Investigating_Compounds_Targeting_nAChR_Descriptor_Dataset_Preparation.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "authorship_tag": "ABX9TyMCcaK4g+gYNlb4OmQ2XpyK",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/Ghaidahazaa/Investigating-Compounds-Targeting-nAChR-/blob/main/Investigating_Compounds_Targeting_nAChR_Descriptor_Dataset_Preparation.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**Download PaDEL-Descriptor**"
      ],
      "metadata": {
        "id": "Ezp-XtmvkVOl"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
        "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ndh0Hcu90d9L",
        "outputId": "6bc0d4b6-3b07-4524-c86b-cf7c27487910"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2024-11-23 11:44:57--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
            "Resolving github.com (github.com)... 140.82.114.4\n",
            "Connecting to github.com (github.com)|140.82.114.4|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip [following]\n",
            "--2024-11-23 11:44:57--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 25768637 (25M) [application/zip]\n",
            "Saving to: ‘padel.zip’\n",
            "\n",
            "padel.zip           100%[===================>]  24.57M   145MB/s    in 0.2s    \n",
            "\n",
            "2024-11-23 11:44:58 (145 MB/s) - ‘padel.zip’ saved [25768637/25768637]\n",
            "\n",
            "--2024-11-23 11:44:58--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n",
            "Resolving github.com (github.com)... 140.82.112.4\n",
            "Connecting to github.com (github.com)|140.82.112.4|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh [following]\n",
            "--2024-11-23 11:44:58--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.110.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 231 [text/plain]\n",
            "Saving to: ‘padel.sh’\n",
            "\n",
            "padel.sh            100%[===================>]     231  --.-KB/s    in 0s      \n",
            "\n",
            "2024-11-23 11:44:58 (5.34 MB/s) - ‘padel.sh’ saved [231/231]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "! unzip padel.zip"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "qvp0Maa01wt-",
        "outputId": "e4287148-0524-4dcf-aeed-751c04b13087"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Archive:  padel.zip\n",
            "   creating: PaDEL-Descriptor/\n",
            "  inflating: __MACOSX/._PaDEL-Descriptor  \n",
            "  inflating: PaDEL-Descriptor/MACCSFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._MACCSFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/AtomPairs2DFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._AtomPairs2DFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/EStateFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._EStateFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/Fingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._Fingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/.DS_Store  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._.DS_Store  \n",
            "   creating: PaDEL-Descriptor/license/\n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._license  \n",
            "  inflating: PaDEL-Descriptor/KlekotaRothFingerprintCount.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._KlekotaRothFingerprintCount.xml  \n",
            "  inflating: PaDEL-Descriptor/config  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._config  \n",
            "  inflating: PaDEL-Descriptor/PubchemFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._PubchemFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/ExtendedFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._ExtendedFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/KlekotaRothFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._KlekotaRothFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/GraphOnlyFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._GraphOnlyFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/SubstructureFingerprinter.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._SubstructureFingerprinter.xml  \n",
            "  inflating: PaDEL-Descriptor/Descriptors.xls  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._Descriptors.xls  \n",
            "   creating: PaDEL-Descriptor/lib/\n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._lib  \n",
            "  inflating: PaDEL-Descriptor/PaDEL-Descriptor.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._PaDEL-Descriptor.jar  \n",
            "  inflating: PaDEL-Descriptor/SubstructureFingerprintCount.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._SubstructureFingerprintCount.xml  \n",
            "  inflating: PaDEL-Descriptor/AtomPairs2DFingerprintCount.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._AtomPairs2DFingerprintCount.xml  \n",
            "  inflating: PaDEL-Descriptor/descriptors.xml  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/._descriptors.xml  \n",
            "  inflating: PaDEL-Descriptor/license/lgpl-2.1.txt  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/license/._lgpl-2.1.txt  \n",
            "  inflating: PaDEL-Descriptor/license/LICENSE.txt  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/license/._LICENSE.txt  \n",
            "  inflating: PaDEL-Descriptor/license/README - CDK  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/license/._README - CDK  \n",
            "  inflating: PaDEL-Descriptor/license/lgpl.license  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/license/._lgpl.license  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(6).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(6).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(4).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(4).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/xom-1.1(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._xom-1.1(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/swing-worker-1.1.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._swing-worker-1.1.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(5).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(5).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/appframework-1.0.3.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._appframework-1.0.3.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(7).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(7).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/vecmath1.2-1.14.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._vecmath1.2-1.14.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(6).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(6).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(6).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(6).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(4).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(4).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-base-2.4.7-SNAPSHOT.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(8).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(8).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(4).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(4).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/xom-1.1.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._xom-1.1.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(5).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(5).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(7).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(7).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(6).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(6).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(4).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(4).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/l2fprod-common-all(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._l2fprod-common-all(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/l2fprod-common-all.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._l2fprod-common-all.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(5).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(5).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(7).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(7).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(4).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(4).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/cdk-1.4.15.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._cdk-1.4.15.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(5).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(5).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(8).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(8).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(6).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(6).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(2).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(2).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/jama(3).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(3).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(1).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(1).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/guava-17.0.jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._guava-17.0.jar  \n",
            "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(4).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(4).jar  \n",
            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(5).jar  \n",
            "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(5).jar  \n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "! rm -rf __MACOSX"
      ],
      "metadata": {
        "id": "apC31HVX51tW"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**Load bioactivity data**\n",
        " Download the curated ChEMBL bioactivity data that has been pre-processed from his Bioinformatics Project. Here we will be using the bioactivity_pIC50 file that essentially contain the pIC50 values that we will be using for building a regression model."
      ],
      "metadata": {
        "id": "AliZYzOm2G5g"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from google.colab import drive\n",
        "drive.mount('/content/drive')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "DMJvxsnc7CIc",
        "outputId": "1ba5ed75-2b69-422c-d4f5-b0a61a7394a0"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount(\"/content/drive\", force_remount=True).\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!cp '/content/drive/My Drive/Colab Notebooks/data2/cleaned_bioactivity_data_IC50.csv' ."
      ],
      "metadata": {
        "id": "Qteg0i3t7FEb"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "! wget cleaned_bioactivity_data_IC50.csv"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "CN4R5mq355a4",
        "outputId": "4c6ad869-f46e-41c6-a8ee-96a5674a2555"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2024-11-23 12:11:38--  http://cleaned_bioactivity_data_ic50.csv/\n",
            "Resolving cleaned_bioactivity_data_ic50.csv (cleaned_bioactivity_data_ic50.csv)... failed: Name or service not known.\n",
            "wget: unable to resolve host address ‘cleaned_bioactivity_data_ic50.csv’\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd"
      ],
      "metadata": {
        "id": "8T-GrKYJ621C"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "ls"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "a-tmwFXg64gh",
        "outputId": "d3da3aa8-d7a5-40d4-9c81-1ff8e5a6e1ec"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "cleaned_bioactivity_data_IC50.csv  \u001b[0m\u001b[01;34mdrive\u001b[0m/  \u001b[01;34mPaDEL-Descriptor\u001b[0m/  padel.sh  padel.zip  \u001b[01;34msample_data\u001b[0m/\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "df3 = pd.read_csv('cleaned_bioactivity_data_IC50.csv')"
      ],
      "metadata": {
        "id": "ONP82aKq79ST"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "df3"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 626
        },
        "id": "N6UPtOf87_ia",
        "outputId": "0c795c07-b301-4e3d-ce68-82f39a380032"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    Unnamed: 0.1  Unnamed: 0 molecule_chembl_id  \\\n",
              "0              0           0      CHEMBL1761821   \n",
              "1              1           1       CHEMBL238979   \n",
              "2              2           2       CHEMBL451442   \n",
              "3              3           3       CHEMBL599735   \n",
              "4              4           4       CHEMBL268074   \n",
              "..           ...         ...                ...   \n",
              "80            80         100      CHEMBL5220652   \n",
              "81            81         101      CHEMBL5220622   \n",
              "82            82         102      CHEMBL5219354   \n",
              "83            83         103      CHEMBL5219058   \n",
              "84            84         104      CHEMBL5219320   \n",
              "\n",
              "                                     canonical_smiles         class     MolWt  \\\n",
              "0   Cc1cc[n+](CC#Cc2ccc(-c3ccc(C#CC[n+]4ccc(C)c(C)...        active   442.606   \n",
              "1   C(#Cc1cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)cc(C#CCC...        active   738.999   \n",
              "2   C(#Cc1cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)c(C#CCCC...        active   959.294   \n",
              "3   Cc1cc[n+](CCCc2ccc(-c3ccc(CCC[n+]4ccc(C)c(C)c4...        active   450.670   \n",
              "4   [Br-].[Br-].[Br-].c1ccc2c(c1)ccc[n+]2CCCCCc1cc...        active   672.981   \n",
              "..                                                ...           ...       ...   \n",
              "80  C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC[C@@H](C(=O)...        active  1746.778   \n",
              "81  C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC(C)(C)[C@@H]...        active  1718.724   \n",
              "82  C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC[C@@H](C(=O)...        active  1718.724   \n",
              "83  C[C@@H](O)[C@@H]1NC(=O)[C@H]2NC(=O)[C@H](NC(=O...        active  1718.724   \n",
              "84  C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC[C@@H](C(=O)...  intermediate  1718.724   \n",
              "\n",
              "        LogP  NumHDonors  NumHAcceptors     pIC50 bioactivity_class  \n",
              "0    5.26568           0              0  7.795880            active  \n",
              "1   10.04580           0              0  6.173925            active  \n",
              "2   12.83220           0              0  8.769551            active  \n",
              "3    6.42788           0              0  8.376751            active  \n",
              "4   10.24770           0              0  8.318759            active  \n",
              "..       ...         ...            ...       ...               ...  \n",
              "80  -4.96533          23             25  6.000000            active  \n",
              "81  -5.74393          23             25  7.619789            active  \n",
              "82  -5.74393          23             25  6.000000            active  \n",
              "83  -5.74393          23             25  8.886057            active  \n",
              "84  -5.74393          23             25  5.920819      intermediate  \n",
              "\n",
              "[85 rows x 11 columns]"
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              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Unnamed: 0.1</th>\n",
              "      <th>Unnamed: 0</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>class</th>\n",
              "      <th>MolWt</th>\n",
              "      <th>LogP</th>\n",
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              "      <th>pIC50</th>\n",
              "      <th>bioactivity_class</th>\n",
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              "      <th>0</th>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>CHEMBL1761821</td>\n",
              "      <td>Cc1cc[n+](CC#Cc2ccc(-c3ccc(C#CC[n+]4ccc(C)c(C)...</td>\n",
              "      <td>active</td>\n",
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              "      <td>CHEMBL238979</td>\n",
              "      <td>C(#Cc1cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)cc(C#CCC...</td>\n",
              "      <td>active</td>\n",
              "      <td>738.999</td>\n",
              "      <td>10.04580</td>\n",
              "      <td>0</td>\n",
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              "      <td>active</td>\n",
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              "      <th>2</th>\n",
              "      <td>2</td>\n",
              "      <td>2</td>\n",
              "      <td>CHEMBL451442</td>\n",
              "      <td>C(#Cc1cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)c(C#CCCC...</td>\n",
              "      <td>active</td>\n",
              "      <td>959.294</td>\n",
              "      <td>12.83220</td>\n",
              "      <td>0</td>\n",
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              "      <td>8.769551</td>\n",
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              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>3</td>\n",
              "      <td>3</td>\n",
              "      <td>CHEMBL599735</td>\n",
              "      <td>Cc1cc[n+](CCCc2ccc(-c3ccc(CCC[n+]4ccc(C)c(C)c4...</td>\n",
              "      <td>active</td>\n",
              "      <td>450.670</td>\n",
              "      <td>6.42788</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>8.376751</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>4</td>\n",
              "      <td>4</td>\n",
              "      <td>CHEMBL268074</td>\n",
              "      <td>[Br-].[Br-].[Br-].c1ccc2c(c1)ccc[n+]2CCCCCc1cc...</td>\n",
              "      <td>active</td>\n",
              "      <td>672.981</td>\n",
              "      <td>10.24770</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>8.318759</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",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
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              "    <tr>\n",
              "      <th>80</th>\n",
              "      <td>80</td>\n",
              "      <td>100</td>\n",
              "      <td>CHEMBL5220652</td>\n",
              "      <td>C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC[C@@H](C(=O)...</td>\n",
              "      <td>active</td>\n",
              "      <td>1746.778</td>\n",
              "      <td>-4.96533</td>\n",
              "      <td>23</td>\n",
              "      <td>25</td>\n",
              "      <td>6.000000</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>81</th>\n",
              "      <td>81</td>\n",
              "      <td>101</td>\n",
              "      <td>CHEMBL5220622</td>\n",
              "      <td>C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC(C)(C)[C@@H]...</td>\n",
              "      <td>active</td>\n",
              "      <td>1718.724</td>\n",
              "      <td>-5.74393</td>\n",
              "      <td>23</td>\n",
              "      <td>25</td>\n",
              "      <td>7.619789</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>82</th>\n",
              "      <td>82</td>\n",
              "      <td>102</td>\n",
              "      <td>CHEMBL5219354</td>\n",
              "      <td>C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC[C@@H](C(=O)...</td>\n",
              "      <td>active</td>\n",
              "      <td>1718.724</td>\n",
              "      <td>-5.74393</td>\n",
              "      <td>23</td>\n",
              "      <td>25</td>\n",
              "      <td>6.000000</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>83</th>\n",
              "      <td>83</td>\n",
              "      <td>103</td>\n",
              "      <td>CHEMBL5219058</td>\n",
              "      <td>C[C@@H](O)[C@@H]1NC(=O)[C@H]2NC(=O)[C@H](NC(=O...</td>\n",
              "      <td>active</td>\n",
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              "      <td>-5.74393</td>\n",
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              "      <td>active</td>\n",
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              "    <tr>\n",
              "      <th>84</th>\n",
              "      <td>84</td>\n",
              "      <td>104</td>\n",
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              "      <td>C[C@@H](O)[C@@H]1NC(=O)[C@@H]2CSSC[C@@H](C(=O)...</td>\n",
              "      <td>intermediate</td>\n",
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              "      <td>-5.74393</td>\n",
              "      <td>23</td>\n",
              "      <td>25</td>\n",
              "      <td>5.920819</td>\n",
              "      <td>intermediate</td>\n",
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              "  </tbody>\n",
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              "<p>85 rows × 11 columns</p>\n",
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              "        border-radius: 50%;\n",
              "        cursor: pointer;\n",
              "        display: none;\n",
              "        fill: #1967D2;\n",
              "        height: 32px;\n",
              "        padding: 0 0 0 0;\n",
              "        width: 32px;\n",
              "      }\n",
              "\n",
              "      .colab-df-generate:hover {\n",
              "        background-color: #E2EBFA;\n",
              "        box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "        fill: #174EA6;\n",
              "      }\n",
              "\n",
              "      [theme=dark] .colab-df-generate {\n",
              "        background-color: #3B4455;\n",
              "        fill: #D2E3FC;\n",
              "      }\n",
              "\n",
              "      [theme=dark] .colab-df-generate:hover {\n",
              "        background-color: #434B5C;\n",
              "        box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "        filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "        fill: #FFFFFF;\n",
              "      }\n",
              "    </style>\n",
              "    <button class=\"colab-df-generate\" onclick=\"generateWithVariable('df3')\"\n",
              "            title=\"Generate code using this dataframe.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
              "    <path d=\"M7,19H8.4L18.45,9,17,7.55,7,17.6ZM5,21V16.75L18.45,3.32a2,2,0,0,1,2.83,0l1.4,1.43a1.91,1.91,0,0,1,.58,1.4,1.91,1.91,0,0,1-.58,1.4L9.25,21ZM18.45,9,17,7.55Zm-12,3A5.31,5.31,0,0,0,4.9,8.1,5.31,5.31,0,0,0,1,6.5,5.31,5.31,0,0,0,4.9,4.9,5.31,5.31,0,0,0,6.5,1,5.31,5.31,0,0,0,8.1,4.9,5.31,5.31,0,0,0,12,6.5,5.46,5.46,0,0,0,6.5,12Z\"/>\n",
              "  </svg>\n",
              "    </button>\n",
              "    <script>\n",
              "      (() => {\n",
              "      const buttonEl =\n",
              "        document.querySelector('#id_f407e41d-4576-4c0b-b500-0f4da4e4f15d button.colab-df-generate');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      buttonEl.onclick = () => {\n",
              "        google.colab.notebook.generateWithVariable('df3');\n",
              "      }\n",
              "      })();\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "    </div>\n",
              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "variable_name": "df3",
              "summary": "{\n  \"name\": \"df3\",\n  \"rows\": 85,\n  \"fields\": [\n    {\n      \"column\": \"Unnamed: 0.1\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 24,\n        \"min\": 0,\n        \"max\": 84,\n        \"num_unique_values\": 85,\n        \"samples\": [\n          78,\n          0,\n          68\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"Unnamed: 0\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 30,\n        \"min\": 0,\n        \"max\": 104,\n        \"num_unique_values\": 85,\n        \"samples\": [\n          98,\n          0,\n          88\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"molecule_chembl_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 85,\n        \"samples\": [\n          \"CHEMBL5220455\",\n          \"CHEMBL1761821\",\n          \"CHEMBL5203781\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"canonical_smiles\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 85,\n        \"samples\": [\n          \"C[C@@H](O)[C@@H]1NC(=O)[C@H]2NC(=O)[C@H](NC(=O)CN)CSSC[C@H](NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H]3CCCN3C(=O)[C@H](CC(=O)O)NC1=O)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](Cc1ccc(O)c(I)c1)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)O)CSSC2(C)C\",\n          \"Cc1cc[n+](CC#Cc2ccc(-c3ccc(C#CC[n+]4ccc(C)c(C)c4)cc3)cc2)cc1C.[Br-].[Br-]\",\n          \"CC[C@H](C)[C@@H]1NC(=O)[C@H](CC(=O)O)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CO)NC(=O)[C@@H]2CSSC[C@H](NC(=O)CN)C(=O)N[C@@H](CSSC[C@@H](C(N)=O)NC1=O)C(=O)NC(CN)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C)C(=O)N2\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"class\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"active\",\n          \"intermediate\",\n          \"inactive\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"MolWt\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 1015.3661501616488,\n        \"min\": 280.391,\n        \"max\": 5673.417999999977,\n        \"num_unique_values\": 76,\n        \"samples\": [\n          672.9810000000001,\n          1929.9450000000015,\n          1652.888\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"LogP\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 8.751320032637786,\n        \"min\": -26.06198000000012,\n        \"max\": 15.156599999999967,\n        \"num_unique_values\": 74,\n        \"samples\": [\n          10.247699999999996,\n          -5.841959999999986,\n          6.672700000000008\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"NumHDonors\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 16,\n        \"min\": 0,\n        \"max\": 71,\n        \"num_unique_values\": 18,\n        \"samples\": [\n          0,\n          28,\n          71\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"NumHAcceptors\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 18,\n        \"min\": 0,\n        \"max\": 95,\n        \"num_unique_values\": 16,\n        \"samples\": [\n          0,\n          25,\n          29\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"pIC50\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 1.4619753791355434,\n        \"min\": 3.604324214730064,\n        \"max\": 10.30102999566398,\n        \"num_unique_values\": 73,\n        \"samples\": [\n          8.318758762624412,\n          9.585026652029182,\n          8.301029995663981\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"bioactivity_class\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"active\",\n          \"intermediate\",\n          \"inactive\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 37
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "selection = ['canonical_smiles','molecule_chembl_id']\n",
        "df3_selection = df3[selection]\n",
        "df3_selection.to_csv('molecule.smi', sep='\\t', index=False, header=False)"
      ],
      "metadata": {
        "id": "QMGZlwr48IgT"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "! cat molecule.smi | head -5"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "uuqomCiG8LeZ",
        "outputId": "783b80f7-31ba-4d39-fdc0-1755a5ee5a03"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Cc1cc[n+](CC#Cc2ccc(-c3ccc(C#CC[n+]4ccc(C)c(C)c4)cc3)cc2)cc1C.[Br-].[Br-]\tCHEMBL1761821\n",
            "C(#Cc1cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)c1)CCC[n+]1cccc(-c2ccccc2)c1.[Br-].[Br-].[Br-]\tCHEMBL238979\n",
            "C(#Cc1cc(C#CCCC[n+]2cccc(-c3ccccc3)c2)c(C#CCCC[n+]2cccc(-c3ccccc3)c2)cc1C#CCCC[n+]1cccc(-c2ccccc2)c1)CCC[n+]1cccc(-c2ccccc2)c1.[Br-].[Br-].[Br-].[Br-]\tCHEMBL451442\n",
            "Cc1cc[n+](CCCc2ccc(-c3ccc(CCC[n+]4ccc(C)c(C)c4)cc3)cc2)cc1C.[Br-].[Br-]\tCHEMBL599735\n",
            "[Br-].[Br-].[Br-].c1ccc2c(c1)ccc[n+]2CCCCCc1cc(CCCCC[n+]2cccc3ccccc32)cc(CCCCC[n+]2cccc3ccccc32)c1\tCHEMBL268074\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "! cat molecule.smi | wc -l"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "c-Mzkuwt8QEY",
        "outputId": "28d9c06f-6281-4c72-bae6-125dba76fb10"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "85\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**Calculate PaDEL descriptors**\n"
      ],
      "metadata": {
        "id": "W8YFScNg8SrE"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "! cat padel.sh"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "29kb1v4I8XC_",
        "outputId": "ab33e667-a5eb-4611-fd69-5e79b7f221af"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "java -Xms1G -Xmx1G -Djava.awt.headless=true -jar ./PaDEL-Descriptor/PaDEL-Descriptor.jar -removesalt -standardizenitro -fingerprints -descriptortypes ./PaDEL-Descriptor/PubchemFingerprinter.xml -dir ./ -file descriptors_output.csv\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "! bash padel.sh"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "RwLB_VJB8ZZy",
        "outputId": "f5abbddb-f1fc-42a9-c8fc-5b6ac6cddb2f"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Processing CHEMBL1761821 in molecule.smi (1/85). \n",
            "Processing CHEMBL451442 in molecule.smi (3/85). \n",
            "Processing CHEMBL238979 in molecule.smi (2/85). \n",
            "Processing CHEMBL599735 in molecule.smi (4/85). Average speed: 5.41 s/mol.\n",
            "Processing CHEMBL268074 in molecule.smi (5/85). Average speed: 4.00 s/mol.\n",
            "Processing CHEMBL241120 in molecule.smi (6/85). Average speed: 3.54 s/mol.\n",
            "Processing CHEMBL267841 in molecule.smi (7/85). Average speed: 2.98 s/mol.\n",
            "Processing CHEMBL454767 in molecule.smi (8/85). Average speed: 3.39 s/mol.\n",
            "Processing CHEMBL3104241 in molecule.smi (9/85). Average speed: 2.63 s/mol.\n",
            "Processing CHEMBL3104242 in molecule.smi (10/85). Average speed: 2.77 s/mol.\n",
            "Processing CHEMBL4228783 in molecule.smi (11/85). Average speed: 2.63 s/mol.\n",
            "Processing CHEMBL4226390 in molecule.smi (12/85). Average speed: 2.40 s/mol.\n",
            "Processing CHEMBL4228263 in molecule.smi (14/85). Average speed: 2.24 s/mol.\n",
            "Processing CHEMBL4229033 in molecule.smi (13/85). Average speed: 2.37 s/mol.\n",
            "Processing CHEMBL4225280 in molecule.smi (15/85). Average speed: 2.21 s/mol.\n",
            "Processing CHEMBL1257065 in molecule.smi (16/85). Average speed: 2.15 s/mol.\n",
            "Processing CHEMBL4287656 in molecule.smi (17/85). Average speed: 2.04 s/mol.\n",
            "Processing CHEMBL4280452 in molecule.smi (18/85). Average speed: 1.95 s/mol.\n",
            "Processing CHEMBL4291079 in molecule.smi (19/85). Average speed: 1.87 s/mol.\n",
            "Processing CHEMBL4293646 in molecule.smi (20/85). Average speed: 1.81 s/mol.\n",
            "Processing CHEMBL4285772 in molecule.smi (21/85). Average speed: 1.73 s/mol.\n",
            "Processing CHEMBL4276776 in molecule.smi (22/85). Average speed: 1.67 s/mol.\n",
            "Processing CHEMBL4526368 in molecule.smi (23/85). Average speed: 1.69 s/mol.\n",
            "Processing CHEMBL3104239 in molecule.smi (24/85). Average speed: 1.69 s/mol.\n",
            "Processing CHEMBL4555265 in molecule.smi (25/85). Average speed: 1.71 s/mol.\n",
            "Processing CHEMBL4574008 in molecule.smi (26/85). Average speed: 2.10 s/mol.\n",
            "Processing CHEMBL3104237 in molecule.smi (27/85). Average speed: 2.12 s/mol.\n",
            "Processing CHEMBL4460879 in molecule.smi (28/85). Average speed: 2.10 s/mol.\n",
            "Processing CHEMBL4460411 in molecule.smi (29/85). Average speed: 2.24 s/mol.\n",
            "Processing CHEMBL3632636 in molecule.smi (30/85). Average speed: 2.43 s/mol.\n",
            "Processing CHEMBL4579708 in molecule.smi (31/85). Average speed: 2.37 s/mol.\n",
            "Processing CHEMBL4647678 in molecule.smi (32/85). Average speed: 2.37 s/mol.\n",
            "Processing CHEMBL4635345 in molecule.smi (33/85). Average speed: 2.37 s/mol.\n",
            "Processing CHEMBL4642677 in molecule.smi (34/85). Average speed: 2.36 s/mol.\n",
            "Processing CHEMBL4634288 in molecule.smi (35/85). Average speed: 2.34 s/mol.\n",
            "Processing CHEMBL4644697 in molecule.smi (36/85). Average speed: 2.32 s/mol.\n",
            "Processing CHEMBL4634686 in molecule.smi (37/85). Average speed: 2.39 s/mol.\n",
            "Processing CHEMBL4644407 in molecule.smi (38/85). Average speed: 2.29 s/mol.\n",
            "Processing CHEMBL4756657 in molecule.smi (39/85). Average speed: 2.30 s/mol.\n",
            "Processing CHEMBL4787614 in molecule.smi (40/85). Average speed: 2.24 s/mol.\n",
            "Processing CHEMBL4791366 in molecule.smi (42/85). Average speed: 2.17 s/mol.\n",
            "Processing CHEMBL4763515 in molecule.smi (41/85). Average speed: 2.22 s/mol.\n",
            "Processing CHEMBL4869892 in molecule.smi (43/85). Average speed: 2.20 s/mol.\n",
            "Processing CHEMBL4872191 in molecule.smi (44/85). Average speed: 2.15 s/mol.\n",
            "Processing CHEMBL1836968 in molecule.smi (45/85). Average speed: 2.14 s/mol.\n",
            "Processing CHEMBL5089881 in molecule.smi (46/85). Average speed: 2.13 s/mol.\n",
            "Processing CHEMBL5086734 in molecule.smi (47/85). Average speed: 2.12 s/mol.\n",
            "Processing CHEMBL5091401 in molecule.smi (48/85). Average speed: 2.11 s/mol.\n",
            "Processing CHEMBL5090616 in molecule.smi (50/85). Average speed: 2.08 s/mol.\n",
            "Processing CHEMBL5080428 in molecule.smi (49/85). Average speed: 2.10 s/mol.\n",
            "Processing CHEMBL5090753 in molecule.smi (51/85). Average speed: 2.05 s/mol.\n",
            "Processing CHEMBL5073182 in molecule.smi (52/85). Average speed: 2.03 s/mol.\n",
            "Processing CHEMBL5197651 in molecule.smi (53/85). Average speed: 2.01 s/mol.\n",
            "Processing CHEMBL5184316 in molecule.smi (54/85). Average speed: 2.04 s/mol.\n",
            "Processing CHEMBL5191958 in molecule.smi (55/85). Average speed: 1.98 s/mol.\n",
            "Processing CHEMBL5195695 in molecule.smi (56/85). Average speed: 1.95 s/mol.\n",
            "Processing CHEMBL5177606 in molecule.smi (57/85). Average speed: 1.92 s/mol.\n",
            "Processing CHEMBL5174508 in molecule.smi (58/85). Average speed: 1.89 s/mol.\n",
            "Processing CHEMBL5190813 in molecule.smi (59/85). Average speed: 1.86 s/mol.\n",
            "Processing CHEMBL5176101 in molecule.smi (60/85). Average speed: 1.83 s/mol.\n",
            "Processing CHEMBL5176690 in molecule.smi (61/85). Average speed: 1.81 s/mol.\n",
            "Processing CHEMBL5201239 in molecule.smi (62/85). Average speed: 1.78 s/mol.\n",
            "Processing CHEMBL5178473 in molecule.smi (63/85). Average speed: 1.75 s/mol.\n",
            "Processing CHEMBL5182514 in molecule.smi (64/85). Average speed: 1.73 s/mol.\n",
            "Processing CHEMBL5171118 in molecule.smi (65/85). Average speed: 1.70 s/mol.\n",
            "Processing CHEMBL5182114 in molecule.smi (66/85). Average speed: 1.68 s/mol.\n",
            "Processing CHEMBL5196098 in molecule.smi (67/85). Average speed: 1.66 s/mol.\n",
            "Processing CHEMBL5192422 in molecule.smi (68/85). Average speed: 1.64 s/mol.\n",
            "Processing CHEMBL5203781 in molecule.smi (69/85). Average speed: 1.65 s/mol.\n",
            "Processing CHEMBL5220002 in molecule.smi (70/85). Average speed: 1.63 s/mol.\n",
            "Processing CHEMBL5220113 in molecule.smi (71/85). Average speed: 1.65 s/mol.\n",
            "Processing CHEMBL5219016 in molecule.smi (72/85). Average speed: 1.63 s/mol.\n",
            "Processing CHEMBL5220467 in molecule.smi (73/85). Average speed: 1.63 s/mol.\n",
            "Processing CHEMBL5219752 in molecule.smi (74/85). Average speed: 1.62 s/mol.\n",
            "Processing CHEMBL5220060 in molecule.smi (75/85). Average speed: 1.61 s/mol.\n",
            "Processing CHEMBL5219936 in molecule.smi (76/85). Average speed: 1.61 s/mol.\n",
            "Processing CHEMBL5218653 in molecule.smi (77/85). Average speed: 1.59 s/mol.\n",
            "Processing CHEMBL5219791 in molecule.smi (78/85). Average speed: 1.59 s/mol.\n",
            "Processing CHEMBL5220455 in molecule.smi (79/85). Average speed: 1.59 s/mol.\n",
            "Processing CHEMBL5221023 in molecule.smi (80/85). Average speed: 1.59 s/mol.\n",
            "Processing CHEMBL5220652 in molecule.smi (81/85). Average speed: 1.58 s/mol.\n",
            "Processing CHEMBL5220622 in molecule.smi (82/85). Average speed: 1.60 s/mol.\n",
            "Processing CHEMBL5219354 in molecule.smi (83/85). Average speed: 1.59 s/mol.\n",
            "Processing CHEMBL5219058 in molecule.smi (84/85). Average speed: 1.58 s/mol.\n",
            "Processing CHEMBL5219320 in molecule.smi (85/85). Average speed: 1.57 s/mol.\n",
            "Descriptor calculation completed in 2 mins 12.201 secs . Average speed: 1.56 s/mol.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "! ls -l"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "zRUsF-ge9B9z",
        "outputId": "d51b74f8-b5c7-4404-be43-18e2af7f44b5"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "total 25396\n",
            "-rw------- 1 root root    27705 Nov 23 12:11 cleaned_bioactivity_data_IC50.csv\n",
            "-rw-r--r-- 1 root root   162471 Nov 23 12:16 descriptors_output.csv\n",
            "drwx------ 6 root root     4096 Nov 23 11:49 drive\n",
            "-rw-r--r-- 1 root root    20813 Nov 23 12:13 molecule.smi\n",
            "drwxrwxr-x 4 root root     4096 May 30  2020 PaDEL-Descriptor\n",
            "-rw-r--r-- 1 root root      231 Nov 23 11:44 padel.sh\n",
            "-rw-r--r-- 1 root root 25768637 Nov 23 11:44 padel.zip\n",
            "drwxr-xr-x 1 root root     4096 Nov 21 14:25 sample_data\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**Preparing the X and Y Data Matrices**\n",
        "**X data matrix**"
      ],
      "metadata": {
        "id": "UtxKh50c9H8X"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "df3_X = pd.read_csv('descriptors_output.csv')"
      ],
      "metadata": {
        "id": "-AJKBHyf9LQl"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "df3_X"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 439
        },
        "id": "VWXtxu5g9NaK",
        "outputId": "db908ee7-06b3-4ea8-b78d-8f5ef86fff63"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "             Name  PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  \\\n",
              "0   CHEMBL1761821           1           1           1           0           0   \n",
              "1    CHEMBL238979           1           1           1           1           0   \n",
              "2    CHEMBL599735           1           1           1           1           0   \n",
              "3    CHEMBL451442           1           1           1           1           0   \n",
              "4    CHEMBL268074           1           1           1           1           0   \n",
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              "<p>85 rows × 882 columns</p>\n",
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              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
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              "  }\n",
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              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
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              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
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              "      quickchartButtonEl.style.display =\n",
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              "        display: none;\n",
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              "        height: 32px;\n",
              "        padding: 0 0 0 0;\n",
              "        width: 32px;\n",
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              "\n",
              "      .colab-df-generate:hover {\n",
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              "\n",
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              "    <button class=\"colab-df-generate\" onclick=\"generateWithVariable('df3_X')\"\n",
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              "  </svg>\n",
              "    </button>\n",
              "    <script>\n",
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              "        document.querySelector('#id_3d421098-fbda-496e-a87c-30ef1e8f5294 button.colab-df-generate');\n",
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              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      buttonEl.onclick = () => {\n",
              "        google.colab.notebook.generateWithVariable('df3_X');\n",
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              "\n",
              "    </div>\n",
              "  </div>\n"
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            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "variable_name": "df3_X"
            }
          },
          "metadata": {},
          "execution_count": 45
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "df3_X = df3_X.drop(columns=['Name'])\n",
        "df3_X"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 439
        },
        "id": "BV2_uvEH9Qmj",
        "outputId": "371cfec1-5250-4e84-f320-92ccfffcfd42"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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              "    PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  PubchemFP5  \\\n",
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              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "    <script>\n",
              "      const buttonEl =\n",
              "        document.querySelector('#df-c3c41401-5742-43d6-8f0a-0a16fc350619 button.colab-df-convert');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      async function convertToInteractive(key) {\n",
              "        const element = document.querySelector('#df-c3c41401-5742-43d6-8f0a-0a16fc350619');\n",
              "        const dataTable =\n",
              "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "          + ' to learn more about interactive tables.';\n",
              "        element.innerHTML = '';\n",
              "        dataTable['output_type'] = 'display_data';\n",
              "        await google.colab.output.renderOutput(dataTable, element);\n",
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              "        docLink.innerHTML = docLinkHtml;\n",
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              "            title=\"Suggest charts\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
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              "    </g>\n",
              "</svg>\n",
              "  </button>\n",
              "\n",
              "<style>\n",
              "  .colab-df-quickchart {\n",
              "      --bg-color: #E8F0FE;\n",
              "      --fill-color: #1967D2;\n",
              "      --hover-bg-color: #E2EBFA;\n",
              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
              "      --disabled-bg-color: #DDD;\n",
              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
              "      --hover-fill-color: #FFFFFF;\n",
              "      --disabled-bg-color: #3B4455;\n",
              "      --disabled-fill-color: #666;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart {\n",
              "    background-color: var(--bg-color);\n",
              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
              "    fill: var(--fill-color);\n",
              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "    fill: var(--button-hover-fill-color);\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
              "    }\n",
              "    20% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    30% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-76ac1670-4eb0-4a21-8040-bb1df69cd347 button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "\n",
              "  <div id=\"id_ed92c36b-c7d9-403c-b0c7-860960e70e29\">\n",
              "    <style>\n",
              "      .colab-df-generate {\n",
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              "        display: none;\n",
              "        fill: #1967D2;\n",
              "        height: 32px;\n",
              "        padding: 0 0 0 0;\n",
              "        width: 32px;\n",
              "      }\n",
              "\n",
              "      .colab-df-generate:hover {\n",
              "        background-color: #E2EBFA;\n",
              "        box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "        fill: #174EA6;\n",
              "      }\n",
              "\n",
              "      [theme=dark] .colab-df-generate {\n",
              "        background-color: #3B4455;\n",
              "        fill: #D2E3FC;\n",
              "      }\n",
              "\n",
              "      [theme=dark] .colab-df-generate:hover {\n",
              "        background-color: #434B5C;\n",
              "        box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "        filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "        fill: #FFFFFF;\n",
              "      }\n",
              "    </style>\n",
              "    <button class=\"colab-df-generate\" onclick=\"generateWithVariable('df3_X')\"\n",
              "            title=\"Generate code using this dataframe.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
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              "  </svg>\n",
              "    </button>\n",
              "    <script>\n",
              "      (() => {\n",
              "      const buttonEl =\n",
              "        document.querySelector('#id_ed92c36b-c7d9-403c-b0c7-860960e70e29 button.colab-df-generate');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      buttonEl.onclick = () => {\n",
              "        google.colab.notebook.generateWithVariable('df3_X');\n",
              "      }\n",
              "      })();\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
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              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "variable_name": "df3_X"
            }
          },
          "metadata": {},
          "execution_count": 46
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**Y variable**\n",
        "Convert IC50 to pIC50"
      ],
      "metadata": {
        "id": "fdWZ3Pyw9TdI"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "df3_Y = df3['pIC50']\n",
        "df3_Y"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 453
        },
        "id": "DDBJZlum9ZQa",
        "outputId": "774b1766-1c60-4716-a65c-a582fd440672"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "0     7.795880\n",
              "1     6.173925\n",
              "2     8.769551\n",
              "3     8.376751\n",
              "4     8.318759\n",
              "        ...   \n",
              "80    6.000000\n",
              "81    7.619789\n",
              "82    6.000000\n",
              "83    8.886057\n",
              "84    5.920819\n",
              "Name: pIC50, Length: 85, dtype: float64"
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              "  </tbody>\n",
              "</table>\n",
              "<p>85 rows × 1 columns</p>\n",
              "</div><br><label><b>dtype:</b> float64</label>"
            ]
          },
          "metadata": {},
          "execution_count": 47
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**Combining X and Y variable**"
      ],
      "metadata": {
        "id": "DSk1eyMc9iCd"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "dataset3 = pd.concat([df3_X,df3_Y], axis=1)\n",
        "dataset3"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 439
        },
        "id": "nl925Wgi9jZX",
        "outputId": "60abc3ed-1eab-40b9-c74a-c101b93e039b"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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              "    PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  PubchemFP5  \\\n",
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              "\n",
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              "      <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",
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              "      <td>0</td>\n",
              "      <td>6.000000</td>\n",
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              "      <th>81</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
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              "      <td>0</td>\n",
              "      <td>7.619789</td>\n",
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              "    <tr>\n",
              "      <th>82</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
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              "      <td>0</td>\n",
              "      <td>1</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>6.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>83</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>...</td>\n",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>8.886057</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>84</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>5.920819</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>85 rows × 882 columns</p>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
              "\n",
              "  <div class=\"colab-df-container\">\n",
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              "    [theme=dark] .colab-df-convert:hover {\n",
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              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
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              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
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              "\n",
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              "      --hover-bg-color: #E2EBFA;\n",
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              "      --disabled-fill-color: #AAA;\n",
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              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
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              "\n",
              "  .colab-df-quickchart {\n",
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              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
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              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
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              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
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              "    20% {\n",
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              "    30% {\n",
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              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
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              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-3091be0b-0564-471e-a55f-2ef1b59cf99b button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
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              "  </script>\n",
              "</div>\n",
              "\n",
              "  <div id=\"id_05a20fe7-dad4-4dcb-b38d-65cc6f8e227c\">\n",
              "    <style>\n",
              "      .colab-df-generate {\n",
              "        background-color: #E8F0FE;\n",
              "        border: none;\n",
              "        border-radius: 50%;\n",
              "        cursor: pointer;\n",
              "        display: none;\n",
              "        fill: #1967D2;\n",
              "        height: 32px;\n",
              "        padding: 0 0 0 0;\n",
              "        width: 32px;\n",
              "      }\n",
              "\n",
              "      .colab-df-generate:hover {\n",
              "        background-color: #E2EBFA;\n",
              "        box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "        fill: #174EA6;\n",
              "      }\n",
              "\n",
              "      [theme=dark] .colab-df-generate {\n",
              "        background-color: #3B4455;\n",
              "        fill: #D2E3FC;\n",
              "      }\n",
              "\n",
              "      [theme=dark] .colab-df-generate:hover {\n",
              "        background-color: #434B5C;\n",
              "        box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "        filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "        fill: #FFFFFF;\n",
              "      }\n",
              "    </style>\n",
              "    <button class=\"colab-df-generate\" onclick=\"generateWithVariable('dataset3')\"\n",
              "            title=\"Generate code using this dataframe.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
              "    <path d=\"M7,19H8.4L18.45,9,17,7.55,7,17.6ZM5,21V16.75L18.45,3.32a2,2,0,0,1,2.83,0l1.4,1.43a1.91,1.91,0,0,1,.58,1.4,1.91,1.91,0,0,1-.58,1.4L9.25,21ZM18.45,9,17,7.55Zm-12,3A5.31,5.31,0,0,0,4.9,8.1,5.31,5.31,0,0,0,1,6.5,5.31,5.31,0,0,0,4.9,4.9,5.31,5.31,0,0,0,6.5,1,5.31,5.31,0,0,0,8.1,4.9,5.31,5.31,0,0,0,12,6.5,5.46,5.46,0,0,0,6.5,12Z\"/>\n",
              "  </svg>\n",
              "    </button>\n",
              "    <script>\n",
              "      (() => {\n",
              "      const buttonEl =\n",
              "        document.querySelector('#id_05a20fe7-dad4-4dcb-b38d-65cc6f8e227c button.colab-df-generate');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      buttonEl.onclick = () => {\n",
              "        google.colab.notebook.generateWithVariable('dataset3');\n",
              "      }\n",
              "      })();\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "    </div>\n",
              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "variable_name": "dataset3"
            }
          },
          "metadata": {},
          "execution_count": 48
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#**download the CSV file to the computer for Model Building**"
      ],
      "metadata": {
        "id": "HrpBMS_G9noP"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "dataset3.to_csv('Neuronal_acetylcholine_06_bioactivity_data_3class_pIC50_pubchem_fp.csv', index=False)"
      ],
      "metadata": {
        "id": "154uAMzC9qa4"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "from google.colab import drive\n",
        "drive.mount('/content/drive')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "2B0YsozwAqPA",
        "outputId": "47d5c67e-968b-4386-85f7-514b1eeef69c"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount(\"/content/drive\", force_remount=True).\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "dataset3.to_csv('/content/drive/My Drive/Colab Notebooks/data2/Neuronal_acetylcholine_06_bioactivity_data_3class_pIC50_pubchem_fp.csv', index=False)"
      ],
      "metadata": {
        "id": "IPWu0QxEBFmY"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}