padelpy.ipynb

{
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  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "padelpy.ipynb",
      "provenance": [],
      "collapsed_sections": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_TwfB5SbRlCl"
      },
      "source": [
        "# **Calculating molecular fingerprints using padelpy**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "RvCr54uPSDxy"
      },
      "source": [
        "# **Install padelpy**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "NZV55YIz4BMx",
        "outputId": "e402368a-a61f-4b64-80ee-18d9eb1b9937"
      },
      "source": [
        "! pip install padelpy"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting padelpy\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/4d/40/57cd08bdbb1e6f2a7f25f7495fe3b4009ee453b401fe1ba457df92bf78c6/padelpy-0.1.9-py2.py3-none-any.whl (20.9MB)\n",
            "\u001b[K     |████████████████████████████████| 20.9MB 1.4MB/s \n",
            "\u001b[?25hInstalling collected packages: padelpy\n",
            "Successfully installed padelpy-0.1.9\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "K7AgkF1havzY"
      },
      "source": [
        "# **Prepare fingerprint XML**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "OSY4PlfDSKi1"
      },
      "source": [
        "### **Download fingerprint XML files**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ZBXNlLXAA14q",
        "outputId": "7a7876f8-0117-4f6b-f292-e8af47883e5e"
      },
      "source": [
        "! wget https://github.com/dataprofessor/padel/raw/main/fingerprints_xml.zip\n",
        "! unzip fingerprints_xml.zip"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-07-04 15:38:39--  https://github.com/dataprofessor/padel/raw/main/fingerprints_xml.zip\n",
            "Resolving github.com (github.com)... 140.82.113.4\n",
            "Connecting to github.com (github.com)|140.82.113.4|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://raw.githubusercontent.com/dataprofessor/padel/main/fingerprints_xml.zip [following]\n",
            "--2021-07-04 15:38:39--  https://raw.githubusercontent.com/dataprofessor/padel/main/fingerprints_xml.zip\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 10871 (11K) [application/zip]\n",
            "Saving to: ‘fingerprints_xml.zip’\n",
            "\n",
            "fingerprints_xml.zi 100%[===================>]  10.62K  --.-KB/s    in 0s      \n",
            "\n",
            "2021-07-04 15:38:39 (105 MB/s) - ‘fingerprints_xml.zip’ saved [10871/10871]\n",
            "\n",
            "Archive:  fingerprints_xml.zip\n",
            "  inflating: AtomPairs2DFingerprintCount.xml  \n",
            "  inflating: AtomPairs2DFingerprinter.xml  \n",
            "  inflating: EStateFingerprinter.xml  \n",
            "  inflating: ExtendedFingerprinter.xml  \n",
            "  inflating: Fingerprinter.xml       \n",
            "  inflating: GraphOnlyFingerprinter.xml  \n",
            "  inflating: KlekotaRothFingerprintCount.xml  \n",
            "  inflating: KlekotaRothFingerprinter.xml  \n",
            "  inflating: MACCSFingerprinter.xml  \n",
            "  inflating: PubchemFingerprinter.xml  \n",
            "  inflating: SubstructureFingerprintCount.xml  \n",
            "  inflating: SubstructureFingerprinter.xml  \n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "AHkFjZ1sSSna"
      },
      "source": [
        "### **List and sort fingerprint XML files**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "-15LyfWQOUz1",
        "outputId": "7d154167-134c-4b0a-c1cb-5e6d4b56c3b0"
      },
      "source": [
        "import glob\n",
        "xml_files = glob.glob(\"*.xml\")\n",
        "xml_files.sort()\n",
        "xml_files"
      ],
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "['AtomPairs2DFingerprintCount.xml',\n",
              " 'AtomPairs2DFingerprinter.xml',\n",
              " 'EStateFingerprinter.xml',\n",
              " 'ExtendedFingerprinter.xml',\n",
              " 'Fingerprinter.xml',\n",
              " 'GraphOnlyFingerprinter.xml',\n",
              " 'KlekotaRothFingerprintCount.xml',\n",
              " 'KlekotaRothFingerprinter.xml',\n",
              " 'MACCSFingerprinter.xml',\n",
              " 'PubchemFingerprinter.xml',\n",
              " 'SubstructureFingerprintCount.xml',\n",
              " 'SubstructureFingerprinter.xml']"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 3
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "LrCmuWI2ZYdk"
      },
      "source": [
        "FP_list = ['AtomPairs2DCount',\n",
        " 'AtomPairs2D',\n",
        " 'EState',\n",
        " 'CDKextended',\n",
        " 'CDK',\n",
        " 'CDKgraphonly',\n",
        " 'KlekotaRothCount',\n",
        " 'KlekotaRoth',\n",
        " 'MACCS',\n",
        " 'PubChem',\n",
        " 'SubstructureCount',\n",
        " 'Substructure']"
      ],
      "execution_count": 4,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "86rnl7iha_8n"
      },
      "source": [
        "### **Create a dictionary**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "2Ir_n8KlbMvs",
        "outputId": "d24b001f-eb7e-4edf-9ee5-bfc0717ef626"
      },
      "source": [
        "fp = dict(zip(FP_list, xml_files))\n",
        "fp"
      ],
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'AtomPairs2D': 'AtomPairs2DFingerprinter.xml',\n",
              " 'AtomPairs2DCount': 'AtomPairs2DFingerprintCount.xml',\n",
              " 'CDK': 'Fingerprinter.xml',\n",
              " 'CDKextended': 'ExtendedFingerprinter.xml',\n",
              " 'CDKgraphonly': 'GraphOnlyFingerprinter.xml',\n",
              " 'EState': 'EStateFingerprinter.xml',\n",
              " 'KlekotaRoth': 'KlekotaRothFingerprinter.xml',\n",
              " 'KlekotaRothCount': 'KlekotaRothFingerprintCount.xml',\n",
              " 'MACCS': 'MACCSFingerprinter.xml',\n",
              " 'PubChem': 'PubchemFingerprinter.xml',\n",
              " 'Substructure': 'SubstructureFingerprinter.xml',\n",
              " 'SubstructureCount': 'SubstructureFingerprintCount.xml'}"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "id": "vLD-W-YULMqb",
        "outputId": "6e08ea57-f80d-429f-d0a2-fd7ffb60f1bf"
      },
      "source": [
        "fp['AtomPairs2D']"
      ],
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'AtomPairs2DFingerprinter.xml'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 6
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Lzw3bMBwShwd"
      },
      "source": [
        "# **Load HCV dataset**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 305
        },
        "id": "HSaojt-N7wAB",
        "outputId": "cbf91865-a5c2-4540-e05a-03cb1fc00f24"
      },
      "source": [
        "import pandas as pd\n",
        "\n",
        "df = pd.read_csv('https://raw.githubusercontent.com/dataprofessor/data/master/HCV_NS5B_Curated.csv')\n",
        "df.head(2)"
      ],
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>CMPD_CHEMBLID</th>\n",
              "      <th>CANONICAL_SMILES</th>\n",
              "      <th>STANDARD_TYPE</th>\n",
              "      <th>RELATION</th>\n",
              "      <th>STANDARD_VALUE</th>\n",
              "      <th>STANDARD_UNITS</th>\n",
              "      <th>pIC50</th>\n",
              "      <th>PROTEIN_ACCESSION</th>\n",
              "      <th>PREF_NAME</th>\n",
              "      <th>DOC_CHEMBLID</th>\n",
              "      <th>ASSAY_SRC_DESCRIPTION</th>\n",
              "      <th>DESCRIPTION</th>\n",
              "      <th>PUBMED_ID</th>\n",
              "      <th>JOURNAL</th>\n",
              "      <th>YEAR</th>\n",
              "      <th>VOLUME</th>\n",
              "      <th>ISSUE</th>\n",
              "      <th>FIRST_PAGE</th>\n",
              "      <th>MOLWEIGHT</th>\n",
              "      <th>ALOGP</th>\n",
              "      <th>PSA</th>\n",
              "      <th>NUM_RO5_VIOLATIONS</th>\n",
              "      <th>Activity</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>CHEMBL179256</td>\n",
              "      <td>OC(=O)c1ccc2c(c1)nc(c3ccc(O)cc3F)n2C4CCCCC4</td>\n",
              "      <td>IC50</td>\n",
              "      <td>=</td>\n",
              "      <td>1.4</td>\n",
              "      <td>nM</td>\n",
              "      <td>8.853872</td>\n",
              "      <td>Q8JXU8</td>\n",
              "      <td>Hepatitis C virus NS5B RNA-dependent RNA polym...</td>\n",
              "      <td>CHEMBL1142688</td>\n",
              "      <td>Scientific Literature</td>\n",
              "      <td>Inhibitory concentration against RNA dependent...</td>\n",
              "      <td>15743173.0</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2005</td>\n",
              "      <td>48.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>1314.0</td>\n",
              "      <td>354.37</td>\n",
              "      <td>4.93</td>\n",
              "      <td>75.35</td>\n",
              "      <td>0</td>\n",
              "      <td>Active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL204350</td>\n",
              "      <td>CC(C)(C)CCN1[C@H](C(=C(C1=O)C2=NS(=O)(=O)c3ccc...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>=</td>\n",
              "      <td>1.7</td>\n",
              "      <td>nM</td>\n",
              "      <td>8.769551</td>\n",
              "      <td>Q8JXU8</td>\n",
              "      <td>Hepatitis C virus NS5B RNA-dependent RNA polym...</td>\n",
              "      <td>CHEMBL1146957</td>\n",
              "      <td>Scientific Literature</td>\n",
              "      <td>Inhibition of HCV NS5B RNA dependent RNA polym...</td>\n",
              "      <td>16455253.0</td>\n",
              "      <td>Bioorg. Med. Chem. Lett.</td>\n",
              "      <td>2006</td>\n",
              "      <td>16.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>2205.0</td>\n",
              "      <td>419.54</td>\n",
              "      <td>2.37</td>\n",
              "      <td>107.45</td>\n",
              "      <td>0</td>\n",
              "      <td>Active</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "  CMPD_CHEMBLID  ... Activity\n",
              "0  CHEMBL179256  ...   Active\n",
              "1  CHEMBL204350  ...   Active\n",
              "\n",
              "[2 rows x 23 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 7
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 305
        },
        "id": "pK-egpYgLq4X",
        "outputId": "ab9d7235-f8ed-4b90-d075-a5dad928fa44"
      },
      "source": [
        "df.tail(2)"
      ],
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>CMPD_CHEMBLID</th>\n",
              "      <th>CANONICAL_SMILES</th>\n",
              "      <th>STANDARD_TYPE</th>\n",
              "      <th>RELATION</th>\n",
              "      <th>STANDARD_VALUE</th>\n",
              "      <th>STANDARD_UNITS</th>\n",
              "      <th>pIC50</th>\n",
              "      <th>PROTEIN_ACCESSION</th>\n",
              "      <th>PREF_NAME</th>\n",
              "      <th>DOC_CHEMBLID</th>\n",
              "      <th>ASSAY_SRC_DESCRIPTION</th>\n",
              "      <th>DESCRIPTION</th>\n",
              "      <th>PUBMED_ID</th>\n",
              "      <th>JOURNAL</th>\n",
              "      <th>YEAR</th>\n",
              "      <th>VOLUME</th>\n",
              "      <th>ISSUE</th>\n",
              "      <th>FIRST_PAGE</th>\n",
              "      <th>MOLWEIGHT</th>\n",
              "      <th>ALOGP</th>\n",
              "      <th>PSA</th>\n",
              "      <th>NUM_RO5_VIOLATIONS</th>\n",
              "      <th>Activity</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>576</th>\n",
              "      <td>CHEMBL175454</td>\n",
              "      <td>OC(=O)c1ccc2c(c1)nc(c3ccccn3)n2c4ccccc4</td>\n",
              "      <td>IC50</td>\n",
              "      <td>=</td>\n",
              "      <td>360000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>3.443697</td>\n",
              "      <td>Q8JXU8</td>\n",
              "      <td>Hepatitis C virus NS5B RNA-dependent RNA polym...</td>\n",
              "      <td>CHEMBL1149223</td>\n",
              "      <td>Scientific Literature</td>\n",
              "      <td>Inhibitory activity against NS5B polymerase of...</td>\n",
              "      <td>14684311.0</td>\n",
              "      <td>Bioorg. Med. Chem. Lett.</td>\n",
              "      <td>2004</td>\n",
              "      <td>14.0</td>\n",
              "      <td>1.0</td>\n",
              "      <td>119.0</td>\n",
              "      <td>315.33</td>\n",
              "      <td>3.96</td>\n",
              "      <td>68.01</td>\n",
              "      <td>0</td>\n",
              "      <td>Inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>577</th>\n",
              "      <td>CHEMBL369640</td>\n",
              "      <td>CC(C)n1c(nc2cc(ccc12)C(=O)O)c3ccccn3</td>\n",
              "      <td>IC50</td>\n",
              "      <td>=</td>\n",
              "      <td>408000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>3.389340</td>\n",
              "      <td>Q8JXU8</td>\n",
              "      <td>Hepatitis C virus NS5B RNA-dependent RNA polym...</td>\n",
              "      <td>CHEMBL1149223</td>\n",
              "      <td>Scientific Literature</td>\n",
              "      <td>Inhibitory activity against NS5B polymerase of...</td>\n",
              "      <td>14684311.0</td>\n",
              "      <td>Bioorg. Med. Chem. Lett.</td>\n",
              "      <td>2004</td>\n",
              "      <td>14.0</td>\n",
              "      <td>1.0</td>\n",
              "      <td>119.0</td>\n",
              "      <td>281.31</td>\n",
              "      <td>3.11</td>\n",
              "      <td>68.01</td>\n",
              "      <td>0</td>\n",
              "      <td>Inactive</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "    CMPD_CHEMBLID  ...  Activity\n",
              "576  CHEMBL175454  ...  Inactive\n",
              "577  CHEMBL369640  ...  Inactive\n",
              "\n",
              "[2 rows x 23 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 8
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "xqrnC9hQSrf_"
      },
      "source": [
        "# **Prepare data subset as input to PaDEL**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 423
        },
        "id": "ix1B4fUfBCCH",
        "outputId": "f8e6636c-a84f-4018-a03e-21198a729023"
      },
      "source": [
        "df2 = pd.concat( [df['CANONICAL_SMILES'],df['CMPD_CHEMBLID']], axis=1 )\n",
        "df2.to_csv('molecule.smi', sep='\\t', index=False, header=False)\n",
        "df2"
      ],
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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              "    .dataframe thead th {\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>CANONICAL_SMILES</th>\n",
              "      <th>CMPD_CHEMBLID</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>OC(=O)c1ccc2c(c1)nc(c3ccc(O)cc3F)n2C4CCCCC4</td>\n",
              "      <td>CHEMBL179256</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CC(C)(C)CCN1[C@H](C(=C(C1=O)C2=NS(=O)(=O)c3ccc...</td>\n",
              "      <td>CHEMBL204350</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>OC(=O)c1ccc2c(c1)nc(c3ccc(O)cc3)n2C4CCCCC4</td>\n",
              "      <td>CHEMBL179257</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>OC(=O)c1ccc2c(C3CCCCC3)c([nH]c2c1)c4ccc(O)cc4</td>\n",
              "      <td>CHEMBL178784</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CN(C)C(=O)Cn1c(c2ccc(OCc3ccccc3)cc2)c(C4CCCCC4...</td>\n",
              "      <td>CHEMBL369319</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>573</th>\n",
              "      <td>CCC(CC)n1c(nc2cc(ccc12)C(=O)O)c3ccccn3</td>\n",
              "      <td>CHEMBL175762</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>574</th>\n",
              "      <td>Cc1sc(cc1\\C(=C\\C(=O)C(=O)O)\\O)c2ccccc2</td>\n",
              "      <td>CHEMBL197882</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>575</th>\n",
              "      <td>OC(=O)c1ccc2c(c1)ncn2C3CCCCC3</td>\n",
              "      <td>CHEMBL177122</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>576</th>\n",
              "      <td>OC(=O)c1ccc2c(c1)nc(c3ccccn3)n2c4ccccc4</td>\n",
              "      <td>CHEMBL175454</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>577</th>\n",
              "      <td>CC(C)n1c(nc2cc(ccc12)C(=O)O)c3ccccn3</td>\n",
              "      <td>CHEMBL369640</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>578 rows × 2 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                                      CANONICAL_SMILES CMPD_CHEMBLID\n",
              "0          OC(=O)c1ccc2c(c1)nc(c3ccc(O)cc3F)n2C4CCCCC4  CHEMBL179256\n",
              "1    CC(C)(C)CCN1[C@H](C(=C(C1=O)C2=NS(=O)(=O)c3ccc...  CHEMBL204350\n",
              "2           OC(=O)c1ccc2c(c1)nc(c3ccc(O)cc3)n2C4CCCCC4  CHEMBL179257\n",
              "3        OC(=O)c1ccc2c(C3CCCCC3)c([nH]c2c1)c4ccc(O)cc4  CHEMBL178784\n",
              "4    CN(C)C(=O)Cn1c(c2ccc(OCc3ccccc3)cc2)c(C4CCCCC4...  CHEMBL369319\n",
              "..                                                 ...           ...\n",
              "573             CCC(CC)n1c(nc2cc(ccc12)C(=O)O)c3ccccn3  CHEMBL175762\n",
              "574             Cc1sc(cc1\\C(=C\\C(=O)C(=O)O)\\O)c2ccccc2  CHEMBL197882\n",
              "575                      OC(=O)c1ccc2c(c1)ncn2C3CCCCC3  CHEMBL177122\n",
              "576            OC(=O)c1ccc2c(c1)nc(c3ccccn3)n2c4ccccc4  CHEMBL175454\n",
              "577               CC(C)n1c(nc2cc(ccc12)C(=O)O)c3ccccn3  CHEMBL369640\n",
              "\n",
              "[578 rows x 2 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 10
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "VeBPQ_TVTMe0"
      },
      "source": [
        "# **Calculate descriptors**\n",
        "\n",
        "There are 12 fingerprint types in PaDEL. To calculate all 12, make sure to make adjustments to the ***descriptortypes*** input argument to any of the ones in the ***fp*** dictionary variable as shown above, e.g. *SubstructureFingerprintCount.xml*"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "cIV6_RB3cE7J",
        "outputId": "ca1a8b7e-b81f-4688-a6e6-811ce5589e44"
      },
      "source": [
        "fp"
      ],
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'AtomPairs2D': 'AtomPairs2DFingerprinter.xml',\n",
              " 'AtomPairs2DCount': 'AtomPairs2DFingerprintCount.xml',\n",
              " 'CDK': 'Fingerprinter.xml',\n",
              " 'CDKextended': 'ExtendedFingerprinter.xml',\n",
              " 'CDKgraphonly': 'GraphOnlyFingerprinter.xml',\n",
              " 'EState': 'EStateFingerprinter.xml',\n",
              " 'KlekotaRoth': 'KlekotaRothFingerprinter.xml',\n",
              " 'KlekotaRothCount': 'KlekotaRothFingerprintCount.xml',\n",
              " 'MACCS': 'MACCSFingerprinter.xml',\n",
              " 'PubChem': 'PubchemFingerprinter.xml',\n",
              " 'Substructure': 'SubstructureFingerprinter.xml',\n",
              " 'SubstructureCount': 'SubstructureFingerprintCount.xml'}"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 11
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "id": "bYYYcHevcHBA",
        "outputId": "75f781bd-f1a4-4e6d-c3e4-928c293a8834"
      },
      "source": [
        "fp['PubChem']"
      ],
      "execution_count": 12,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'PubchemFingerprinter.xml'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 12
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "g926DY4M4PdF"
      },
      "source": [
        "from padelpy import padeldescriptor\n",
        "\n",
        "fingerprint = 'Substructure'\n",
        "\n",
        "fingerprint_output_file = ''.join([fingerprint,'.csv']) #Substructure.csv\n",
        "fingerprint_descriptortypes = fp[fingerprint]\n",
        "\n",
        "padeldescriptor(mol_dir='molecule.smi', \n",
        "                d_file=fingerprint_output_file, #'Substructure.csv'\n",
        "                #descriptortypes='SubstructureFingerprint.xml', \n",
        "                descriptortypes= fingerprint_descriptortypes,\n",
        "                detectaromaticity=True,\n",
        "                standardizenitro=True,\n",
        "                standardizetautomers=True,\n",
        "                threads=2,\n",
        "                removesalt=True,\n",
        "                log=True,\n",
        "                fingerprints=True)"
      ],
      "execution_count": 13,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "jEn8ayPAVM8f"
      },
      "source": [
        "# **Display calculated fingerprints**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 443
        },
        "id": "kI5L4yRP4tke",
        "outputId": "746b6fa1-df0f-40ac-fae8-2b3cef0c8a53"
      },
      "source": [
        "descriptors = pd.read_csv(fingerprint_output_file)\n",
        "descriptors"
      ],
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
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              "    .dataframe tbody tr th:only-of-type {\n",
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              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Name</th>\n",
              "      <th>SubFP1</th>\n",
              "      <th>SubFP2</th>\n",
              "      <th>SubFP3</th>\n",
              "      <th>SubFP4</th>\n",
              "      <th>SubFP5</th>\n",
              "      <th>SubFP6</th>\n",
              "      <th>SubFP7</th>\n",
              "      <th>SubFP8</th>\n",
              "      <th>SubFP9</th>\n",
              "      <th>SubFP10</th>\n",
              "      <th>SubFP11</th>\n",
              "      <th>SubFP12</th>\n",
              "      <th>SubFP13</th>\n",
              "      <th>SubFP14</th>\n",
              "      <th>SubFP15</th>\n",
              "      <th>SubFP16</th>\n",
              "      <th>SubFP17</th>\n",
              "      <th>SubFP18</th>\n",
              "      <th>SubFP19</th>\n",
              "      <th>SubFP20</th>\n",
              "      <th>SubFP21</th>\n",
              "      <th>SubFP22</th>\n",
              "      <th>SubFP23</th>\n",
              "      <th>SubFP24</th>\n",
              "      <th>SubFP25</th>\n",
              "      <th>SubFP26</th>\n",
              "      <th>SubFP27</th>\n",
              "      <th>SubFP28</th>\n",
              "      <th>SubFP29</th>\n",
              "      <th>SubFP30</th>\n",
              "      <th>SubFP31</th>\n",
              "      <th>SubFP32</th>\n",
              "      <th>SubFP33</th>\n",
              "      <th>SubFP34</th>\n",
              "      <th>SubFP35</th>\n",
              "      <th>SubFP36</th>\n",
              "      <th>SubFP37</th>\n",
              "      <th>SubFP38</th>\n",
              "      <th>SubFP39</th>\n",
              "      <th>...</th>\n",
              "      <th>SubFP268</th>\n",
              "      <th>SubFP269</th>\n",
              "      <th>SubFP270</th>\n",
              "      <th>SubFP271</th>\n",
              "      <th>SubFP272</th>\n",
              "      <th>SubFP273</th>\n",
              "      <th>SubFP274</th>\n",
              "      <th>SubFP275</th>\n",
              "      <th>SubFP276</th>\n",
              "      <th>SubFP277</th>\n",
              "      <th>SubFP278</th>\n",
              "      <th>SubFP279</th>\n",
              "      <th>SubFP280</th>\n",
              "      <th>SubFP281</th>\n",
              "      <th>SubFP282</th>\n",
              "      <th>SubFP283</th>\n",
              "      <th>SubFP284</th>\n",
              "      <th>SubFP285</th>\n",
              "      <th>SubFP286</th>\n",
              "      <th>SubFP287</th>\n",
              "      <th>SubFP288</th>\n",
              "      <th>SubFP289</th>\n",
              "      <th>SubFP290</th>\n",
              "      <th>SubFP291</th>\n",
              "      <th>SubFP292</th>\n",
              "      <th>SubFP293</th>\n",
              "      <th>SubFP294</th>\n",
              "      <th>SubFP295</th>\n",
              "      <th>SubFP296</th>\n",
              "      <th>SubFP297</th>\n",
              "      <th>SubFP298</th>\n",
              "      <th>SubFP299</th>\n",
              "      <th>SubFP300</th>\n",
              "      <th>SubFP301</th>\n",
              "      <th>SubFP302</th>\n",
              "      <th>SubFP303</th>\n",
              "      <th>SubFP304</th>\n",
              "      <th>SubFP305</th>\n",
              "      <th>SubFP306</th>\n",
              "      <th>SubFP307</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>CHEMBL204350</td>\n",
              "      <td>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
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              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL179256</td>\n",
              "      <td>0</td>\n",
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              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>CHEMBL179257</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>1</td>\n",
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              "      <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>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>CHEMBL178784</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>1</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",
              "      <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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CHEMBL369319</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>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>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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</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>573</th>\n",
              "      <td>CHEMBL178067</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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>574</th>\n",
              "      <td>CHEMBL197882</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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>575</th>\n",
              "      <td>CHEMBL177122</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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>576</th>\n",
              "      <td>CHEMBL175454</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>577</th>\n",
              "      <td>CHEMBL369640</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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>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>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>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>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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>578 rows × 308 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "             Name  SubFP1  SubFP2  ...  SubFP305  SubFP306  SubFP307\n",
              "0    CHEMBL204350       1       1  ...         0         0         1\n",
              "1    CHEMBL179256       0       1  ...         0         0         1\n",
              "2    CHEMBL179257       0       1  ...         0         0         1\n",
              "3    CHEMBL178784       0       1  ...         0         0         1\n",
              "4    CHEMBL369319       0       1  ...         0         0         1\n",
              "..            ...     ...     ...  ...       ...       ...       ...\n",
              "573  CHEMBL178067       1       1  ...         0         0         1\n",
              "574  CHEMBL197882       1       1  ...         0         0         1\n",
              "575  CHEMBL177122       0       1  ...         0         0         1\n",
              "576  CHEMBL175454       0       0  ...         0         0         1\n",
              "577  CHEMBL369640       1       0  ...         0         0         1\n",
              "\n",
              "[578 rows x 308 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 14
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iNWwQ-ZHnp-v"
      },
      "source": [
        "# **Build a Random Forest Model**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "g2bEH5KIDrxB"
      },
      "source": [
        "X = descriptors.drop('Name', axis=1)\n",
        "y = df['Activity']"
      ],
      "execution_count": 15,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "28idzdgUnxDp"
      },
      "source": [
        "### **Remove low variance features**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 443
        },
        "id": "hdJ4O3jqi9St",
        "outputId": "4db6342d-e079-4acd-b54f-7d1a8b7d9ac6"
      },
      "source": [
        "from sklearn.feature_selection import VarianceThreshold\n",
        "\n",
        "def remove_low_variance(input_data, threshold=0.1):\n",
        "    selection = VarianceThreshold(threshold)\n",
        "    selection.fit(input_data)\n",
        "    return input_data[input_data.columns[selection.get_support(indices=True)]]\n",
        "\n",
        "X = remove_low_variance(X, threshold=0.1)\n",
        "X"
      ],
      "execution_count": 16,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>SubFP1</th>\n",
              "      <th>SubFP2</th>\n",
              "      <th>SubFP3</th>\n",
              "      <th>SubFP18</th>\n",
              "      <th>SubFP49</th>\n",
              "      <th>SubFP84</th>\n",
              "      <th>SubFP101</th>\n",
              "      <th>SubFP109</th>\n",
              "      <th>SubFP135</th>\n",
              "      <th>SubFP137</th>\n",
              "      <th>SubFP171</th>\n",
              "      <th>SubFP172</th>\n",
              "      <th>SubFP180</th>\n",
              "      <th>SubFP181</th>\n",
              "      <th>SubFP183</th>\n",
              "      <th>SubFP184</th>\n",
              "      <th>SubFP214</th>\n",
              "      <th>SubFP275</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>1</td>\n",
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              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
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              "      <td>1</td>\n",
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              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
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              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\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>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>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\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>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</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",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>573</th>\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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>574</th>\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>1</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>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>575</th>\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>0</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>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>576</th>\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>1</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>577</th>\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>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</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>1</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>578 rows × 18 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     SubFP1  SubFP2  SubFP3  SubFP18  ...  SubFP183  SubFP184  SubFP214  SubFP275\n",
              "0         1       1       0        0  ...         0         0         1         1\n",
              "1         0       1       0        0  ...         0         1         0         1\n",
              "2         0       1       0        0  ...         0         1         0         1\n",
              "3         0       1       1        0  ...         0         1         0         1\n",
              "4         0       1       1        1  ...         0         1         0         1\n",
              "..      ...     ...     ...      ...  ...       ...       ...       ...       ...\n",
              "573       1       1       0        0  ...         0         1         0         1\n",
              "574       1       1       0        0  ...         1         1         0         1\n",
              "575       0       1       0        0  ...         0         1         0         1\n",
              "576       0       0       0        0  ...         0         1         0         1\n",
              "577       1       0       0        0  ...         0         1         0         1\n",
              "\n",
              "[578 rows x 18 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 16
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "4ExPVzFDq8S5"
      },
      "source": [
        "### **Data splitting**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "39J79FaCqHVg"
      },
      "source": [
        "from sklearn.model_selection import train_test_split\n",
        "\n",
        "X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)"
      ],
      "execution_count": 19,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "a26XeU6sO8hp",
        "outputId": "0781e69a-314c-4f26-c52a-2a2dfa64e79d"
      },
      "source": [
        "X_train.shape, X_test.shape"
      ],
      "execution_count": 20,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "((462, 18), (116, 18))"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 20
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "MvZaDWBrq-ek"
      },
      "source": [
        "### **Model building**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "f3O_duyXn2U5",
        "outputId": "0430ead2-253d-4160-a088-b92a2c84adcb"
      },
      "source": [
        "from sklearn.ensemble import RandomForestClassifier\n",
        "from sklearn.metrics import matthews_corrcoef\n",
        "\n",
        "model = RandomForestClassifier(n_estimators=500, random_state=42)\n",
        "model.fit(X_train, y_train)"
      ],
      "execution_count": 21,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "RandomForestClassifier(bootstrap=True, ccp_alpha=0.0, class_weight=None,\n",
              "                       criterion='gini', max_depth=None, max_features='auto',\n",
              "                       max_leaf_nodes=None, max_samples=None,\n",
              "                       min_impurity_decrease=0.0, min_impurity_split=None,\n",
              "                       min_samples_leaf=1, min_samples_split=2,\n",
              "                       min_weight_fraction_leaf=0.0, n_estimators=500,\n",
              "                       n_jobs=None, oob_score=False, random_state=42, verbose=0,\n",
              "                       warm_start=False)"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 21
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "JDON4_R0rBJX"
      },
      "source": [
        "### **Apply model to make prediction**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "uBhxt1eKoCMR"
      },
      "source": [
        "y_train_pred = model.predict(X_train)\n",
        "y_test_pred = model.predict(X_test)"
      ],
      "execution_count": 22,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "BfbbWsfjrHcc"
      },
      "source": [
        "### **Calculate model performance metrics**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "wanGN7sJp1rq",
        "outputId": "21223e1a-b2bc-403d-a1cb-e8cfe3e9df71"
      },
      "source": [
        "mcc_train = matthews_corrcoef(y_train, y_train_pred)\n",
        "mcc_train"
      ],
      "execution_count": 23,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "0.8328828266116973"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 23
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "sLRUcvBkp6CY",
        "outputId": "aed230b6-ec66-4b04-dbef-0de8301404c3"
      },
      "source": [
        "mcc_test = matthews_corrcoef(y_test, y_test_pred)\n",
        "mcc_test"
      ],
      "execution_count": 24,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "0.5219385334290642"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 24
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "XQO9Ch9_r381"
      },
      "source": [
        "### **Cross-validation**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "glASiECVrNla",
        "outputId": "e29b2ba5-2320-4a87-8cc3-16df9d30a5ee"
      },
      "source": [
        "from sklearn.model_selection import cross_val_score\n",
        "\n",
        "rf = RandomForestClassifier(n_estimators=500, random_state=42)\n",
        "cv_scores = cross_val_score(rf, X_train, y_train, cv=5)\n",
        "cv_scores"
      ],
      "execution_count": 25,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "array([0.86021505, 0.86021505, 0.88043478, 0.83695652, 0.79347826])"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 25
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "LLB-A-1QsZwb",
        "outputId": "213f40ac-e18e-4578-d290-392473f74e51"
      },
      "source": [
        "mcc_cv = cv_scores.mean()\n",
        "mcc_cv"
      ],
      "execution_count": 26,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "0.8462599345488545"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 26
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 81
        },
        "id": "-zYBGR7Bsf0E",
        "outputId": "61de0c71-b37c-48a1-9d46-0f31c489d227"
      },
      "source": [
        "model_name = pd.Series(['Random forest'], name='Name')\n",
        "mcc_train_series = pd.Series(mcc_train, name='MCC_train')\n",
        "mcc_cv_series = pd.Series(mcc_cv, name='MCC_cv')\n",
        "mcc_test_series = pd.Series(mcc_test, name='MCC_test')\n",
        "\n",
        "performance_metrics = pd.concat([model_name, mcc_train_series, mcc_cv_series, mcc_test_series], axis=1)\n",
        "performance_metrics"
      ],
      "execution_count": 27,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Name</th>\n",
              "      <th>MCC_train</th>\n",
              "      <th>MCC_cv</th>\n",
              "      <th>MCC_test</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>Random forest</td>\n",
              "      <td>0.832883</td>\n",
              "      <td>0.84626</td>\n",
              "      <td>0.521939</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "            Name  MCC_train   MCC_cv  MCC_test\n",
              "0  Random forest   0.832883  0.84626  0.521939"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 27
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "nyXWoG6dswDp"
      },
      "source": [
        ""
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}