Curado_de_base_de_datos.ipynb

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        "id": "view-in-github",
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      "source": [
        "<a href=\"https://colab.research.google.com/github/DIFACQUIM/Cursos/blob/main/Curado_de_base_de_datos.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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    },
    {
      "cell_type": "markdown",
      "source": [
        "Python script based on the implementation of paper: Sánchez-Cruz N, Pilón-Jiménez BA and Medina-Franco JL. Functional group and diversity analysis of BIOFACQUIM: A Mexican natural product database. F1000Research 2020, 8(Chem Inf Sci):2071 DOI:[10.12688/f1000research.21540](https://doi.org/10.12688/f1000research.21540.2).                                                                        [GitHub](https://github.com/DIFACQUIM/IFG_General/blob/master/Compounds_Curation.py)  "
      ],
      "metadata": {
        "id": "XnghYpDCHvRw"
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      "execution_count": null,
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        "outputId": "fa0e2b45-3d9a-4cd0-cc82-0dddf47c35cb"
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      "outputs": [
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          "name": "stdout",
          "text": [
            "Requirement already satisfied: rdkit in /usr/local/lib/python3.10/dist-packages (2023.3.3)\n",
            "Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from rdkit) (1.23.5)\n",
            "Requirement already satisfied: Pillow in /usr/local/lib/python3.10/dist-packages (from rdkit) (9.4.0)\n"
          ]
        }
      ],
      "source": [
        "!pip install rdkit"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install molvs"
      ],
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        "id": "l1mXaVq7tiDP",
        "outputId": "df3367c7-68e7-456c-96a2-b9e2f2d7e5df"
      },
      "execution_count": null,
      "outputs": [
        {
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          "name": "stdout",
          "text": [
            "Requirement already satisfied: molvs in /usr/local/lib/python3.10/dist-packages (0.1.1)\n",
            "Requirement already satisfied: six in /usr/local/lib/python3.10/dist-packages (from molvs) (1.16.0)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd\n",
        "from rdkit import Chem\n",
        "from rdkit.Chem import PandasTools\n",
        "from rdkit.Chem import rdMolDescriptors\n",
        "from molvs.standardize import Standardizer\n",
        "from molvs.charge import Uncharger, Reionizer\n",
        "from molvs.fragment import LargestFragmentChooser\n",
        "from molvs.tautomer import TautomerCanonicalizer\n",
        "from rdkit.Chem.rdmolops import GetFormalCharge, RemoveStereochemistry"
      ],
      "metadata": {
        "id": "aXRa_W3wuEI1"
      },
      "execution_count": null,
      "outputs": []
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    {
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          "height": 129
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        "outputId": "b39517a4-eb0e-41a1-ae9d-5f8639bc014b"
      },
      "source": [
        "#DNMT1\n",
        "url_dnmt1 = \"https://raw.githubusercontent.com/DIFACQUIM/Cursos/main/Datasets/DNMT1.csv\"\n",
        "DNMT1 = pd.read_csv(url_dnmt1)\n",
        "DNMT1.head(2)  # Muestra las dos primeras filas de información, para corroborar que cargó la información correctamente"
      ],
      "execution_count": null,
      "outputs": [
        {
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              "  \"Molecule ChEMBL ID Molecule Name  Molecule Max Phase  Molecular Weight  \\\n",
              "0      \"CHEMBL2336409           NaN                   0            461.53   \n",
              "1      \"CHEMBL1916683           NaN                   0            261.28   \n",
              "\n",
              "   #RO5 Violations  AlogP                                             Smiles  \\\n",
              "0                1   5.65  Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...   \n",
              "1                0   1.45            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1   \n",
              "\n",
              "  Standard Type Standard Relation  Standard Value Standard Units  \\\n",
              "0          IC50               '='         11220.0             nM   \n",
              "1          IC50               '='        310000.0             nM   \n",
              "\n",
              "   pChEMBL Value  \n",
              "0           4.95  \n",
              "1            NaN  "
            ],
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              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
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          },
          "metadata": {},
          "execution_count": 50
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "set(list(DNMT1[\"Molecule Name\"]))"
      ],
      "metadata": {
        "id": "txOXhZCKhjSy",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "ee3f3c17-dfb1-4679-fa35-98e3639e3685"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "{'AZACITIDINE',\n",
              " 'BENZANTHRONE',\n",
              " 'CEPHALOTHIN',\n",
              " 'DAPHNORIN',\n",
              " 'DECITABINE',\n",
              " 'Dichlon',\n",
              " 'EPIGALOCATECHIN GALLATE',\n",
              " 'GENISTEIN',\n",
              " 'PROCAINAMIDE',\n",
              " 'PSAMMAPLIN A',\n",
              " 'S-ADENOSYLHOMOCYSTEINE',\n",
              " 'VORINOSTAT',\n",
              " nan}"
            ]
          },
          "metadata": {},
          "execution_count": 51
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "print(DNMT1.columns)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "o9gup9Psg6jp",
        "outputId": "9a10f6aa-9a00-4480-9f01-c4b1500a646a"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Index(['\"Molecule ChEMBL ID', 'Molecule Name', 'Molecule Max Phase',\n",
            "       'Molecular Weight', '#RO5 Violations', 'AlogP', 'Smiles',\n",
            "       'Standard Type', 'Standard Relation', 'Standard Value',\n",
            "       'Standard Units', 'pChEMBL Value'],\n",
            "      dtype='object')\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#Select SMILES_chiral column\n",
        "DNMT1 = DNMT1[['\"Molecule ChEMBL ID',\"Smiles\",'Standard Type', 'Standard Relation', 'Standard Value',\n",
        "       'Standard Units', 'pChEMBL Value']]\n",
        "DNMT1"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
        },
        "id": "qngJ-bUCUADp",
        "outputId": "bf9068c0-ea87-4724-dd96-d61c25df0bce"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    \"Molecule ChEMBL ID                                             Smiles  \\\n",
              "0        \"CHEMBL2336409  Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...   \n",
              "1        \"CHEMBL1916683            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1   \n",
              "2        \"CHEMBL3109075  O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...   \n",
              "3        \"CHEMBL3109080     O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O   \n",
              "4        \"CHEMBL3126645  Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...   \n",
              "..                  ...                                                ...   \n",
              "466      \"CHEMBL4866673  COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...   \n",
              "467      \"CHEMBL4871621  COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...   \n",
              "468      \"CHEMBL4878570  O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...   \n",
              "469      \"CHEMBL4454542  COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...   \n",
              "470      \"CHEMBL1231795  COc1cc2c(NC3CCN(C(C)C)CC3)nc(C3CCCCC3)nc2cc1OC...   \n",
              "\n",
              "    Standard Type Standard Relation  Standard Value Standard Units  \\\n",
              "0            IC50               '='         11220.0             nM   \n",
              "1            IC50               '='        310000.0             nM   \n",
              "2            IC50               '='        128000.0             nM   \n",
              "3            IC50               '='        230000.0             nM   \n",
              "4            IC50               '='        265000.0             nM   \n",
              "..            ...               ...             ...            ...   \n",
              "466          IC50               '='          2570.0             nM   \n",
              "467          IC50               '>'            10.0             nM   \n",
              "468          IC50               '='          2020.0             nM   \n",
              "469          IC50               '='          3100.0             nM   \n",
              "470          IC50               '='        107000.0             nM   \n",
              "\n",
              "     pChEMBL Value  \n",
              "0             4.95  \n",
              "1              NaN  \n",
              "2              NaN  \n",
              "3              NaN  \n",
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              "..             ...  \n",
              "466           5.59  \n",
              "467            NaN  \n",
              "468           5.70  \n",
              "469           5.51  \n",
              "470            NaN  \n",
              "\n",
              "[471 rows x 7 columns]"
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              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>\"Molecule ChEMBL ID</th>\n",
              "      <th>Smiles</th>\n",
              "      <th>Standard Type</th>\n",
              "      <th>Standard Relation</th>\n",
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              "      <th>Standard Units</th>\n",
              "      <th>pChEMBL Value</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>\"CHEMBL2336409</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>11220.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>4.95</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>\"CHEMBL1916683</td>\n",
              "      <td>CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>310000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>\"CHEMBL3109075</td>\n",
              "      <td>O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>128000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>\"CHEMBL3109080</td>\n",
              "      <td>O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>230000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>\"CHEMBL3126645</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>265000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</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",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>466</th>\n",
              "      <td>\"CHEMBL4866673</td>\n",
              "      <td>COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2570.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.59</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>467</th>\n",
              "      <td>\"CHEMBL4871621</td>\n",
              "      <td>COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'&gt;'</td>\n",
              "      <td>10.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>468</th>\n",
              "      <td>\"CHEMBL4878570</td>\n",
              "      <td>O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2020.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>469</th>\n",
              "      <td>\"CHEMBL4454542</td>\n",
              "      <td>COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>3100.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.51</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>470</th>\n",
              "      <td>\"CHEMBL1231795</td>\n",
              "      <td>COc1cc2c(NC3CCN(C(C)C)CC3)nc(C3CCCCC3)nc2cc1OC...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>107000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>471 rows × 7 columns</p>\n",
              "</div>\n",
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              "      spin 1s steps(1) infinite;\n",
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              "\n",
              "  @keyframes spin {\n",
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              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
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              "      border-bottom-color: var(--fill-color);\n",
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              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
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              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-e11461ce-29b3-46f0-9d06-b505e0e853f1 button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
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              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ]
          },
          "metadata": {},
          "execution_count": 53
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "DNMT1.columns = ['Molecule ChEMBL ID',\"Smiles\",'Standard Type', 'Standard Relation', 'Standard Value',\n",
        "       'Standard Units', 'pChEMBL Value']"
      ],
      "metadata": {
        "id": "YyCnzNAgjDEN"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "DNMT1"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
        },
        "id": "bMRwT40LjMPo",
        "outputId": "9a296ba4-cb96-4e9b-a114-7b7a67be4901"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    Molecule ChEMBL ID                                             Smiles  \\\n",
              "0       \"CHEMBL2336409  Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...   \n",
              "1       \"CHEMBL1916683            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1   \n",
              "2       \"CHEMBL3109075  O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...   \n",
              "3       \"CHEMBL3109080     O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O   \n",
              "4       \"CHEMBL3126645  Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...   \n",
              "..                 ...                                                ...   \n",
              "466     \"CHEMBL4866673  COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...   \n",
              "467     \"CHEMBL4871621  COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...   \n",
              "468     \"CHEMBL4878570  O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...   \n",
              "469     \"CHEMBL4454542  COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...   \n",
              "470     \"CHEMBL1231795  COc1cc2c(NC3CCN(C(C)C)CC3)nc(C3CCCCC3)nc2cc1OC...   \n",
              "\n",
              "    Standard Type Standard Relation  Standard Value Standard Units  \\\n",
              "0            IC50               '='         11220.0             nM   \n",
              "1            IC50               '='        310000.0             nM   \n",
              "2            IC50               '='        128000.0             nM   \n",
              "3            IC50               '='        230000.0             nM   \n",
              "4            IC50               '='        265000.0             nM   \n",
              "..            ...               ...             ...            ...   \n",
              "466          IC50               '='          2570.0             nM   \n",
              "467          IC50               '>'            10.0             nM   \n",
              "468          IC50               '='          2020.0             nM   \n",
              "469          IC50               '='          3100.0             nM   \n",
              "470          IC50               '='        107000.0             nM   \n",
              "\n",
              "     pChEMBL Value  \n",
              "0             4.95  \n",
              "1              NaN  \n",
              "2              NaN  \n",
              "3              NaN  \n",
              "4              NaN  \n",
              "..             ...  \n",
              "466           5.59  \n",
              "467            NaN  \n",
              "468           5.70  \n",
              "469           5.51  \n",
              "470            NaN  \n",
              "\n",
              "[471 rows x 7 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-a5525eee-200d-4c0f-a863-9e8236bada57\" class=\"colab-df-container\">\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Molecule ChEMBL ID</th>\n",
              "      <th>Smiles</th>\n",
              "      <th>Standard Type</th>\n",
              "      <th>Standard Relation</th>\n",
              "      <th>Standard Value</th>\n",
              "      <th>Standard Units</th>\n",
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              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>\"CHEMBL2336409</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>11220.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>4.95</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>\"CHEMBL1916683</td>\n",
              "      <td>CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>310000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>\"CHEMBL3109075</td>\n",
              "      <td>O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>128000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>\"CHEMBL3109080</td>\n",
              "      <td>O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>230000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>\"CHEMBL3126645</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>265000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</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",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>466</th>\n",
              "      <td>\"CHEMBL4866673</td>\n",
              "      <td>COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2570.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.59</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>467</th>\n",
              "      <td>\"CHEMBL4871621</td>\n",
              "      <td>COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'&gt;'</td>\n",
              "      <td>10.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>468</th>\n",
              "      <td>\"CHEMBL4878570</td>\n",
              "      <td>O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2020.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>469</th>\n",
              "      <td>\"CHEMBL4454542</td>\n",
              "      <td>COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>3100.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.51</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>470</th>\n",
              "      <td>\"CHEMBL1231795</td>\n",
              "      <td>COc1cc2c(NC3CCN(C(C)C)CC3)nc(C3CCCCC3)nc2cc1OC...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>107000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>471 rows × 7 columns</p>\n",
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              "\n",
              "  .colab-df-quickchart:hover {\n",
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              "  .colab-df-quickchart-complete:disabled,\n",
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              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
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              "\n",
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              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-771c1822-e123-447f-84f5-c7a7a5305104 button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ]
          },
          "metadata": {},
          "execution_count": 55
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#Select five compounds\n",
        "#DNMT1 = DNMT1.iloc[:5,:]\n",
        "DNMT1.shape"
      ],
      "metadata": {
        "id": "ft6ic3dV7DT7",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "6f249aaa-a306-421f-8783-fd5c21a7bb07"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "(471, 7)"
            ]
          },
          "metadata": {},
          "execution_count": 56
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Define functions\n",
        "STD = Standardizer() # Get the standardized version of a given SMILES string (canonical SMILES).\n",
        "LFC = LargestFragmentChooser() # Select the largest fragment from a salt (ionic compound).\n",
        "UC = Uncharger() # Charge corrections are applied to ensure, for example, that free metals are correctly ionized.\n",
        "RI = Reionizer() # Neutralize molecule by adding/removing hydrogens.\n",
        "TC = TautomerCanonicalizer()  # Return a tautormer “reasonable” from a chemist’s point, but isn’t guaranteed to be the most energetically favourable."
      ],
      "metadata": {
        "id": "YrWYYlezyVpV"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "def pretreatment(smi):\n",
        "    try:\n",
        "        mol = Chem.MolFromSmiles(smi)\n",
        "        if mol == None:\n",
        "            #If rdkit could not parse the smiles, returns Error 1\n",
        "            return \"Error 1\"\n",
        "        else:\n",
        "            mol = STD(mol)\n",
        "            mol = LFC(mol)\n",
        "\n",
        "            allowed_elements = {\"H\",\"B\",\"C\",\"N\",\"O\",\"F\",\"Si\",\"P\",\"S\",\"Cl\",\"Se\",\"Br\",\"I\"}\n",
        "            actual_elements = set([atom.GetSymbol() for atom in mol.GetAtoms()])\n",
        "            if len(actual_elements-allowed_elements) == 0:\n",
        "                mol = UC(mol)\n",
        "                mol = RI(mol)\n",
        "                RemoveStereochemistry(mol)\n",
        "                mol = TC(mol)\n",
        "                return Chem.MolToSmiles(mol)\n",
        "            else:\n",
        "                # If molecule contains other than the allowed elements, return \"Error 2\"\n",
        "                return \"Error 2\"\n",
        "    except:\n",
        "        return \"Something else was found\""
      ],
      "metadata": {
        "id": "iBdEbe6NxY7y"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "DNMT1[\"NEW_SMILES\"] = [pretreatment(x) for x in DNMT1[\"Smiles\"]]\n",
        "DNMT1"
      ],
      "metadata": {
        "id": "tcqSbRYY6VNK",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 493
        },
        "outputId": "fe3d27c6-d195-4828-fc4c-6997b9dd0754"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "WARNING:molvs.tautomer:Tautomer enumeration stopped at maximum 1000\n",
            "WARNING:molvs.tautomer:Tautomer enumeration stopped at maximum 1000\n",
            "WARNING:molvs.tautomer:Tautomer enumeration stopped at maximum 1000\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    Molecule ChEMBL ID                                             Smiles  \\\n",
              "0       \"CHEMBL2336409  Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...   \n",
              "1       \"CHEMBL1916683            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1   \n",
              "2       \"CHEMBL3109075  O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...   \n",
              "3       \"CHEMBL3109080     O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O   \n",
              "4       \"CHEMBL3126645  Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...   \n",
              "..                 ...                                                ...   \n",
              "466     \"CHEMBL4866673  COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...   \n",
              "467     \"CHEMBL4871621  COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...   \n",
              "468     \"CHEMBL4878570  O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...   \n",
              "469     \"CHEMBL4454542  COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...   \n",
              "470     \"CHEMBL1231795  COc1cc2c(NC3CCN(C(C)C)CC3)nc(C3CCCCC3)nc2cc1OC...   \n",
              "\n",
              "    Standard Type Standard Relation  Standard Value Standard Units  \\\n",
              "0            IC50               '='         11220.0             nM   \n",
              "1            IC50               '='        310000.0             nM   \n",
              "2            IC50               '='        128000.0             nM   \n",
              "3            IC50               '='        230000.0             nM   \n",
              "4            IC50               '='        265000.0             nM   \n",
              "..            ...               ...             ...            ...   \n",
              "466          IC50               '='          2570.0             nM   \n",
              "467          IC50               '>'            10.0             nM   \n",
              "468          IC50               '='          2020.0             nM   \n",
              "469          IC50               '='          3100.0             nM   \n",
              "470          IC50               '='        107000.0             nM   \n",
              "\n",
              "     pChEMBL Value                                         NEW_SMILES  \n",
              "0             4.95  Cc1cc(=Nc2ccc(NC(=O)c3ccc(N=c4cc[nH]c5ccccc45)...  \n",
              "1              NaN            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1  \n",
              "2              NaN  O=C(O)C1C(Cc2c[nH]c3ccccc23)CCN1C(=O)c1ccc2ccc...  \n",
              "3              NaN         O=C(O)C(Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O  \n",
              "4              NaN  Cc1cc(=Nc2ccc(NC(=O)c3cccc(N=c4cc[nH]c5ccccc45...  \n",
              "..             ...                                                ...  \n",
              "466           5.59  COc1cc2c(=NCc3ccc(-c4ccc(C(O)=NO)cc4)cc3)cc(-c...  \n",
              "467            NaN  COc1cc2[nH]c(-c3ccc(C)s3)cc(=NCC3CCN(c4ncc(C(O...  \n",
              "468           5.70  ON=C(O)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...  \n",
              "469           5.51  COc1cc2c(cc1OCCCN1CCCC1)=NC(C1CCCCC1)C=NC=2NC1...  \n",
              "470            NaN  COc1cc2c(=NC3CCN(C(C)C)CC3)[nH]c(C3CCCCC3)nc2c...  \n",
              "\n",
              "[471 rows x 8 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-2086bdb8-5c33-471a-894d-397d25d86bd3\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Molecule ChEMBL ID</th>\n",
              "      <th>Smiles</th>\n",
              "      <th>Standard Type</th>\n",
              "      <th>Standard Relation</th>\n",
              "      <th>Standard Value</th>\n",
              "      <th>Standard Units</th>\n",
              "      <th>pChEMBL Value</th>\n",
              "      <th>NEW_SMILES</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>\"CHEMBL2336409</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>11220.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>4.95</td>\n",
              "      <td>Cc1cc(=Nc2ccc(NC(=O)c3ccc(N=c4cc[nH]c5ccccc45)...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>\"CHEMBL1916683</td>\n",
              "      <td>CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>310000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>\"CHEMBL3109075</td>\n",
              "      <td>O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>128000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>O=C(O)C1C(Cc2c[nH]c3ccccc23)CCN1C(=O)c1ccc2ccc...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>\"CHEMBL3109080</td>\n",
              "      <td>O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>230000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>O=C(O)C(Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>\"CHEMBL3126645</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>265000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>Cc1cc(=Nc2ccc(NC(=O)c3cccc(N=c4cc[nH]c5ccccc45...</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",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>466</th>\n",
              "      <td>\"CHEMBL4866673</td>\n",
              "      <td>COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2570.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.59</td>\n",
              "      <td>COc1cc2c(=NCc3ccc(-c4ccc(C(O)=NO)cc4)cc3)cc(-c...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>467</th>\n",
              "      <td>\"CHEMBL4871621</td>\n",
              "      <td>COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'&gt;'</td>\n",
              "      <td>10.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>COc1cc2[nH]c(-c3ccc(C)s3)cc(=NCC3CCN(c4ncc(C(O...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>468</th>\n",
              "      <td>\"CHEMBL4878570</td>\n",
              "      <td>O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2020.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.70</td>\n",
              "      <td>ON=C(O)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>469</th>\n",
              "      <td>\"CHEMBL4454542</td>\n",
              "      <td>COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>3100.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.51</td>\n",
              "      <td>COc1cc2c(cc1OCCCN1CCCC1)=NC(C1CCCCC1)C=NC=2NC1...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>470</th>\n",
              "      <td>\"CHEMBL1231795</td>\n",
              "      <td>COc1cc2c(NC3CCN(C(C)C)CC3)nc(C3CCCCC3)nc2cc1OC...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>107000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>COc1cc2c(=NC3CCN(C(C)C)CC3)[nH]c(C3CCCCC3)nc2c...</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>471 rows × 8 columns</p>\n",
              "</div>\n",
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              "        element.innerHTML = '';\n",
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              "  </button>\n",
              "\n",
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              "  .colab-df-quickchart {\n",
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              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
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              "\n",
              "  .colab-df-quickchart {\n",
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              "    width: 32px;\n",
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              "\n",
              "  .colab-df-quickchart:hover {\n",
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              "  .colab-df-quickchart-complete:disabled,\n",
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              "\n",
              "  .colab-df-spinner {\n",
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              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
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              "    20% {\n",
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              "      border-right-color: var(--fill-color);\n",
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              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-cde5ea44-ec2e-4298-8051-4549c991369e button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ]
          },
          "metadata": {},
          "execution_count": 59
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Delate smiles that rdkit could not read\n",
        "DNMT1 = DNMT1[DNMT1[\"NEW_SMILES\"] != \"Error 1\"]\n",
        "# Delate smiles that no contain allowed atoms\n",
        "DNMT1 = DNMT1[DNMT1[\"NEW_SMILES\"] != \"Error 2\"]\n",
        "# Delate other errors\n",
        "DNMT1 = DNMT1[DNMT1[\"NEW_SMILES\"] != \"Something else was found\"].reset_index(drop=True)"
      ],
      "metadata": {
        "id": "pjHv3Em7xdfE"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# Delete duplicates\n",
        "DNMT1 = DNMT1.drop_duplicates(subset=[\"NEW_SMILES\"], keep=\"first\").reset_index(drop=True)\n",
        "DNMT1"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 441
        },
        "id": "WQHbHHDrHkhp",
        "outputId": "c02bb744-ba0f-4884-b4cd-b94e81087ac7"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    Molecule ChEMBL ID                                             Smiles  \\\n",
              "0       \"CHEMBL2336409  Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...   \n",
              "1       \"CHEMBL1916683            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1   \n",
              "2       \"CHEMBL3109075  O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...   \n",
              "3       \"CHEMBL3109080     O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O   \n",
              "4       \"CHEMBL3126645  Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...   \n",
              "..                 ...                                                ...   \n",
              "413     \"CHEMBL4850570  COc1cc2nc(-c3cc(C)oc3C)cc(NCC3CCN(c4ncc(C(=O)N...   \n",
              "414     \"CHEMBL4866673  COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...   \n",
              "415     \"CHEMBL4871621  COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...   \n",
              "416     \"CHEMBL4878570  O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...   \n",
              "417     \"CHEMBL4454542  COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...   \n",
              "\n",
              "    Standard Type Standard Relation  Standard Value Standard Units  \\\n",
              "0            IC50               '='         11220.0             nM   \n",
              "1            IC50               '='        310000.0             nM   \n",
              "2            IC50               '='        128000.0             nM   \n",
              "3            IC50               '='        230000.0             nM   \n",
              "4            IC50               '='        265000.0             nM   \n",
              "..            ...               ...             ...            ...   \n",
              "413          IC50               '>'            10.0             nM   \n",
              "414          IC50               '='          2570.0             nM   \n",
              "415          IC50               '>'            10.0             nM   \n",
              "416          IC50               '='          2020.0             nM   \n",
              "417          IC50               '='          3100.0             nM   \n",
              "\n",
              "     pChEMBL Value                                         NEW_SMILES  \n",
              "0             4.95  Cc1cc(=Nc2ccc(NC(=O)c3ccc(N=c4cc[nH]c5ccccc45)...  \n",
              "1              NaN            CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1  \n",
              "2              NaN  O=C(O)C1C(Cc2c[nH]c3ccccc23)CCN1C(=O)c1ccc2ccc...  \n",
              "3              NaN         O=C(O)C(Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O  \n",
              "4              NaN  Cc1cc(=Nc2ccc(NC(=O)c3cccc(N=c4cc[nH]c5ccccc45...  \n",
              "..             ...                                                ...  \n",
              "413            NaN  COc1cc2[nH]c(-c3cc(C)oc3C)cc(=NCC3CCN(c4ncc(C(...  \n",
              "414           5.59  COc1cc2c(=NCc3ccc(-c4ccc(C(O)=NO)cc4)cc3)cc(-c...  \n",
              "415            NaN  COc1cc2[nH]c(-c3ccc(C)s3)cc(=NCC3CCN(c4ncc(C(O...  \n",
              "416           5.70  ON=C(O)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...  \n",
              "417           5.51  COc1cc2c(cc1OCCCN1CCCC1)=NC(C1CCCCC1)C=NC=2NC1...  \n",
              "\n",
              "[418 rows x 8 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-0a18022a-e247-4d28-8129-dd0163266ae1\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Molecule ChEMBL ID</th>\n",
              "      <th>Smiles</th>\n",
              "      <th>Standard Type</th>\n",
              "      <th>Standard Relation</th>\n",
              "      <th>Standard Value</th>\n",
              "      <th>Standard Units</th>\n",
              "      <th>pChEMBL Value</th>\n",
              "      <th>NEW_SMILES</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>\"CHEMBL2336409</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3ccc(Nc4ccnc5ccccc45)cc3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>11220.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>4.95</td>\n",
              "      <td>Cc1cc(=Nc2ccc(NC(=O)c3ccc(N=c4cc[nH]c5ccccc45)...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>\"CHEMBL1916683</td>\n",
              "      <td>CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>310000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>CN1CC2ON=C(Cc3ccc([N+](=O)[O-])cc3)C2C1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>\"CHEMBL3109075</td>\n",
              "      <td>O=C(O)[C@@H]1[C@H](Cc2c[nH]c3ccccc23)CCN1C(=O)...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>128000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>O=C(O)C1C(Cc2c[nH]c3ccccc23)CCN1C(=O)c1ccc2ccc...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>\"CHEMBL3109080</td>\n",
              "      <td>O=C(O)[C@H](Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>230000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>O=C(O)C(Cc1csc2ccccc12)N1C(=O)c2ccccc2C1=O</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>\"CHEMBL3126645</td>\n",
              "      <td>Cc1cc(Nc2ccc(NC(=O)c3cccc(Nc4ccnc5ccccc45)c3)c...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>265000.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>Cc1cc(=Nc2ccc(NC(=O)c3cccc(N=c4cc[nH]c5ccccc45...</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",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>413</th>\n",
              "      <td>\"CHEMBL4850570</td>\n",
              "      <td>COc1cc2nc(-c3cc(C)oc3C)cc(NCC3CCN(c4ncc(C(=O)N...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'&gt;'</td>\n",
              "      <td>10.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>COc1cc2[nH]c(-c3cc(C)oc3C)cc(=NCC3CCN(c4ncc(C(...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>414</th>\n",
              "      <td>\"CHEMBL4866673</td>\n",
              "      <td>COc1cc2c(NCc3ccc(-c4ccc(C(=O)NO)cc4)cc3)cc(-c3...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2570.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.59</td>\n",
              "      <td>COc1cc2c(=NCc3ccc(-c4ccc(C(O)=NO)cc4)cc3)cc(-c...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>415</th>\n",
              "      <td>\"CHEMBL4871621</td>\n",
              "      <td>COc1cc2nc(-c3ccc(C)s3)cc(NCC3CCN(c4ncc(C(=O)NO...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'&gt;'</td>\n",
              "      <td>10.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>NaN</td>\n",
              "      <td>COc1cc2[nH]c(-c3ccc(C)s3)cc(=NCC3CCN(c4ncc(C(O...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>416</th>\n",
              "      <td>\"CHEMBL4878570</td>\n",
              "      <td>O=C(NO)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>2020.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.70</td>\n",
              "      <td>ON=C(O)C1CCN(CC(O)COC(Cn2c3ccccc3c3ccccc32)Cn2...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>417</th>\n",
              "      <td>\"CHEMBL4454542</td>\n",
              "      <td>COc1cc2c(cc1OCCCN1CCCC1)N=C(C1CCCCC1)CN=C2NC1C...</td>\n",
              "      <td>IC50</td>\n",
              "      <td>'='</td>\n",
              "      <td>3100.0</td>\n",
              "      <td>nM</td>\n",
              "      <td>5.51</td>\n",
              "      <td>COc1cc2c(cc1OCCCN1CCCC1)=NC(C1CCCCC1)C=NC=2NC1...</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>418 rows × 8 columns</p>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
              "\n",
              "  <div class=\"colab-df-container\">\n",
              "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-0a18022a-e247-4d28-8129-dd0163266ae1')\"\n",
              "            title=\"Convert this dataframe to an interactive table.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
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              "  </svg>\n",
              "    </button>\n",
              "\n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    .colab-df-buttons div {\n",
              "      margin-bottom: 4px;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "    <script>\n",
              "      const buttonEl =\n",
              "        document.querySelector('#df-0a18022a-e247-4d28-8129-dd0163266ae1 button.colab-df-convert');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      async function convertToInteractive(key) {\n",
              "        const element = document.querySelector('#df-0a18022a-e247-4d28-8129-dd0163266ae1');\n",
              "        const dataTable =\n",
              "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "          + ' to learn more about interactive tables.';\n",
              "        element.innerHTML = '';\n",
              "        dataTable['output_type'] = 'display_data';\n",
              "        await google.colab.output.renderOutput(dataTable, element);\n",
              "        const docLink = document.createElement('div');\n",
              "        docLink.innerHTML = docLinkHtml;\n",
              "        element.appendChild(docLink);\n",
              "      }\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "\n",
              "<div id=\"df-6490649a-4e39-4156-bec1-25a60bc41eb7\">\n",
              "  <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-6490649a-4e39-4156-bec1-25a60bc41eb7')\"\n",
              "            title=\"Suggest charts.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "     width=\"24px\">\n",
              "    <g>\n",
              "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
              "    </g>\n",
              "</svg>\n",
              "  </button>\n",
              "\n",
              "<style>\n",
              "  .colab-df-quickchart {\n",
              "      --bg-color: #E8F0FE;\n",
              "      --fill-color: #1967D2;\n",
              "      --hover-bg-color: #E2EBFA;\n",
              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
              "      --disabled-bg-color: #DDD;\n",
              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
              "      --hover-fill-color: #FFFFFF;\n",
              "      --disabled-bg-color: #3B4455;\n",
              "      --disabled-fill-color: #666;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart {\n",
              "    background-color: var(--bg-color);\n",
              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
              "    fill: var(--fill-color);\n",
              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "    fill: var(--button-hover-fill-color);\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
              "    }\n",
              "    20% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    30% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-6490649a-4e39-4156-bec1-25a60bc41eb7 button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ]
          },
          "metadata": {},
          "execution_count": 61
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Delete rows with NaN (Not a Number) and None values from pandas DataFrame.\n",
        "DNMT1 = DNMT1.dropna()"
      ],
      "metadata": {
        "id": "6nKdv3ghM-_s"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "DNMT1.to_csv(\"DNMT1_curada.csv\", sep=\",\", index=False)"
      ],
      "metadata": {
        "id": "CNz_t0gZ6gA1"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}