Genotoxicity_all_DeploymentModel.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "Genotoxicity_all_DeploymentModel.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "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/stawiskm/QSAR_Modelbuilding_amesTest/blob/main/Genotoxicity_all_DeploymentModel.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "l0Y7_lgN4jzM"
      },
      "source": [
        "# **Bioinformatics Project - Computational Ames test [Part 1] Descriptor Calculation and Dataset Preparation**\n",
        "\n",
        "Marc Jermann\n",
        "\n",
        "In this Jupyter notebook, we will be building a real-life **data science project**. Particularly, we will be building a machine learning model using the ChEMBL bioactivity data.\n",
        "\n",
        "In **Part 1**, we will be calculating molecular descriptors that are essentially quantitative description of the compounds in the dataset. Finally, we will be preparing this into a dataset for subsequent model building in Part 2.\n",
        "\n",
        "**with all available data**\n",
        "\n",
        "---"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "o-4IOizard4P"
      },
      "source": [
        "## **Download PaDEL-Descriptor**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "H0mjQ2PcrSe5",
        "outputId": "e83e054d-9bf7-4b1c-bd65-ce2a8eba46ee",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
        "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2022-05-18 22:09:05--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
            "Resolving github.com (github.com)... 140.82.114.3\n",
            "Connecting to github.com (github.com)|140.82.114.3|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip [following]\n",
            "--2022-05-18 22:09:05--  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  --.-KB/s    in 0.1s    \n",
            "\n",
            "2022-05-18 22:09:05 (165 MB/s) - ‘padel.zip’ saved [25768637/25768637]\n",
            "\n",
            "--2022-05-18 22:09:06--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n",
            "Resolving github.com (github.com)... 140.82.114.3\n",
            "Connecting to github.com (github.com)|140.82.114.3|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh [following]\n",
            "--2022-05-18 22:09:06--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.111.133, 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: 231 [text/plain]\n",
            "Saving to: ‘padel.sh’\n",
            "\n",
            "padel.sh            100%[===================>]     231  --.-KB/s    in 0s      \n",
            "\n",
            "2022-05-18 22:09:06 (15.3 MB/s) - ‘padel.sh’ saved [231/231]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "64HnTL4tS-nA",
        "outputId": "b405ed80-8590-40e8-a776-78bebf45cc48",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "! unzip padel.zip"
      ],
      "execution_count": 2,
      "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",
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            "  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",
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            "  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",
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            "  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",
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            "  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",
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            "  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",
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            "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(2).jar  \n",
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            "  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",
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            "  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": "markdown",
      "metadata": {
        "id": "QmxXXFa4wTNG"
      },
      "source": [
        "## **Load bioactivity data**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fcBvxkPWKFRV"
      },
      "source": [
        "Download the curated ChEMBL bioactivity data that has been pre-processed from Parts 1 and 2 of this Bioinformatics Project series. Here we will be using the **bioactivity_data_3class_pIC50.csv** file that essentially contain the pIC50 values that we will be using for building a regression model."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Fpu5C7HlwV9s"
      },
      "source": [
        "import pandas as pd"
      ],
      "execution_count": 3,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "GCcE8J5XwjtB"
      },
      "source": [
        "# CHEMBL data\n",
        "df1 = pd.read_csv(\"https://raw.githubusercontent.com/stawiskm/QSAR_Modelbuilding_amesTest/main/data/QSAR_ames_raw-data.csv\")\n",
        "df1 = df1.drop(labels=['molecule_chembl_id'],axis=1)\n",
        "df1.columns = ['canonical_smiles', 'class']"
      ],
      "execution_count": 4,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "df1"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
        },
        "id": "CWvVtxcT6qbd",
        "outputId": "aff45724-4f7c-41b2-fd1f-32e15aea88b3"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "                                      canonical_smiles      class\n",
              "0    CC(C)(N)C(=O)N[C@H](COCc1ccccc1)c1nnnn1CCOC(=O...  Non-toxic\n",
              "1    C=C1C(=O)O[C@@H]2C[C@@]3(C)CCCC(=C)[C@@H]3C[C@...      Toxic\n",
              "2    C=C1CCC[C@]2(C)C[C@H]3OC(=O)[C@@H](C)[C@H]3C[C...  Non-toxic\n",
              "3                                     O=c1ccc2ccccc2o1  Non-toxic\n",
              "4                            COc1c2ccoc2cc2oc(=O)ccc12  Non-toxic\n",
              "..                                                 ...        ...\n",
              "650  COCCCOc1cc2c(cc1OC)-c1cc(=O)c(C(=O)O)cn1[C@H](...  Non-toxic\n",
              "651           N#C/C(=C\\c1cccc2cnccc12)c1c[nH]c2ccccc12  Non-toxic\n",
              "652  O=c1cc(NC2CCN(S(=O)(=O)C(F)(F)F)CC2)c2cc(C(c3c...  Non-toxic\n",
              "653    N#Cc1cnc2ccc(-c3c(-c4ccc(F)c(Cl)c4)ncn3CCO)nn12  Non-toxic\n",
              "654  CC(C)(C)OC(=O)Nc1ccc(-c2cc(C(=O)NCCc3cc(C(=O)N...  Non-toxic\n",
              "\n",
              "[655 rows x 2 columns]"
            ],
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              "<style scoped>\n",
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              "\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>class</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>CC(C)(N)C(=O)N[C@H](COCc1ccccc1)c1nnnn1CCOC(=O...</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>C=C1C(=O)O[C@@H]2C[C@@]3(C)CCCC(=C)[C@@H]3C[C@...</td>\n",
              "      <td>Toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>C=C1CCC[C@]2(C)C[C@H]3OC(=O)[C@@H](C)[C@H]3C[C...</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>O=c1ccc2ccccc2o1</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>COc1c2ccoc2cc2oc(=O)ccc12</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>650</th>\n",
              "      <td>COCCCOc1cc2c(cc1OC)-c1cc(=O)c(C(=O)O)cn1[C@H](...</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>651</th>\n",
              "      <td>N#C/C(=C\\c1cccc2cnccc12)c1c[nH]c2ccccc12</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>652</th>\n",
              "      <td>O=c1cc(NC2CCN(S(=O)(=O)C(F)(F)F)CC2)c2cc(C(c3c...</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>653</th>\n",
              "      <td>N#Cc1cnc2ccc(-c3c(-c4ccc(F)c(Cl)c4)ncn3CCO)nn12</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>654</th>\n",
              "      <td>CC(C)(C)OC(=O)Nc1ccc(-c2cc(C(=O)NCCc3cc(C(=O)N...</td>\n",
              "      <td>Non-toxic</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>655 rows × 2 columns</p>\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "df2 = pd.read_csv('https://github.com/stawiskm/QSAR_Modelbuilding_amesTest/raw/main/data/paperData1.csv')\n",
        "df3 = pd.read_csv('https://github.com/stawiskm/QSAR_Modelbuilding_amesTest/raw/main/data/paperData2.csv')\n",
        "df2.columns = ['canonical_smiles', 'class']\n",
        "df3.columns = ['canonical_smiles', 'class']\n",
        "df2['class'] = df2['class'].replace({'non-mutagens':'Non-toxic'})\n",
        "df2['class'] = df2['class'].replace({'mutagens':'Toxic'})\n",
        "df3['class'] = df3['class'].replace({'non-mutagens':'Non-toxic'})\n",
        "df3['class'] = df3['class'].replace({'mutagens':'Toxic'})"
      ],
      "metadata": {
        "id": "k689uxFb3cD9"
      },
      "execution_count": 6,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "df_all = pd.concat([df1,df2,df3], axis=0)"
      ],
      "metadata": {
        "id": "E92KvDRjL_R-"
      },
      "execution_count": 7,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "def cleanSMILES(row):\n",
        "    cpd = str(row.canonical_smiles).split('.')\n",
        "    cpd_longest = max(cpd, key = len)\n",
        "    return cpd_longest"
      ],
      "metadata": {
        "id": "N-VHNDe4QRLn"
      },
      "execution_count": 8,
      "outputs": []
    },
    {
      "cell_type": "code",
      "execution_count": 9,
      "metadata": {
        "id": "7AMm19NW0bJR"
      },
      "outputs": [],
      "source": [
        "df_all['smiles'] = df_all.apply(cleanSMILES ,axis=1)\n",
        "df_all = df_all.drop(\"canonical_smiles\",axis=1)\n",
        "df_all = df_all.rename({\"smiles\":\"canonical_smiles\"},axis=1)\n",
        "\n",
        "df_all=df_all.drop_duplicates(subset=['canonical_smiles'], keep='last')"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "BJDJkY43R-9F"
      },
      "source": [
        "selection = [\"canonical_smiles\",\"class\"]\n",
        "df_all[selection].to_csv('molecule.smi', sep='\\t', index=False, header=False)"
      ],
      "execution_count": 10,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "YzN_S4Quro5S"
      },
      "source": [
        "## **Calculate fingerprint descriptors**\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "JsgTV-ByxdMa"
      },
      "source": [
        "### **Calculate PaDEL descriptors**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "6kN9jrGpS5nE",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "825eb57a-8228-44ad-b805-b0f67456d990"
      },
      "source": [
        "! bash padel.sh"
      ],
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\u001b[1;30;43mDie letzten 5000 Zeilen der Streamingausgabe wurden abgeschnitten.\u001b[0m\n",
            "Processing Toxic in molecule.smi (1043/6041). Average speed: 0.19 s/mol.\n",
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            "Descriptor calculation completed in 12 mins 35.455 secs . Average speed: 0.13 s/mol.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "3g319qxVl7tY"
      },
      "source": [
        "df = pd.read_csv('descriptors_output.csv')\n",
        "df = df.rename({'Name': 'class'}, axis='columns')\n",
        "df.to_csv('QSAR_DescriptorData_ALL.csv', index=False)"
      ],
      "execution_count": 17,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Final Model for deployment"
      ],
      "metadata": {
        "id": "WPbYGiqHCzD5"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import pickle\n",
        "import pandas as pd\n",
        "from sklearn.ensemble import RandomForestClassifier"
      ],
      "metadata": {
        "id": "OdFb70DVCZNW"
      },
      "execution_count": 11,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "df = pd.read_csv(\"https://raw.githubusercontent.com/stawiskm/QSAR_Modelbuilding_amesTest/main/data/QSAR_DescriptorData_ALL.csv\")"
      ],
      "metadata": {
        "id": "Vjf2fqEtM65p"
      },
      "execution_count": 12,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "X = df.drop(['class'], axis=1)\n",
        "X.to_csv('descriptor_list.csv', index = False)\n",
        "y = df[\"class\"]"
      ],
      "metadata": {
        "id": "f2AtPjoODvCC"
      },
      "execution_count": 13,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "clfmodel = {'max_depth': 40,\n",
        "            'min_samples_leaf': 1,\n",
        "            'min_samples_split': 5,\n",
        "            'n_estimators': 800}\n",
        "\n",
        "model =  RandomForestClassifier(max_depth=clfmodel[\"max_depth\"],\n",
        "                                min_samples_leaf=clfmodel[\"min_samples_leaf\"],\n",
        "                                min_samples_split=clfmodel[\"min_samples_split\"],\n",
        "                                n_estimators=clfmodel[\"n_estimators\"])\n",
        "\n",
        "model.fit(X,y)\n",
        "\n",
        "# save\n",
        "with open('amesTest_model.pkl','wb') as f:\n",
        "    pickle.dump(model,f)\n",
        "\n",
        "# load\n",
        "with open('amesTest_model.pkl', 'rb') as f:\n",
        "    model_reloaded = pickle.load(f)\n",
        "\n",
        "\n",
        "model_reloaded.predict(X)"
      ],
      "metadata": {
        "id": "VOYMFNNlDON4",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "d4b91314-3688-4cb8-82af-9072bd0e754f"
      },
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "array(['Toxic', 'Non-toxic', 'Non-toxic', ..., 'Non-toxic', 'Non-toxic',\n",
              "       'Non-toxic'], dtype=object)"
            ]
          },
          "metadata": {},
          "execution_count": 14
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        ""
      ],
      "metadata": {
        "id": "KyhxLizzyRR3"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}