Descriptor_Dataset_Preparation.ipynb

{
  "cells": [
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 572
        },
        "colab_type": "code",
        "id": "H0mjQ2PcrSe5",
        "outputId": "7cd24f88-a9b5-445e-90fc-a2bde1f2aef8"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "--2020-06-09 16:58:49--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
            "Resolving github.com (github.com)... 140.82.113.3\n",
            "Connecting to github.com (github.com)|140.82.113.3|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip [following]\n",
            "--2020-06-09 16:58:50--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|: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  40.2MB/s    in 0.6s    \n",
            "\n",
            "2020-06-09 16:58:51 (40.2 MB/s) - ‘padel.zip’ saved [25768637/25768637]\n",
            "\n",
            "--2020-06-09 16:58:52--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n",
            "Resolving github.com (github.com)... 140.82.113.3\n",
            "Connecting to github.com (github.com)|140.82.113.3|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh [following]\n",
            "--2020-06-09 16:58:52--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|: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",
            "2020-06-09 16:58:52 (11.1 MB/s) - ‘padel.sh’ saved [231/231]\n",
            "\n"
          ]
        }
      ],
      "source": [
        "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
        "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 2,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "colab_type": "code",
        "id": "64HnTL4tS-nA",
        "outputId": "b082c979-db9f-48dd-8050-0462b6cf4979"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "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",
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            "  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"
          ]
        }
      ],
      "source": [
        "! unzip padel.zip"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "QmxXXFa4wTNG"
      },
      "source": [
        "## **Load bioactivity data**"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 3,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 208
        },
        "colab_type": "code",
        "id": "JBs7QdJoubWC",
        "outputId": "3d6bfdcd-1eb9-4930-8e43-45d217f7d22b"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "--2020-06-09 17:00:26--  https://raw.githubusercontent.com/dataprofessor/data/master/acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 655414 (640K) [text/plain]\n",
            "Saving to: ‘acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv’\n",
            "\n",
            "\r          acetylcho   0%[                    ]       0  --.-KB/s               \racetylcholinesteras 100%[===================>] 640.05K  --.-KB/s    in 0.07s   \n",
            "\n",
            "2020-06-09 17:00:26 (9.21 MB/s) - ‘acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv’ saved [655414/655414]\n",
            "\n"
          ]
        }
      ],
      "source": [
        "! wget https://raw.githubusercontent.com/dataprofessor/data/master/acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 0,
      "metadata": {
        "colab": {},
        "colab_type": "code",
        "id": "Fpu5C7HlwV9s"
      },
      "outputs": [],
      "source": [
        "import pandas as pd"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 0,
      "metadata": {
        "colab": {},
        "colab_type": "code",
        "id": "GCcE8J5XwjtB"
      },
      "outputs": [],
      "source": [
        "df3 = pd.read_csv('acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv')"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 6,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 467
        },
        "colab_type": "code",
        "id": "60z_N6egNiSJ",
        "outputId": "4419acc9-ced7-4a45-b849-665ed5e0fd99"
      },
      "outputs": [
        {
          "data": {
            "text/html": [
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              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Unnamed: 0</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>class</th>\n",
              "      <th>MW</th>\n",
              "      <th>LogP</th>\n",
              "      <th>NumHDonors</th>\n",
              "      <th>NumHAcceptors</th>\n",
              "      <th>pIC50</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>0</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
              "      <td>active</td>\n",
              "      <td>312.325</td>\n",
              "      <td>2.80320</td>\n",
              "      <td>0.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>6.124939</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>1</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
              "      <td>active</td>\n",
              "      <td>376.913</td>\n",
              "      <td>4.55460</td>\n",
              "      <td>0.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>7.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>2</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
              "      <td>inactive</td>\n",
              "      <td>426.851</td>\n",
              "      <td>5.35740</td>\n",
              "      <td>0.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>4.301030</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>3</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
              "      <td>active</td>\n",
              "      <td>404.845</td>\n",
              "      <td>4.70690</td>\n",
              "      <td>0.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>6.522879</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>4</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
              "      <td>active</td>\n",
              "      <td>346.334</td>\n",
              "      <td>3.09530</td>\n",
              "      <td>0.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>6.096910</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",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4690</th>\n",
              "      <td>4690</td>\n",
              "      <td>CHEMBL4293155</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
              "      <td>intermediate</td>\n",
              "      <td>511.150</td>\n",
              "      <td>7.07230</td>\n",
              "      <td>2.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>5.612610</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4691</th>\n",
              "      <td>4691</td>\n",
              "      <td>CHEMBL4282558</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
              "      <td>intermediate</td>\n",
              "      <td>511.150</td>\n",
              "      <td>7.07230</td>\n",
              "      <td>2.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>5.595166</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4692</th>\n",
              "      <td>4692</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
              "      <td>intermediate</td>\n",
              "      <td>555.601</td>\n",
              "      <td>7.18140</td>\n",
              "      <td>2.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>5.419075</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4693</th>\n",
              "      <td>4693</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
              "      <td>intermediate</td>\n",
              "      <td>521.702</td>\n",
              "      <td>6.32710</td>\n",
              "      <td>2.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>5.460924</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4694</th>\n",
              "      <td>4694</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
              "      <td>intermediate</td>\n",
              "      <td>501.715</td>\n",
              "      <td>6.29058</td>\n",
              "      <td>2.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>5.555955</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 9 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "      Unnamed: 0 molecule_chembl_id  ... NumHAcceptors     pIC50\n",
              "0              0       CHEMBL133897  ...           6.0  6.124939\n",
              "1              1       CHEMBL336398  ...           5.0  7.000000\n",
              "2              2       CHEMBL131588  ...           5.0  4.301030\n",
              "3              3       CHEMBL130628  ...           5.0  6.522879\n",
              "4              4       CHEMBL130478  ...           6.0  6.096910\n",
              "...          ...                ...  ...           ...       ...\n",
              "4690        4690      CHEMBL4293155  ...           3.0  5.612610\n",
              "4691        4691      CHEMBL4282558  ...           3.0  5.595166\n",
              "4692        4692      CHEMBL4281727  ...           3.0  5.419075\n",
              "4693        4693      CHEMBL4292349  ...           5.0  5.460924\n",
              "4694        4694      CHEMBL4278260  ...           4.0  5.555955\n",
              "\n",
              "[4695 rows x 9 columns]"
            ]
          },
          "execution_count": 6,
          "metadata": {
            "tags": []
          },
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df3"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 0,
      "metadata": {
        "colab": {},
        "colab_type": "code",
        "id": "BJDJkY43R-9F"
      },
      "outputs": [],
      "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)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 8,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 104
        },
        "colab_type": "code",
        "id": "nRSCoPVDSkf5",
        "outputId": "2be43c1d-d8b8-42a8-93fc-4c1b29855a8a"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1\tCHEMBL133897\n",
            "O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1\tCHEMBL336398\n",
            "CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1\tCHEMBL131588\n",
            "O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F\tCHEMBL130628\n",
            "CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C\tCHEMBL130478\n"
          ]
        }
      ],
      "source": [
        "! cat molecule.smi | head -5"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 9,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "colab_type": "code",
        "id": "GlYaJ9pzUGjS",
        "outputId": "6dab2be5-172a-4efb-8b42-7ceef402bfa3"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "4695\n"
          ]
        }
      ],
      "source": [
        "! cat molecule.smi | wc -l"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "YzN_S4Quro5S"
      },
      "source": [
        "## **Calculate fingerprint descriptors**\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "JsgTV-ByxdMa"
      },
      "source": [
        "### **Calculate PaDEL descriptors**"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 10,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 55
        },
        "colab_type": "code",
        "id": "hSCopQvEiSMj",
        "outputId": "77fe3614-69ef-4bd1-9dca-2a9b2c975fbb"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "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"
          ]
        }
      ],
      "source": [
        "! cat padel.sh"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 11,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "colab_type": "code",
        "id": "6kN9jrGpS5nE",
        "outputId": "456a4161-b3dd-44b9-bc82-2523976f25ea"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "Processing CHEMBL133897 in molecule.smi (1/4695). \n",
            "Processing CHEMBL336398 in molecule.smi (2/4695). \n",
            "Processing CHEMBL130628 in molecule.smi (4/4695). Average speed: 2.98 s/mol.\n",
            "Processing CHEMBL131588 in molecule.smi (3/4695). Average speed: 5.85 s/mol.\n",
            "Processing CHEMBL130478 in molecule.smi (5/4695). Average speed: 2.15 s/mol.\n",
            "Processing CHEMBL130098 in molecule.smi (7/4695). Average speed: 1.40 s/mol.\n",
            "Processing CHEMBL130112 in molecule.smi (6/4695). Average speed: 1.71 s/mol.\n",
            "Processing CHEMBL337486 in molecule.smi (8/4695). Average speed: 1.25 s/mol.\n",
            "Processing CHEMBL336538 in molecule.smi (9/4695). Average speed: 1.08 s/mol.\n",
            "Processing CHEMBL131051 in molecule.smi (10/4695). Average speed: 1.01 s/mol.\n",
            "Processing CHEMBL341437 in molecule.smi (11/4695). Average speed: 0.93 s/mol.\n",
            "Processing CHEMBL335033 in molecule.smi (12/4695). Average speed: 0.88 s/mol.\n",
            "Processing CHEMBL122983 in molecule.smi (13/4695). Average speed: 0.90 s/mol.\n",
            "Processing CHEMBL338720 in molecule.smi (14/4695). Average speed: 0.80 s/mol.\n",
            "Processing CHEMBL339995 in molecule.smi (15/4695). Average speed: 0.79 s/mol.\n",
            "Processing CHEMBL131536 in molecule.smi (17/4695). Average speed: 0.71 s/mol.\n",
            "Processing CHEMBL335158 in molecule.smi (16/4695). Average speed: 0.75 s/mol.\n",
            "Processing CHEMBL106126 in molecule.smi (18/4695). Average speed: 0.70 s/mol.\n",
            "Processing CHEMBL336625 in molecule.smi (20/4695). Average speed: 0.64 s/mol.\n",
            "Processing CHEMBL334971 in molecule.smi (19/4695). Average speed: 0.68 s/mol.\n",
            "Processing CHEMBL130666 in molecule.smi (21/4695). Average speed: 0.66 s/mol.\n",
            "Processing CHEMBL134061 in molecule.smi (22/4695). Average speed: 0.63 s/mol.\n",
            "Processing CHEMBL133388 in molecule.smi (23/4695). Average speed: 0.62 s/mol.\n",
            "Processing CHEMBL130645 in molecule.smi (24/4695). Average speed: 0.60 s/mol.\n",
            "Processing CHEMBL133580 in molecule.smi (25/4695). Average speed: 0.59 s/mol.\n",
            "Processing CHEMBL336524 in molecule.smi (26/4695). Average speed: 0.57 s/mol.\n",
            "Processing CHEMBL336276 in molecule.smi (27/4695). Average speed: 0.56 s/mol.\n",
            "Processing CHEMBL334395 in molecule.smi (28/4695). Average speed: 0.56 s/mol.\n",
            "Processing CHEMBL131320 in molecule.smi (29/4695). Average speed: 0.54 s/mol.\n",
            "Processing CHEMBL339297 in molecule.smi (30/4695). Average speed: 0.53 s/mol.\n",
            "Processing CHEMBL337714 in molecule.smi (31/4695). Average speed: 0.52 s/mol.\n",
            "Processing CHEMBL122575 in molecule.smi (32/4695). Average speed: 0.51 s/mol.\n",
            "Processing CHEMBL130704 in molecule.smi (33/4695). Average speed: 0.51 s/mol.\n",
            "Processing CHEMBL46151 in molecule.smi (34/4695). Average speed: 0.50 s/mol.\n",
            "Processing CHEMBL54126 in molecule.smi (35/4695). Average speed: 0.49 s/mol.\n",
            "Processing CHEMBL297316 in molecule.smi (36/4695). Average speed: 0.48 s/mol.\n",
            "Processing CHEMBL65667 in molecule.smi (37/4695). Average speed: 0.47 s/mol.\n",
            "Processing CHEMBL431519 in molecule.smi (38/4695). Average speed: 0.46 s/mol.\n",
            "Processing CHEMBL296429 in molecule.smi (39/4695). Average speed: 0.46 s/mol.\n",
            "Processing CHEMBL154972 in molecule.smi (40/4695). Average speed: 0.45 s/mol.\n",
            "Processing CHEMBL152722 in molecule.smi (41/4695). Average speed: 0.45 s/mol.\n",
            "Processing CHEMBL544022 in molecule.smi (42/4695). Average speed: 0.45 s/mol.\n",
            "Processing CHEMBL349127 in molecule.smi (43/4695). Average speed: 0.44 s/mol.\n",
            "Processing CHEMBL156659 in molecule.smi (44/4695). Average speed: 0.44 s/mol.\n",
            "Processing CHEMBL45118 in molecule.smi (45/4695). Average speed: 0.43 s/mol.\n",
            "Processing CHEMBL155322 in molecule.smi (47/4695). Average speed: 0.42 s/mol.\n",
            "Processing CHEMBL542609 in molecule.smi (46/4695). Average speed: 0.43 s/mol.\n",
            "Processing CHEMBL1203537 in molecule.smi (49/4695). Average speed: 0.41 s/mol.\n",
            "Processing CHEMBL154211 in molecule.smi (48/4695). Average speed: 0.42 s/mol.\n",
            "Processing CHEMBL86 in molecule.smi (50/4695). Average speed: 0.41 s/mol.\n",
            "Processing CHEMBL47375 in molecule.smi (51/4695). Average speed: 0.41 s/mol.\n",
            "Processing CHEMBL542360 in molecule.smi (52/4695). Average speed: 0.40 s/mol.\n",
            "Processing CHEMBL345849 in molecule.smi (53/4695). Average speed: 0.41 s/mol.\n",
            "Processing CHEMBL154689 in molecule.smi (54/4695). Average speed: 0.39 s/mol.\n",
            "Processing CHEMBL346733 in molecule.smi (55/4695). Average speed: 0.39 s/mol.\n",
            "Processing CHEMBL416464 in molecule.smi (56/4695). Average speed: 0.39 s/mol.\n",
            "Processing CHEMBL1203539 in molecule.smi (57/4695). Average speed: 0.38 s/mol.\n",
            "Processing CHEMBL347729 in molecule.smi (58/4695). Average speed: 0.38 s/mol.\n",
            "Processing CHEMBL63173 in molecule.smi (60/4695). Average speed: 0.37 s/mol.\n",
            "Processing CHEMBL296786 in molecule.smi (59/4695). Average speed: 0.37 s/mol.\n",
            "Processing CHEMBL292788 in molecule.smi (62/4695). Average speed: 0.37 s/mol.\n",
            "Processing CHEMBL433041 in molecule.smi (61/4695). Average speed: 0.37 s/mol.\n",
            "Processing CHEMBL155392 in molecule.smi (64/4695). Average speed: 0.37 s/mol.\n",
            "Processing CHEMBL33051 in molecule.smi (63/4695). Average speed: 0.37 s/mol.\n",
            "Processing CHEMBL543546 in molecule.smi (66/4695). Average speed: 0.36 s/mol.\n",
            "Processing CHEMBL153311 in molecule.smi (65/4695). Average speed: 0.36 s/mol.\n",
            "Processing CHEMBL556172 in molecule.smi (68/4695). Average speed: 0.35 s/mol.\n",
            "Processing CHEMBL1420 in molecule.smi (67/4695). Average speed: 0.36 s/mol.\n",
            "Processing CHEMBL154263 in molecule.smi (69/4695). Average speed: 0.35 s/mol.\n",
            "Processing CHEMBL544669 in molecule.smi (70/4695). Average speed: 0.34 s/mol.\n",
            "Processing CHEMBL62664 in molecule.smi (71/4695). Average speed: 0.35 s/mol.\n",
            "Processing CHEMBL155111 in molecule.smi (72/4695). Average speed: 0.34 s/mol.\n",
            "Processing CHEMBL1203534 in molecule.smi (73/4695). Average speed: 0.34 s/mol.\n",
            "Processing CHEMBL541044 in molecule.smi (74/4695). Average speed: 0.34 s/mol.\n",
            "Processing CHEMBL543779 in molecule.smi (75/4695). Average speed: 0.33 s/mol.\n",
            "Processing CHEMBL155495 in molecule.smi (76/4695). Average speed: 0.33 s/mol.\n",
            "Processing CHEMBL64011 in molecule.smi (77/4695). Average speed: 0.33 s/mol.\n",
            "Processing CHEMBL65585 in molecule.smi (78/4695). Average speed: 0.33 s/mol.\n",
            "Processing CHEMBL347539 in molecule.smi (79/4695). Average speed: 0.33 s/mol.\n",
            "Processing CHEMBL154433 in molecule.smi (80/4695). Average speed: 0.33 s/mol.\n",
            "Processing CHEMBL157208 in molecule.smi (81/4695). Average speed: 0.32 s/mol.\n",
            "Processing CHEMBL1790041 in molecule.smi (82/4695). Average speed: 0.32 s/mol.\n",
            "Processing CHEMBL65356 in molecule.smi (83/4695). Average speed: 0.32 s/mol.\n",
            "Processing CHEMBL154366 in molecule.smi (84/4695). Average speed: 0.32 s/mol.\n",
            "Processing CHEMBL153821 in molecule.smi (85/4695). Average speed: 0.32 s/mol.\n",
            "Processing CHEMBL416644 in molecule.smi (86/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL94 in molecule.smi (87/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL303574 in molecule.smi (88/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL296277 in molecule.smi (90/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL65018 in molecule.smi (89/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL1203535 in molecule.smi (92/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL66309 in molecule.smi (91/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL296560 in molecule.smi (93/4695). Average speed: 0.31 s/mol.\n",
            "Processing CHEMBL152260 in molecule.smi (94/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL296669 in molecule.smi (96/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL154950 in molecule.smi (95/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL1203538 in molecule.smi (97/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL19060 in molecule.smi (98/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL422977 in molecule.smi (99/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL11805 in molecule.smi (100/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL302179 in molecule.smi (101/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL27673 in molecule.smi (102/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL132377 in molecule.smi (103/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL132133 in molecule.smi (104/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL95 in molecule.smi (105/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL134488 in molecule.smi (106/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL134382 in molecule.smi (107/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL59109 in molecule.smi (108/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL286990 in molecule.smi (109/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL294891 in molecule.smi (110/4695). Average speed: 0.30 s/mol.\n",
            "Processing CHEMBL1255901 in molecule.smi (111/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL89011 in molecule.smi (112/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL748 in molecule.smi (113/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL29300 in molecule.smi (115/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL50608 in molecule.smi (114/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL27675 in molecule.smi (116/4695). Average speed: 0.29 s/mol.\n",
            "Processing CHEMBL60167 in molecule.smi (118/4695). Average speed: 0.28 s/mol.\n",
            "Processing CHEMBL435373 in molecule.smi (117/4695). Average speed: 0.29 s/mol.\n",
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            "Processing CHEMBL283509 in molecule.smi (444/4695). Average speed: 0.23 s/mol.\n",
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            "Processing CHEMBL95020 in molecule.smi (446/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL24844 in molecule.smi (448/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL61486 in molecule.smi (449/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL292480 in molecule.smi (450/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL61715 in molecule.smi (451/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL11833 in molecule.smi (452/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL64615 in molecule.smi (454/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL24519 in molecule.smi (453/4695). Average speed: 0.23 s/mol.\n",
            "Processing CHEMBL61986 in molecule.smi (455/4695). Average speed: 0.23 s/mol.\n",
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            "Processing CHEMBL153934 in molecule.smi (467/4695). Average speed: 0.24 s/mol.\n",
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            "Processing CHEMBL344656 in molecule.smi (470/4695). Average speed: 0.24 s/mol.\n",
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            "Processing CHEMBL344736 in molecule.smi (500/4695). Average speed: 0.23 s/mol.\n",
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            "Processing CHEMBL122834 in molecule.smi (504/4695). Average speed: 0.23 s/mol.\n",
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            "Processing CHEMBL149084 in molecule.smi (506/4695). Average speed: 0.22 s/mol.\n",
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            "Processing CHEMBL328715 in molecule.smi (514/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL93241 in molecule.smi (513/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL2448609 in molecule.smi (515/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL34222 in molecule.smi (516/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL416586 in molecule.smi (517/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL32964 in molecule.smi (518/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL288549 in molecule.smi (519/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL34002 in molecule.smi (520/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL33098 in molecule.smi (521/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL32966 in molecule.smi (523/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL284938 in molecule.smi (522/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL33173 in molecule.smi (524/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL287691 in molecule.smi (525/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL286690 in molecule.smi (527/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL32543 in molecule.smi (526/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL32453 in molecule.smi (529/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL33727 in molecule.smi (528/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL62373 in molecule.smi (530/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL32452 in molecule.smi (532/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL33161 in molecule.smi (531/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL33642 in molecule.smi (533/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL284369 in molecule.smi (534/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL284519 in molecule.smi (535/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL32653 in molecule.smi (536/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL1127 in molecule.smi (537/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL318026 in molecule.smi (538/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL319451 in molecule.smi (539/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL324975 in molecule.smi (540/4695). Average speed: 0.22 s/mol.\n",
            "Processing CHEMBL325505 in molecule.smi (541/4695). Average speed: 0.22 s/mol.\n"
          ]
        }
      ],
      "source": [
        "! bash padel.sh"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 14,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 173
        },
        "colab_type": "code",
        "id": "2p7rAVy_k_hH",
        "outputId": "7404029f-4d69-486c-97a2-faf6d4574971"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "total 34296\n",
            "-rw-r--r-- 1 root root   655414 Jun  9 17:00 acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv\n",
            "-rw-r--r-- 1 root root  8356701 Jun  9 17:08 descriptors_output.csv\n",
            "drwxr-xr-x 3 root root     4096 Jun  9 17:00 __MACOSX\n",
            "-rw-r--r-- 1 root root   310658 Jun  9 17:01 molecule.smi\n",
            "drwxrwxr-x 4 root root     4096 May 30 10:10 PaDEL-Descriptor\n",
            "-rw-r--r-- 1 root root      231 Jun  9 16:58 padel.sh\n",
            "-rw-r--r-- 1 root root 25768637 Jun  9 16:58 padel.zip\n",
            "drwxr-xr-x 1 root root     4096 May 29 18:19 sample_data\n"
          ]
        }
      ],
      "source": [
        "! ls -l"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "gUMlPfFrxicj"
      },
      "source": [
        "## **Preparing the X and Y Data Matrices**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "30aa4WP4ZA8M"
      },
      "source": [
        "### **X data matrix**"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 0,
      "metadata": {
        "colab": {},
        "colab_type": "code",
        "id": "3g319qxVl7tY"
      },
      "outputs": [],
      "source": [
        "df3_X = pd.read_csv('descriptors_output.csv')"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 16,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 435
        },
        "colab_type": "code",
        "id": "hBp1PTObFQDd",
        "outputId": "26a4603a-d1b2-4d64-e1c8-cf5fd0612bbf"
      },
      "outputs": [
        {
          "data": {
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              "      <th>PubchemFP852</th>\n",
              "      <th>PubchemFP853</th>\n",
              "      <th>PubchemFP854</th>\n",
              "      <th>PubchemFP855</th>\n",
              "      <th>PubchemFP856</th>\n",
              "      <th>PubchemFP857</th>\n",
              "      <th>PubchemFP858</th>\n",
              "      <th>PubchemFP859</th>\n",
              "      <th>PubchemFP860</th>\n",
              "      <th>PubchemFP861</th>\n",
              "      <th>PubchemFP862</th>\n",
              "      <th>PubchemFP863</th>\n",
              "      <th>PubchemFP864</th>\n",
              "      <th>PubchemFP865</th>\n",
              "      <th>PubchemFP866</th>\n",
              "      <th>PubchemFP867</th>\n",
              "      <th>PubchemFP868</th>\n",
              "      <th>PubchemFP869</th>\n",
              "      <th>PubchemFP870</th>\n",
              "      <th>PubchemFP871</th>\n",
              "      <th>PubchemFP872</th>\n",
              "      <th>PubchemFP873</th>\n",
              "      <th>PubchemFP874</th>\n",
              "      <th>PubchemFP875</th>\n",
              "      <th>PubchemFP876</th>\n",
              "      <th>PubchemFP877</th>\n",
              "      <th>PubchemFP878</th>\n",
              "      <th>PubchemFP879</th>\n",
              "      <th>PubchemFP880</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>CHEMBL336398</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL133897</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>CHEMBL130628</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4690</th>\n",
              "      <td>CHEMBL4293155</td>\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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4691</th>\n",
              "      <td>CHEMBL4282558</td>\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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</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>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4692</th>\n",
              "      <td>CHEMBL4281727</td>\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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</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",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
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              "    <tr>\n",
              "      <th>4693</th>\n",
              "      <td>CHEMBL4292349</td>\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>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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",
              "      <td>0</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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <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>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4694</th>\n",
              "      <td>CHEMBL4278260</td>\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",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
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              "      <td>1</td>\n",
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              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 882 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "               Name  PubchemFP0  ...  PubchemFP879  PubchemFP880\n",
              "0      CHEMBL336398           1  ...             0             0\n",
              "1      CHEMBL133897           1  ...             0             0\n",
              "2      CHEMBL130628           1  ...             0             0\n",
              "3      CHEMBL131588           1  ...             0             0\n",
              "4      CHEMBL130478           1  ...             0             0\n",
              "...             ...         ...  ...           ...           ...\n",
              "4690  CHEMBL4293155           1  ...             0             0\n",
              "4691  CHEMBL4282558           1  ...             0             0\n",
              "4692  CHEMBL4281727           1  ...             0             0\n",
              "4693  CHEMBL4292349           1  ...             0             0\n",
              "4694  CHEMBL4278260           1  ...             0             0\n",
              "\n",
              "[4695 rows x 882 columns]"
            ]
          },
          "execution_count": 16,
          "metadata": {
            "tags": []
          },
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df3_X"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 17,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 435
        },
        "colab_type": "code",
        "id": "dTJsDPBKq_hr",
        "outputId": "c92c4d7d-6df7-40b0-a7b8-ce644bacb52a"
      },
      "outputs": [
        {
          "data": {
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              "      <th></th>\n",
              "      <th>PubchemFP0</th>\n",
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              "      <th>PubchemFP848</th>\n",
              "      <th>PubchemFP849</th>\n",
              "      <th>PubchemFP850</th>\n",
              "      <th>PubchemFP851</th>\n",
              "      <th>PubchemFP852</th>\n",
              "      <th>PubchemFP853</th>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4690</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4691</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</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",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
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              "      <td>0</td>\n",
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              "      <th>4693</th>\n",
              "      <td>1</td>\n",
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              "      <td>1</td>\n",
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              "      <td>1</td>\n",
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              "    </tr>\n",
              "    <tr>\n",
              "      <th>4694</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
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              "      <td>0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 881 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "      PubchemFP0  PubchemFP1  ...  PubchemFP879  PubchemFP880\n",
              "0              1           1  ...             0             0\n",
              "1              1           1  ...             0             0\n",
              "2              1           1  ...             0             0\n",
              "3              1           1  ...             0             0\n",
              "4              1           1  ...             0             0\n",
              "...          ...         ...  ...           ...           ...\n",
              "4690           1           1  ...             0             0\n",
              "4691           1           1  ...             0             0\n",
              "4692           1           1  ...             0             0\n",
              "4693           1           1  ...             0             0\n",
              "4694           1           1  ...             0             0\n",
              "\n",
              "[4695 rows x 881 columns]"
            ]
          },
          "execution_count": 17,
          "metadata": {
            "tags": []
          },
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df3_X = df3_X.drop(columns=['Name'])\n",
        "df3_X"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "6ePu814KZNBG"
      },
      "source": [
        "## **Y variable**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "9ssfxFCdr7ua"
      },
      "source": [
        "### **Convert IC50 to pIC50**"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 18,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 225
        },
        "colab_type": "code",
        "id": "FlhsSEW5FXTG",
        "outputId": "ef224d6b-4cf3-4bde-fe83-d2e43f6e246c"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "0       6.124939\n",
              "1       7.000000\n",
              "2       4.301030\n",
              "3       6.522879\n",
              "4       6.096910\n",
              "          ...   \n",
              "4690    5.612610\n",
              "4691    5.595166\n",
              "4692    5.419075\n",
              "4693    5.460924\n",
              "4694    5.555955\n",
              "Name: pIC50, Length: 4695, dtype: float64"
            ]
          },
          "execution_count": 18,
          "metadata": {
            "tags": []
          },
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df3_Y = df3['pIC50']\n",
        "df3_Y"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "eET6iZ1Aw3oe"
      },
      "source": [
        "## **Combining X and Y variable**"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 19,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 435
        },
        "colab_type": "code",
        "id": "FRBfBP3QxFJp",
        "outputId": "ee900c26-ff5c-4e20-a3fb-7b1f9367db66"
      },
      "outputs": [
        {
          "data": {
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              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>PubchemFP0</th>\n",
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              "      <th>PubchemFP21</th>\n",
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              "      <th>...</th>\n",
              "      <th>PubchemFP842</th>\n",
              "      <th>PubchemFP843</th>\n",
              "      <th>PubchemFP844</th>\n",
              "      <th>PubchemFP845</th>\n",
              "      <th>PubchemFP846</th>\n",
              "      <th>PubchemFP847</th>\n",
              "      <th>PubchemFP848</th>\n",
              "      <th>PubchemFP849</th>\n",
              "      <th>PubchemFP850</th>\n",
              "      <th>PubchemFP851</th>\n",
              "      <th>PubchemFP852</th>\n",
              "      <th>PubchemFP853</th>\n",
              "      <th>PubchemFP854</th>\n",
              "      <th>PubchemFP855</th>\n",
              "      <th>PubchemFP856</th>\n",
              "      <th>PubchemFP857</th>\n",
              "      <th>PubchemFP858</th>\n",
              "      <th>PubchemFP859</th>\n",
              "      <th>PubchemFP860</th>\n",
              "      <th>PubchemFP861</th>\n",
              "      <th>PubchemFP862</th>\n",
              "      <th>PubchemFP863</th>\n",
              "      <th>PubchemFP864</th>\n",
              "      <th>PubchemFP865</th>\n",
              "      <th>PubchemFP866</th>\n",
              "      <th>PubchemFP867</th>\n",
              "      <th>PubchemFP868</th>\n",
              "      <th>PubchemFP869</th>\n",
              "      <th>PubchemFP870</th>\n",
              "      <th>PubchemFP871</th>\n",
              "      <th>PubchemFP872</th>\n",
              "      <th>PubchemFP873</th>\n",
              "      <th>PubchemFP874</th>\n",
              "      <th>PubchemFP875</th>\n",
              "      <th>PubchemFP876</th>\n",
              "      <th>PubchemFP877</th>\n",
              "      <th>PubchemFP878</th>\n",
              "      <th>PubchemFP879</th>\n",
              "      <th>PubchemFP880</th>\n",
              "      <th>pIC50</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>7.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>4.301030</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>6.522879</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>6.096910</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4690</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>5.612610</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4691</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",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>...</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>5.595166</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4692</th>\n",
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              "      <td>1</td>\n",
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              "      <td>5.555955</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 882 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "      PubchemFP0  PubchemFP1  PubchemFP2  ...  PubchemFP879  PubchemFP880     pIC50\n",
              "0              1           1           1  ...             0             0  6.124939\n",
              "1              1           1           1  ...             0             0  7.000000\n",
              "2              1           1           1  ...             0             0  4.301030\n",
              "3              1           1           0  ...             0             0  6.522879\n",
              "4              1           1           0  ...             0             0  6.096910\n",
              "...          ...         ...         ...  ...           ...           ...       ...\n",
              "4690           1           1           1  ...             0             0  5.612610\n",
              "4691           1           1           1  ...             0             0  5.595166\n",
              "4692           1           1           1  ...             0             0  5.419075\n",
              "4693           1           1           1  ...             0             0  5.460924\n",
              "4694           1           1           1  ...             0             0  5.555955\n",
              "\n",
              "[4695 rows x 882 columns]"
            ]
          },
          "execution_count": 19,
          "metadata": {
            "tags": []
          },
          "output_type": "execute_result"
        }
      ],
      "source": [
        "dataset3 = pd.concat([df3_X,df3_Y], axis=1)\n",
        "dataset3"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 0,
      "metadata": {
        "colab": {},
        "colab_type": "code",
        "id": "75npGyvhae0e"
      },
      "outputs": [],
      "source": [
        "dataset3.to_csv('acetylcholinesterase_06_bioactivity_data_3class_pIC50_pubchem_fp.csv', index=False)"
      ]
    }
  ],
  "metadata": {
    "colab": {
      "collapsed_sections": [],
      "name": "CDD-ML-Part-3-Acetylcholinesterase-Descriptor-Dataset-Preparation.ipynb",
      "provenance": []
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}