9
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "cfajS5q-uVpw",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 779
        },
        "outputId": "4bc44e49-af2e-4b31-f216-edb5fdf64f9d"
      },
      "source": [
        "# dropping duplicate compounds of canonical_smiles (same compounds)\n",
        "df2_nr = df2.drop_duplicates(['canonical_smiles'])\n",
        "df2_nr"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>assay_variant_accession</th>\n",
              "      <th>assay_variant_mutation</th>\n",
              "      <th>bao_endpoint</th>\n",
              "      <th>bao_format</th>\n",
              "      <th>bao_label</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>data_validity_comment</th>\n",
              "      <th>data_validity_description</th>\n",
              "      <th>document_chembl_id</th>\n",
              "      <th>document_journal</th>\n",
              "      <th>document_year</th>\n",
              "      <th>ligand_efficiency</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>molecule_pref_name</th>\n",
              "      <th>parent_molecule_chembl_id</th>\n",
              "      <th>pchembl_value</th>\n",
              "      <th>potential_duplicate</th>\n",
              "      <th>qudt_units</th>\n",
              "      <th>record_id</th>\n",
              "      <th>relation</th>\n",
              "      <th>src_id</th>\n",
              "      <th>standard_flag</th>\n",
              "      <th>standard_relation</th>\n",
              "      <th>standard_text_value</th>\n",
              "      <th>standard_type</th>\n",
              "      <th>standard_units</th>\n",
              "      <th>standard_upper_value</th>\n",
              "      <th>standard_value</th>\n",
              "      <th>target_chembl_id</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '19.61', 'le': '0.36', 'lle': '3.32', ...</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>6.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252547</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>750.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '18.57', 'le': '0.38', 'lle': '2.45', ...</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>7.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252533</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>100.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252530</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '16.11', 'le': '0.34', 'lle': '1.81', ...</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>6.52</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252534</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>300.0</td>\n",
              "      <td>CHEMBL220</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>None</td>\n",
              "      <td>None</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>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '17.60', 'le': '0.36', 'lle': '3.00', ...</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>6.10</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252552</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>800.0</td>\n",
              "      <td>CHEMBL220</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",
              "      <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",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7473</th>\n",
              "      <td>None</td>\n",
              "      <td>19468458</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4cccc(F)c4)CC3)sc2-...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4554172</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4554172</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255437</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>CHEMBL220</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7474</th>\n",
              "      <td>None</td>\n",
              "      <td>19468459</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C(F)(F)F)CC3...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>{'bei': '9.32', 'le': '0.18', 'lle': '-2.84', ...</td>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>5.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255436</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>7570.0</td>\n",
              "      <td>CHEMBL220</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>7.57</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7475</th>\n",
              "      <td>None</td>\n",
              "      <td>19468460</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4478126</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ATC...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C)CC3)sc2-c2...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4477206</td>\n",
              "      <td>J Med Chem</td>\n",
              "      <td>2016.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3255435</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>CHEMBL220</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7477</th>\n",
              "      <td>None</td>\n",
              "      <td>19487204</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(O)c2c(c1)C1=C(c3c(O)c(O)cc(C)c3-c3cc(OC...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '8.34', 'le': '0.16', 'lle': '0.75', '...</td>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>4.81</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258961</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>15500.0</td>\n",
              "      <td>CHEMBL220</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>15.5</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7478</th>\n",
              "      <td>None</td>\n",
              "      <td>19487205</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4481753</td>\n",
              "      <td>Inhibition of AChE (unknown origin) using acet...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(O)c(C(C)=O)c(-c2c(C)cc(O)c3oc4c(O)cc(C)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4480424</td>\n",
              "      <td>J Nat Prod</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>{'bei': '7.46', 'le': '0.14', 'lle': '-2.11', ...</td>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>4.17</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3258960</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>68300.0</td>\n",
              "      <td>CHEMBL220</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>68.3</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5043 rows × 45 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value value\n",
              "0                None        33969  ...        None  0.75\n",
              "1                None        37563  ...        None   0.1\n",
              "2                None        37565  ...        None  50.0\n",
              "3                None        38902  ...        None   0.3\n",
              "4                None        41170  ...        None   0.8\n",
              "...               ...          ...  ...         ...   ...\n",
              "7473             None     19468458  ...        None  10.0\n",
              "7474             None     19468459  ...        None  7.57\n",
              "7475             None     19468460  ...        None  10.0\n",
              "7477             None     19487204  ...        None  15.5\n",
              "7478             None     19487205  ...        None  68.3\n",
              "\n",
              "[5043 rows x 45 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 10
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "749L2U9kYAi6",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        },
        "outputId": "402b3e18-2edb-45b4-9bba-5ed1f52746a6"
      },
      "source": [
        "# combining the 3 columns and bioactivity_class\n",
        "selection = [\"molecule_chembl_id\", \"canonical_smiles\", \"standard_value\"]\n",
        "df3 = df2_nr[selection]\n",
        "df3"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
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              "\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>7473</th>\n",
              "      <td>CHEMBL4554172</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4cccc(F)c4)CC3)sc2-...</td>\n",
              "      <td>10000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7474</th>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C(F)(F)F)CC3...</td>\n",
              "      <td>7570.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7475</th>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C)CC3)sc2-c2...</td>\n",
              "      <td>10000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7477</th>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>COc1cc(O)c2c(c1)C1=C(c3c(O)c(O)cc(C)c3-c3cc(OC...</td>\n",
              "      <td>15500.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7478</th>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>COc1cc(O)c(C(C)=O)c(-c2c(C)cc(O)c3oc4c(O)cc(C)...</td>\n",
              "      <td>68300.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5043 rows × 3 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     molecule_chembl_id  ... standard_value\n",
              "0          CHEMBL133897  ...          750.0\n",
              "1          CHEMBL336398  ...          100.0\n",
              "2          CHEMBL131588  ...        50000.0\n",
              "3          CHEMBL130628  ...          300.0\n",
              "4          CHEMBL130478  ...          800.0\n",
              "...                 ...  ...            ...\n",
              "7473      CHEMBL4554172  ...        10000.0\n",
              "7474      CHEMBL4533844  ...         7570.0\n",
              "7475      CHEMBL4570655  ...        10000.0\n",
              "7477      CHEMBL4571704  ...        15500.0\n",
              "7478      CHEMBL4556664  ...        68300.0\n",
              "\n",
              "[5043 rows x 3 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 11
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "XUvbdxPOun1d"
      },
      "source": [
        "df3.to_csv('acetylcholinesterase_02_bioactivity_data_preprocessed.csv', index=False)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "R0gV4018yMHQ"
      },
      "source": [
        "df4 = pd.read_csv('acetylcholinesterase_02_bioactivity_data_preprocessed.csv')"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "BOC4_9GGWLOb"
      },
      "source": [
        "# labeling data as either being active, inactive, or intermediate\n",
        "# compounds with standard_value < 1000 nM are considered active\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\")"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "99fwj3KrQkcD",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        },
        "outputId": "592647b8-1ea3-42bd-cc8f-c24f7452dfeb"
      },
      "source": [
        "bioactivity_class = pd.Series(bioactivity_threshold, name='class')\n",
        "df5 = pd.concat([df4, bioactivity_class], axis=1)\n",
        "df5"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>5038</th>\n",
              "      <td>CHEMBL4554172</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4cccc(F)c4)CC3)sc2-...</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5039</th>\n",
              "      <td>CHEMBL4533844</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C(F)(F)F)CC3...</td>\n",
              "      <td>7570.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5040</th>\n",
              "      <td>CHEMBL4570655</td>\n",
              "      <td>Cc1ccc(-c2nc(NC(=O)C3CCN(Cc4ccccc4C)CC3)sc2-c2...</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5041</th>\n",
              "      <td>CHEMBL4571704</td>\n",
              "      <td>COc1cc(O)c2c(c1)C1=C(c3c(O)c(O)cc(C)c3-c3cc(OC...</td>\n",
              "      <td>15500.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5042</th>\n",
              "      <td>CHEMBL4556664</td>\n",
              "      <td>COc1cc(O)c(C(C)=O)c(-c2c(C)cc(O)c3oc4c(O)cc(C)...</td>\n",
              "      <td>68300.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5043 rows × 4 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     molecule_chembl_id  ...         class\n",
              "0          CHEMBL133897  ...        active\n",
              "1          CHEMBL336398  ...        active\n",
              "2          CHEMBL131588  ...      inactive\n",
              "3          CHEMBL130628  ...        active\n",
              "4          CHEMBL130478  ...        active\n",
              "...                 ...  ...           ...\n",
              "5038      CHEMBL4554172  ...      inactive\n",
              "5039      CHEMBL4533844  ...  intermediate\n",
              "5040      CHEMBL4570655  ...      inactive\n",
              "5041      CHEMBL4571704  ...      inactive\n",
              "5042      CHEMBL4556664  ...      inactive\n",
              "\n",
              "[5043 rows x 4 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 15
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "J5V-ilgtYQWF"
      },
      "source": [
        "# converting the dataframe to a csv file\n",
        "df5.to_csv('acetylcholinesterase_03_bioactivity_data_curated.csv', index=False)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "-dd9LgcqYQby",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "8f273d69-3278-4bc5-cab4-c2e5217dd967"
      },
      "source": [
        "! zip acetylcholinesterase.zip *.csv"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "  adding: acetylcholinesterase_01_bioactivity_data_raw.csv (deflated 91%)\n",
            "  adding: acetylcholinesterase_02_bioactivity_data_preprocessed.csv (deflated 81%)\n",
            "  adding: acetylcholinesterase_03_bioactivity_data_curated.csv (deflated 82%)\n"
          ],
          "name": "stdout"
        }
      ]
    }
  ]
}