notebooks/regression-transformer-demo.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "id": "302355e8",
      "metadata": {
        "id": "302355e8"
      },
      "source": [
        "<img align=\"right\" src=\"https://raw.githubusercontent.com/GT4SD/gt4sd-core/main/docs/_static/gt4sd_logo.png\" alt=\"logo\" width=\"100\" height=\"100\"/>\n",
        "\n",
        "##  Demo: Regression Transformer in the Generative Toolkit for Scientific Discovery\n"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "**The code below**\n",
        "1. installs the gt4sd library\n",
        "2. configures logging to disable log messages\n",
        "3. imports modules and classes for regression-based conditional generation of molecules and proteins\n",
        "4. imports RDKit and Selfies for cheminformatics and molecular data processing"
      ],
      "metadata": {
        "id": "b-lx6yuHyWFv"
      },
      "id": "b-lx6yuHyWFv"
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "cb8d7e46",
      "metadata": {
        "id": "cb8d7e46",
        "outputId": "d74076d8-c141-4d94-8df5-f05a5517fc94"
      },
      "outputs": [
        {
          "name": "stderr",
          "output_type": "stream",
          "text": [
            "Using TensorFlow backend.\n"
          ]
        }
      ],
      "source": [
        "import logging, sys\n",
        "logging.disable(sys.maxsize)\n",
        "\n",
        "\n",
        "from gt4sd.algorithms.conditional_generation.regression_transformer import (\n",
        "    RegressionTransformer, RegressionTransformerMolecules, RegressionTransformerProteins\n",
        ")\n",
        "import mols2grid\n",
        "from rdkit import Chem\n",
        "from selfies import encoder\n",
        "import pandas as pd"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "67314a02",
      "metadata": {
        "id": "67314a02"
      },
      "source": [
        "# Let us have a look at Buturon, a common herbicide"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "731cf426",
      "metadata": {
        "id": "731cf426",
        "outputId": "79a59ef7-9943-41a6-9c31-4997a41e2bf6"
      },
      "outputs": [
        {
          "data": {
            "image/png": 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\n",
            "text/plain": [
              "<rdkit.Chem.rdchem.Mol at 0x7f96b36dd530>"
            ]
          },
          "execution_count": 2,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "smi = \"CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1\"\n",
        "true_esol = -3.9\n",
        "Chem.MolFromSmiles(smi)"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "8738635c",
      "metadata": {
        "id": "8738635c"
      },
      "source": [
        "## Buturon has a water solubility score of -3.90\n",
        "## We can predict its ESOL (estimated solubility) value with the RegressionTransformer"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "**The code below:**\n",
        "1. configures a regression transformer model for molecules using the \"solubility\" algorithm version and a \"greedy\" search strategy\n",
        "2. defines a target string, which includes a masked ESOL value and the encoded SMILES representation of a chemical compound *smi*\n",
        "3. initializes the regression transformer model with the provided configuration and target\n",
        "4. generates a predicted ESOL value for the given SMILES representation using the sample(1) method and extracts the predicted value from the generated string."
      ],
      "metadata": {
        "id": "aO7kxLTuyZfU"
      },
      "id": "aO7kxLTuyZfU"
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "0ae41998",
      "metadata": {
        "id": "0ae41998",
        "outputId": "bff3f377-6b71-490b-9657-745f16f5ef38"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "For Buturuon, the predicted ESOL is -5.2467\n"
          ]
        }
      ],
      "source": [
        "config = RegressionTransformerMolecules(algorithm_version=\"solubility\", search=\"greedy\")\n",
        "target = f\"<esol>[MASK][MASK][MASK][MASK][MASK]|{encoder(smi)}\"\n",
        "esol_predictor = RegressionTransformer(configuration=config, target=target)\n",
        "score_str = list(esol_predictor.sample(1))[0]\n",
        "print(f\"For Buturuon, the predicted ESOL is {score_str.split('>')[-1]}\")"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "1319596d",
      "metadata": {
        "id": "1319596d"
      },
      "outputs": [],
      "source": []
    },
    {
      "cell_type": "markdown",
      "id": "e7fb878d",
      "metadata": {
        "id": "e7fb878d"
      },
      "source": [
        "#### Ok, we can see that the prediction was decently close but not perfect\n",
        "#### Now let us try to improve Buturuon to a molecule with higher solubility\n",
        "#### Note, that we will use the same model to do so!\n"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "5484a56f",
      "metadata": {
        "id": "5484a56f"
      },
      "source": [
        "#### We simply set the hyperparameters for the search"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "**The code below:**\n",
        "1. uses a \"sample\" search strategy, which is recommended for generative tasks. 2. the model is set to have a temperature of 2, which controls the level of randomness in generation\n",
        "3. the tolerance is set to 5%, meaning that the model can deviate by up to 5% from the target property value\n",
        "4. specifies that 20% of the tokens in the generated sequences will be masked"
      ],
      "metadata": {
        "id": "EN4Rgb6PycCF"
      },
      "id": "EN4Rgb6PycCF"
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "921eff13",
      "metadata": {
        "id": "921eff13",
        "outputId": "0e731e71-37f7-4cd7-ad92-0b68de4db484"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "[('CC(C)=CN(C)C(=O)NC1=CC=C(Cl)C=C1', '<esol>-2.6173'),\n",
              " ('CC(C#CN(C)C(=O)NC1)=CC=C(Cl)C=C1', '<esol>-2.5757'),\n",
              " ('CC(C#C)N(C)C(=O)NC=CCl', '<esol>-2.5757'),\n",
              " ('CCC#CN(C)C(=O)NC1=CC=C(Cl)C=C1', '<esol>-4.0012'),\n",
              " ('CCSCC#CN(C)C(=O)NC1=CC=C(Cl)C=C1', '<esol>-4.0012'),\n",
              " ('CC(C#C)N(C)C(=O)OC1=CC=C(Cl)C=C1', '<esol>-2.6173'),\n",
              " ('CC(C#C)N(C)C(=O)[NH]C1=CC=C(Cl)C=C1', '<esol>-2.6173'),\n",
              " ('CC(C#C)(CC)C(=O)NC1=CC=C(Cl)C=C1', '<esol>-4.0012')]"
            ]
          },
          "execution_count": 4,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "target_esol = -3.53\n",
        "config = RegressionTransformerMolecules(\n",
        "    algorithm_version=\"solubility\",\n",
        "    search=\"sample\", # the alternative is 'greedy' but 'sample' is recommended for generative tasks\n",
        "    temperature=2,\n",
        "    tolerance=5, # percentage of tolerated deviation from the desired property value (here -3.53)\n",
        "    sampling_wrapper={\n",
        "        'property_goal': {'<esol>': target_esol},\n",
        "        'fraction_to_mask': 0.2\n",
        "    }\n",
        ")\n",
        "esol_generator = RegressionTransformer(\n",
        "    configuration=config, target=smi\n",
        ")\n",
        "generations = list(esol_generator.sample(8))\n",
        "generations"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "**The code below:**\n",
        "1. extracts the SMILES representations (chemical notations) from the generated sequences (generations) and stores them in the smiles list\n",
        "2. extracts the ESOL values from the generated sequences and converts them to floating-point numbers, storing them in the esols list\n",
        "3. prints a header indicating that it's displaying molecules with higher solubility scores\n",
        "4. creates a DataFrame (result) to organize the information"
      ],
      "metadata": {
        "id": "MI5GhQzQyeLE"
      },
      "id": "MI5GhQzQyeLE"
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "719e5ae1",
      "metadata": {
        "id": "719e5ae1",
        "outputId": "1ab41768-27c4-46d2-bf92-27c76495da9e"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "\u001b[1m\t\t\tButuruon-inspired molecules with a higher solubility score \n"
          ]
        },
        {
          "data": {
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              "    &lt;script&gt;\n",
              "    // list.js\n",
              "var listObj = new List(&#x27;mols2grid&#x27;, {\n",
              "    valueNames: [{data: [&#x27;mols2grid-id&#x27;]}, &#x27;data-img&#x27;, &#x27;data-mols2grid-id&#x27;, &#x27;data-ESOL&#x27;, &#x27;data-SMILES&#x27;, &#x27;data-Name&#x27;, &#x27;data-mols2grid-id-copy&#x27;, {attr: &#x27;data-content&#x27;, name: &#x27;mols2grid-tooltip&#x27;}],\n",
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              "    page: 9,\n",
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              "        item: &#x27;&lt;li class=&quot;page-item&quot;&gt;&lt;a class=&quot;page page-link&quot; href=&quot;#&quot; onclick=&quot;event.preventDefault()&quot;&gt;&lt;/a&gt;&lt;/li&gt;&#x27;,\n",
              "        innerWindow: 1,\n",
              "        outerWindow: 1,\n",
              "    },\n",
              "});\n",
              "listObj.remove(&quot;mols2grid-id&quot;, &quot;0&quot;);\n",
              "listObj.add([{&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 0, &quot;data-ESOL&quot;: -3.9, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Buturon&quot;, &quot;data-mols2grid-id-copy&quot;: 0, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Buturon&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -3.9&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 1, &quot;data-ESOL&quot;: -2.617, &quot;data-SMILES&quot;: &quot;CC(C)=CN(C)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 1, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C)=CN(C)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.617&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 2, &quot;data-ESOL&quot;: -2.576, &quot;data-SMILES&quot;: &quot;CC(C#CN(C)C(=O)NC1)=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 2, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#CN(C)C(=O)NC1)=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.576&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 3, &quot;data-ESOL&quot;: -2.576, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)NC=CCl&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 3, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)NC=CCl&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.576&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 4, &quot;data-ESOL&quot;: -4.001, &quot;data-SMILES&quot;: &quot;CCC#CN(C)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 4, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CCC#CN(C)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -4.001&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 5, &quot;data-ESOL&quot;: -4.001, &quot;data-SMILES&quot;: &quot;CCSCC#CN(C)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 5, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CCSCC#CN(C)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -4.001&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 6, &quot;data-ESOL&quot;: -2.617, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)OC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 6, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)OC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.617&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 7, &quot;data-ESOL&quot;: -2.617, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)[NH]C1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 7, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)[NH]C1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.617&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 8, &quot;data-ESOL&quot;: -4.001, &quot;data-SMILES&quot;: &quot;CC(C#C)(CC)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 8, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)(CC)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -4.001&quot;}]);\n",
              "// filter\n",
              "if (window.parent.mols2grid_lists === undefined) {\n",
              "    window.parent.mols2grid_lists = {};\n",
              "}\n",
              "window.parent.mols2grid_lists[&quot;Results&quot;] = listObj;\n",
              "\n",
              "\n",
              "// selection\n",
              "class MolStorage extends Map {\n",
              "    multi_set(_id, _smiles) {\n",
              "        for (let i=0; i &lt; _id.length; i++) {\n",
              "            this.set(_id[i], _smiles[i]);\n",
              "        }\n",
              "    }\n",
              "    multi_del(_id) {\n",
              "        for (let i=0; i &lt; _id.length; i++) {\n",
              "            this.delete(_id[i]);\n",
              "        };\n",
              "    }\n",
              "    to_dict() {\n",
              "        var content = &quot;{&quot;;\n",
              "        for (let [key, value] of this) {\n",
              "            content += key + &quot;:&quot; + JSON.stringify(value) + &quot;,&quot;;\n",
              "        }\n",
              "        content = content.length &gt; 1 ? content.slice(0, -1) : content;\n",
              "        content += &quot;}&quot;;\n",
              "        return content\n",
              "    }\n",
              "    download_smi(fileName) {\n",
              "        var content = &quot;SMILES index\\n&quot;;\n",
              "        for (let [key, value] of this) {\n",
              "            content += value + &quot; &quot; + key + &quot;\\n&quot;;\n",
              "        }\n",
              "        var a = document.createElement(&quot;a&quot;);\n",
              "        var file = new Blob([content], {type: &quot;text/plain&quot;});\n",
              "        a.href = URL.createObjectURL(file);\n",
              "        a.download = fileName;\n",
              "        a.click();\n",
              "        a.remove();\n",
              "    }\n",
              "}\n",
              "var SELECTION = new MolStorage();\n",
              "\n",
              "\n",
              "\n",
              "// kernel\n",
              "var kernel_env = null;\n",
              "if (window.parent.IPython !== undefined) {\n",
              "    // Jupyter notebook\n",
              "    kernel_env = &quot;jupyter&quot;;\n",
              "    var kernel = window.parent.IPython.notebook.kernel;\n",
              "    kernel.execute(&#x27;from mols2grid.select import register as _m2g_reg&#x27;)\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "        kernel.execute(&quot;_m2g_reg.add_selection(&#x27;&quot;+grid_id+&quot;&#x27;, &quot;+JSON.stringify(_id)+&quot;,&quot;+JSON.stringify(smiles)+&quot;)&quot;);\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "        kernel.execute(&quot;_m2g_reg.del_selection(&#x27;&quot;+grid_id+&quot;&#x27;, &quot;+JSON.stringify(_id)+&quot;)&quot;);\n",
              "    }\n",
              "} else if (window.parent.google !== undefined) {\n",
              "    // Google colab\n",
              "    kernel_env = &quot;colab&quot;;\n",
              "    var kernel = window.parent.google.colab.kernel;\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "        (async function() {\n",
              "        const result = await kernel.invokeFunction(&#x27;_m2g_reg.add_selection&#x27;,\n",
              "                                                   [grid_id, _id, smiles], {});\n",
              "        })();\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "        (async function() {\n",
              "        const result = await kernel.invokeFunction(&#x27;_m2g_reg.del_selection&#x27;,\n",
              "                                                   [grid_id, _id], {});\n",
              "        })();\n",
              "    }\n",
              "} else {\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "    }\n",
              "}\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// sort\n",
              "var sort_field = &quot;mols2grid-id&quot;;\n",
              "var sort_order = &quot;asc&quot;;\n",
              "function mols2gridSortFunction(itemA, itemB, options) {\n",
              "    var x = itemA.values()[options.valueName];\n",
              "    var y = itemB.values()[options.valueName];\n",
              "    if (typeof x === &quot;number&quot;) {\n",
              "        if (isFinite(x - y)) {\n",
              "            return x - y; \n",
              "        } else {\n",
              "            return isFinite(x) ? -1 : 1;\n",
              "        }\n",
              "    } else {\n",
              "        x = x.toLowerCase();\n",
              "        y = y.toLowerCase();\n",
              "        return (x &lt; y) ? -1: (x &gt; y) ? 1: 0;\n",
              "    }\n",
              "}\n",
              "function checkboxSort(itemA, itemB, options) {\n",
              "    if (itemA.elm !== undefined) {\n",
              "        var checkedA = itemA.elm.firstChild.checked;\n",
              "        if (itemB.elm !== undefined) {\n",
              "            var checkedB = itemB.elm.firstChild.checked;\n",
              "            if (checkedA &amp;&amp; !checkedB) {\n",
              "                return -1;\n",
              "            } else if (!checkedA &amp;&amp; checkedB) {\n",
              "                return 1;\n",
              "            } else {\n",
              "                return 0;\n",
              "            }\n",
              "        } else {\n",
              "            return -1;\n",
              "        }\n",
              "    } else if (itemB.elm !== undefined) {\n",
              "        return 1;\n",
              "    } else {\n",
              "        return 0;\n",
              "    }\n",
              "}\n",
              "$(&#x27;#mols2grid button.sort-btn&#x27;).click(function(e) {\n",
              "    var _field = $(this).attr(&quot;data-name&quot;);\n",
              "    if (_field == sort_field) {\n",
              "        $(this).removeClass(&quot;arrow-&quot; + sort_order)\n",
              "        sort_order = (sort_order === &quot;desc&quot;) ? &quot;asc&quot; : &quot;desc&quot;;\n",
              "    } else {\n",
              "        $(&#x27;#mols2grid button.sort-btn.active&#x27;).removeClass(&quot;active arrow-&quot; + sort_order);\n",
              "        sort_order = &quot;asc&quot;;\n",
              "        sort_field = _field;\n",
              "        $(this).addClass(&quot;active&quot;);\n",
              "    }\n",
              "    $(this).addClass(&quot;arrow-&quot; + sort_order)\n",
              "    if (sort_field == &quot;checkbox&quot;) {\n",
              "        listObj.sort(&quot;mols2grid-id&quot;, {order: sort_order, sortFunction: checkboxSort});\n",
              "    } else {\n",
              "        listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction});\n",
              "    }\n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// tooltips\n",
              "$.fn.tooltip.Constructor.Default.whiteList.span = [&#x27;style&#x27;]\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    $(function () {\n",
              "        // hide previous popovers\n",
              "        $(&#x27;#mols2grid a.page-link&#x27;).click(function(e) {\n",
              "            $(&#x27;.mols2grid-tooltip[data-toggle=&quot;popover&quot;]&#x27;).popover(&#x27;hide&#x27;)\n",
              "        });\n",
              "        // create new popover\n",
              "        $(&#x27;.mols2grid-tooltip[data-toggle=&quot;popover&quot;]&#x27;).popover({\n",
              "            placement: &#x27;bottom&#x27;,\n",
              "            trigger: &#x27;click hover&#x27;,\n",
              "            html: true,\n",
              "            sanitize: false,\n",
              "        });\n",
              "    })\n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "// selection modifyers and export options\n",
              "// check all\n",
              "$(&#x27;#btn-chkbox-all&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id = [];\n",
              "    var _smiles = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox&quot;).each(function() {\n",
              "            this.checked = true;\n",
              "            _id.push(parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;)));\n",
              "            _smiles.push($($(this).siblings(&quot;.data-SMILES&quot;)[0]).text());\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    add_selection(&quot;Results&quot;, _id, _smiles);\n",
              "});\n",
              "// uncheck all\n",
              "$(&#x27;#btn-chkbox-none&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox:checked&quot;).each(function() {\n",
              "            this.checked = false;\n",
              "            _id.push(parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;)));\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    del_selection(&quot;Results&quot;, _id);\n",
              "});\n",
              "// invert\n",
              "$(&#x27;#btn-chkbox-invert&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id_add = [];\n",
              "    var _id_del = [];\n",
              "    var _smiles = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox&quot;).each(function() {\n",
              "            this.checked = !this.checked;\n",
              "            var _id = parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;));\n",
              "            if (this.checked) {\n",
              "                _id_add.push(_id);\n",
              "                _smiles.push($(this).siblings(&quot;.data-SMILES&quot;).first().text());\n",
              "            } else {\n",
              "                _id_del.push(_id);\n",
              "            }\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    del_selection(&quot;Results&quot;, _id_del);\n",
              "    add_selection(&quot;Results&quot;, _id_add, _smiles);\n",
              "});\n",
              "// copy to clipboard\n",
              "$(&quot;#btn-chkbox-copy&quot;).click(function(e) {\n",
              "    navigator.clipboard.writeText(SELECTION.to_dict());\n",
              "});\n",
              "// export smiles\n",
              "$(&quot;#btn-chkbox-dlsmi&quot;).click(function(e) {\n",
              "    SELECTION.download_smi(&quot;selection.smi&quot;);\n",
              "});\n",
              "// export CSV\n",
              "$(&quot;#btn-chkbox-dlcsv&quot;).click(function(e) {\n",
              "    var sep = &quot;\\t&quot;\n",
              "    // same order as subset + tooltip\n",
              "    var columns = Array.from(listObj.items[0].elm.querySelectorAll(&quot;div.data&quot;))\n",
              "                       .map(elm =&gt; elm.classList[1]);\n",
              "    // remove &#x27;data-&#x27;\n",
              "    var header = columns.map(name =&gt; name.slice(5));\n",
              "    // csv content\n",
              "    header = [&quot;index&quot;].concat(header).join(sep);\n",
              "    var content = header + &quot;\\n&quot;;\n",
              "    for (let [index, smiles] of SELECTION.entries()) {\n",
              "        var data = listObj.items[index].values();\n",
              "        content += index;\n",
              "        columns.forEach((key) =&gt; {\n",
              "            content += sep + data[key];\n",
              "        })\n",
              "        content += &quot;\\n&quot;;\n",
              "    }\n",
              "    var a = document.createElement(&quot;a&quot;);\n",
              "    var file = new Blob([content], {type: &quot;text/csv&quot;});\n",
              "    a.href = URL.createObjectURL(file);\n",
              "    a.download = &quot;selection.csv&quot;;\n",
              "    a.click();\n",
              "    a.remove();\n",
              "});\n",
              "// update selection on checkbox click\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    $(&quot;input:checkbox&quot;).change(function() {\n",
              "        var _id = parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;));\n",
              "        if (this.checked) {\n",
              "            var _smiles = $($(this).siblings(&quot;.data-SMILES&quot;)[0]).text();\n",
              "            add_selection(&quot;Results&quot;, [_id], [_smiles]);\n",
              "        } else {\n",
              "            del_selection(&quot;Results&quot;, [_id]);\n",
              "        }\n",
              "    }); \n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// generate images for the currently displayed molecules\n",
              "var draw_opts = {&quot;fixedBondLength&quot;: 25, &quot;width&quot;: 300, &quot;height&quot;: 150};\n",
              "var json_draw_opts = JSON.stringify(draw_opts);\n",
              "\n",
              "var smarts_matches = {};\n",
              "\n",
              "// Load RDKit\n",
              "window\n",
              ".initRDKitModule()\n",
              ".then(function(RDKit) {\n",
              "    console.log(&#x27;RDKit version: &#x27;, RDKit.version());\n",
              "    window.RDKit = RDKit;\n",
              "    window.RDKitModule = RDKit;\n",
              "\n",
              "    // search bar\n",
              "    function SmartsSearch(query, columns) {\n",
              "    var smiles_col = columns[0];\n",
              "    smarts_matches = {};\n",
              "    var query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "    var qmol = RDKit.get_qmol(query);\n",
              "    if (qmol.is_valid()) {\n",
              "        for (var k = 0, kl = listObj.items.length; k &lt; kl; k++) {\n",
              "            var item = listObj.items[k];\n",
              "            var smiles = item.values()[smiles_col]\n",
              "            var mol = RDKit.get_mol(smiles);\n",
              "            if (mol.is_valid()) {\n",
              "                var results = JSON.parse(mol.get_substruct_match(qmol));\n",
              "                if (results.atoms) {\n",
              "                    item.found = true;\n",
              "                    \n",
              "                    smarts_matches[smiles] = results;\n",
              "                    \n",
              "                } else {\n",
              "                    item.found = false;\n",
              "                }\n",
              "            } else {\n",
              "                item.found = false;\n",
              "            }\n",
              "            mol.delete();\n",
              "        }\n",
              "    }\n",
              "    qmol.delete();\n",
              "}\n",
              "var search_type = &quot;Text&quot;;\n",
              "$(&#x27;#mols2grid .search-btn&#x27;).click(function() {\n",
              "    search_type = $(this).text();\n",
              "    $(&#x27;#mols2grid button.search-btn.active&#x27;).removeClass(&quot;active&quot;);\n",
              "    $(this).addClass(&quot;active&quot;);\n",
              "});\n",
              "$(&#x27;#mols2grid #searchbar&#x27;).on(&quot;keyup&quot;, function(e) {\n",
              "    var query = e.target.value;\n",
              "    if (search_type === &quot;Text&quot;) {\n",
              "        smarts_matches = {};\n",
              "        listObj.search(query, [&#x27;data-SMILES&#x27;, &#x27;data-Name&#x27;, &#x27;data-ESOL&#x27;, &#x27;data-mols2grid-id&#x27;, &#x27;mols2grid-tooltip&#x27;]);\n",
              "    } else {\n",
              "        listObj.search(query, [&quot;data-SMILES&quot;], SmartsSearch);\n",
              "    }\n",
              "});\n",
              "\n",
              "    \n",
              "    // generate images for the currently displayed molecules\n",
              "RDKit.prefer_coordgen(true);\n",
              "function draw_mol(smiles) {\n",
              "    var mol = RDKit.get_mol(smiles, &#x27;{&quot;removeHs&quot;: false }&#x27;);\n",
              "    var svg = &quot;&quot;;\n",
              "    if (mol.is_valid()) {\n",
              "        var highlights = smarts_matches[smiles];\n",
              "        if (highlights) {\n",
              "            var details = Object.assign({}, draw_opts, highlights);\n",
              "            details = JSON.stringify(details);\n",
              "        } else {\n",
              "            var details = json_draw_opts;\n",
              "        }\n",
              "        svg = mol.get_svg_with_highlights(details);\n",
              "    }\n",
              "    mol.delete();\n",
              "    if (svg == &quot;&quot;) {\n",
              "        return &#x27;&lt;svg width=&quot;300&quot; height=&quot;150&quot; xmlns=&quot;http://www.w3.org/2000/svg&quot; version=&quot;1.1&quot; viewBox=&quot;0 0 300 150&quot;&gt;&lt;/svg&gt;&#x27;;\n",
              "    }\n",
              "    return svg;\n",
              "}\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    var query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "    if (query === &quot;&quot;) {\n",
              "        smarts_matches = {};\n",
              "    }\n",
              "    $(&#x27;#mols2grid .cell&#x27;).each(function() {\n",
              "        var $t = $(this);\n",
              "        var smiles = $t.children(&quot;.data-SMILES&quot;).first().text()\n",
              "        var svg = draw_mol(smiles);\n",
              "        $t.children(&quot;.data-img&quot;).html(svg);\n",
              "    });\n",
              "});\n",
              "    \n",
              "\n",
              "    // trigger update to activate tooltips, draw images, setup callbacks...\n",
              "    listObj.update();\n",
              "    // resize iframe to fit content\n",
              "    if (window.frameElement) {\n",
              "        window.parent.fit_height(window.frameElement);\n",
              "    }\n",
              "});\n",
              "    &lt;/script&gt;\n",
              "  &lt;/body&gt;\n",
              "&lt;/html&gt;\">\n",
              "</iframe>"
            ],
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ]
          },
          "execution_count": 5,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "smiles = [g[0] for g in generations]\n",
        "esols = [float(g[1].split('>')[-1]) for g in generations]\n",
        "print(\"\\033[1m\" \"\\t\\t\\tButuruon-inspired molecules with a higher solubility score \")\n",
        "result = pd.DataFrame({\n",
        "    \"SMILES\": [smi] + smiles,\n",
        "    \"Name\": [\"Buturon\"] + len(smiles)*[\"Novel (from RT)\"],\n",
        "    \"ESOL\": [true_esol] + [round(e, 3) for e in esols]\n",
        "})\n",
        "mols2grid.display(\n",
        "    result, tooltip=[\"Name\", \"SMILES\", \"ESOL\"], size=(300,150),\n",
        "    fixedBondLength=25, n_cols=3, width=\"100%\", height=None,\n",
        "    name='Results'\n",
        ")"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "71d23e58",
      "metadata": {
        "id": "71d23e58"
      },
      "source": [
        "### If you want, you can constrain the masking to be on specific atom types only\n",
        "### For example we might want to replace only the Chlorine and Nitrogen atoms"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "0b379843",
      "metadata": {
        "id": "0b379843",
        "outputId": "f08b3811-003c-4541-8312-f6073cf4596e"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "[('CC(C#C)OCCC(=O)NC1=CC=C([NH])C=C1', '<esol>-1.6485'),\n",
              " ('CC(C#C)N(C)C(=O)NC1=CC=C(C)C=C1', '<esol>-2.5757'),\n",
              " ('CC(C#C)C(C)C(=O)NC1=CC=C(N)C=C1', '<esol>-3.0878'),\n",
              " ('CC(C#C)N(C)C(=O)SC1=CC=C(Cl)C=C1', '<esol>-4.0012'),\n",
              " ('CC(C#C)=C(C)C(=O)NC1=CC=C(F)C=C1', '<esol>-2.7141'),\n",
              " ('CC(C#C)(CCC)C=O', '<esol>-3.9735'),\n",
              " ('CC(C#C)C(C)C(=O)NC1=CC=C(C)C=C1', '<esol>-2.5757'),\n",
              " ('CC(C#C)OCCC(=O)OC1=CC=C(F)C=C1', '<esol>-3.0324')]"
            ]
          },
          "execution_count": 6,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "target_esol = -3.53\n",
        "config = RegressionTransformerMolecules(\n",
        "    algorithm_version=\"solubility\",\n",
        "    search=\"sample\", # the alternative is 'greedy' but 'sample' is recommended for generative tasks\n",
        "    temperature=2,\n",
        "    tolerance=5, # percentage of tolerated deviation from the desired property value (here -3.53)\n",
        "    sampling_wrapper={\n",
        "        'property_goal': {'<esol>': target_esol},\n",
        "        'fraction_to_mask': 1.0,\n",
        "        'tokens_to_mask': ['Cl', 'N']\n",
        "    }\n",
        ")\n",
        "esol_generator = RegressionTransformer(\n",
        "    configuration=config, target=smi\n",
        ")\n",
        "generations = list(esol_generator.sample(8))\n",
        "generations"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "4078e3ca",
      "metadata": {
        "id": "4078e3ca",
        "outputId": "a8858a7a-15af-43a9-84b1-4aa082f93597"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "\u001b[1m\t\t\tButuruon-inspired molecules with a higher solubility score \n"
          ]
        },
        {
          "data": {
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              "        obj.style.height = 0;\n",
              "        var height = obj.contentDocument.body.scrollHeight + 18 + 'px';\n",
              "        obj.style.height = height;\n",
              "    }\n",
              "</script>\n",
              "<iframe class=\"mols2grid-iframe\" frameborder=\"0\" width=\"100%\"\n",
              "\n",
              "height=\"200\"\n",
              "\n",
              "\n",
              "allow=\"clipboard-write\"\n",
              "\n",
              "srcdoc=\"&lt;html&gt;\n",
              "  &lt;meta charset=&quot;utf-8&quot;&gt;\n",
              "  &lt;head&gt;\n",
              "    &lt;style&gt;\n",
              "    #mols2grid.gridcontainer {\n",
              "    display: block;\n",
              "    padding-left: 1em;\n",
              "    max-width: 912px;\n",
              "    width: 912px;\n",
              "}\n",
              "#mols2grid .cell {\n",
              "    border: 1px solid #cccccc;\n",
              "    text-align: center;\n",
              "    vertical-align: top;\n",
              "    max-width: 300px;\n",
              "    width: 300px;\n",
              "    font-family: &#x27;DejaVu&#x27;, sans-serif;\n",
              "    font-size: 12pt;\n",
              "    padding: 0;\n",
              "    margin: 0px;\n",
              "    float: left;\n",
              "}\n",
              "#mols2grid .cell:hover {\n",
              "    background-color: #e7e7e7 !important;\n",
              "}\n",
              "#mols2grid .cell .data-img {\n",
              "    padding: 0;\n",
              "    margin: 0;\n",
              "}\n",
              "#mols2grid .cell img, #mols2grid .cell svg {\n",
              "    max-width: 100%;\n",
              "    height: auto;\n",
              "    padding: 0;\n",
              "}\n",
              "#mols2grid .data {\n",
              "    overflow: hidden;\n",
              "    white-space: nowrap;\n",
              "    text-overflow: ellipsis;\n",
              "    display: block;\n",
              "}\n",
              "#mols2grid .arrow-asc:after {\n",
              "    content: &#x27;↑&#x27;;\n",
              "    text-align: right;\n",
              "    float:right;\n",
              "}\n",
              "#mols2grid .arrow-desc:after {\n",
              "    content: &#x27;↓&#x27;;\n",
              "    text-align: right;\n",
              "    float:right;\n",
              "}\n",
              "    /* custom CSS */\n",
              "    \n",
              "    &lt;/style&gt;\n",
              "    &lt;script src=&quot;https://cdnjs.cloudflare.com/ajax/libs/list.js/2.3.1/list.min.js&quot;&gt;&lt;/script&gt;\n",
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              "&lt;script src=&quot;https://code.jquery.com/jquery-3.5.1.slim.min.js&quot; integrity=&quot;sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj&quot; crossorigin=&quot;anonymous&quot;&gt;&lt;/script&gt;\n",
              "&lt;script src=&quot;https://cdn.jsdelivr.net/npm/bootstrap@4.6.0/dist/js/bootstrap.bundle.min.js&quot; integrity=&quot;sha384-Piv4xVNRyMGpqkS2by6br4gNJ7DXjqk09RmUpJ8jgGtD7zP9yug3goQfGII0yAns&quot; crossorigin=&quot;anonymous&quot;&gt;&lt;/script&gt;\n",
              "&lt;script src=&quot;https://unpkg.com/@rdkit/rdkit@2021.9.4/Code/MinimalLib/dist/RDKit_minimal.js&quot;&gt;&lt;/script&gt;\n",
              "    &lt;!-- custom header --&gt;\n",
              "    \n",
              "  &lt;/head&gt;\n",
              "  &lt;body&gt;\n",
              "    &lt;div id=&quot;mols2grid&quot; class=&quot;gridcontainer grid-Results&quot;&gt;\n",
              "      &lt;div class=&quot;row mb-3&quot;&gt;\n",
              "        &lt;div class=&quot;list&quot;&gt;&lt;div class=&quot;cell&quot; data-mols2grid-id=&quot;0&quot;&gt;&lt;input type=&quot;checkbox&quot; class=&quot;position-relative float-left cached_checkbox&quot;&gt;&lt;a tabindex=&quot;0&quot; class=&quot;data data-img mols2grid-tooltip&quot; data-toggle=&quot;popover&quot; data-content=&quot;.&quot;&gt;&lt;/a&gt;&lt;div class=&quot;data data-SMILES&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-Name&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-ESOL&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-mols2grid-id-copy&quot;&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;\n",
              "      &lt;/div&gt;\n",
              "      &lt;div class=&quot;d-inline&quot;&gt;\n",
              "        &lt;ul class=&quot;pagination float-left&quot;&gt;&lt;/ul&gt;\n",
              "        &lt;div id=&quot;controls&quot; class=&quot;d-flex flex-row float-right&quot;&gt;\n",
              "          \n",
              "          &lt;div id=&quot;chkbox-dropdown&quot; class=&quot;dropdown&quot;&gt;\n",
              "    &lt;button class=&quot;btn btn-light dropdown-toggle&quot; type=&quot;button&quot; id=&quot;chkboxDropdown&quot; data-toggle=&quot;dropdown&quot; aria-haspopup=&quot;true&quot; aria-expanded=&quot;false&quot;&gt;☑&lt;/button&gt;\n",
              "    &lt;div class=&quot;dropdown-menu&quot; aria-labelledby=&quot;checkboxDropdownMenu&quot;&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-all&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Check all&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-none&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Uncheck all&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-invert&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Invert&lt;/button&gt;\n",
              "        &lt;div class=&quot;dropdown-divider&quot;&gt;&lt;/div&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-copy&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Copy to clipboard&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-dlsmi&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Save SMILES&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-dlcsv&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Save CSV&lt;/button&gt;\n",
              "    &lt;/div&gt;\n",
              "&lt;/div&gt;\n",
              "          \n",
              "          &lt;div id=&quot;sort-dropdown&quot; class=&quot;dropdown pl-2&quot;&gt;\n",
              "            &lt;button class=&quot;btn btn-light dropdown-toggle&quot; type=&quot;button&quot; id=&quot;sortDropdown&quot; data-toggle=&quot;dropdown&quot; aria-haspopup=&quot;true&quot; aria-expanded=&quot;false&quot;&gt;\n",
              "              Sort by\n",
              "            &lt;/button&gt;\n",
              "            &lt;div class=&quot;dropdown-menu&quot; aria-labelledby=&quot;sortDropdownMenu&quot;&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn arrow-asc active&quot; type=&quot;button&quot; data-name=&quot;mols2grid-id&quot;&gt;Index&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn &quot; type=&quot;button&quot; data-name=&quot;data-SMILES&quot;&gt;SMILES&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn &quot; type=&quot;button&quot; data-name=&quot;data-Name&quot;&gt;Name&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn &quot; type=&quot;button&quot; data-name=&quot;data-ESOL&quot;&gt;ESOL&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn arrow-asc active&quot; type=&quot;button&quot; data-name=&quot;data-mols2grid-id&quot;&gt;mols2grid-id&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn&quot; type=&quot;button&quot; data-name=&quot;checkbox&quot;&gt;Selected&lt;/button&gt;\n",
              "              \n",
              "            &lt;/div&gt;\n",
              "          &lt;/div&gt;\n",
              "          &lt;div class=&quot;input-group row pl-4&quot;&gt;\n",
              "            &lt;input type=&quot;text&quot; id=&quot;searchbar&quot; class=&quot;form-control&quot; placeholder=&quot;Search&quot; aria-label=&quot;Search&quot; aria-describedby=&quot;basic-addon1&quot;&gt;\n",
              "            &lt;div class=&quot;input-group-append&quot;&gt;\n",
              "              &lt;button id=&quot;searchBtn&quot; class=&quot;btn btn-light dropdown-toggle&quot; type=&quot;button&quot; data-toggle=&quot;dropdown&quot; aria-haspopup=&quot;true&quot; aria-expanded=&quot;false&quot;&gt;🔎&lt;/button&gt;\n",
              "              &lt;div class=&quot;dropdown-menu dropdown-menu-right&quot;&gt;\n",
              "                &lt;button id=&quot;txtSearch&quot; class=&quot;search-btn dropdown-item active&quot;&gt;Text&lt;/button&gt;\n",
              "                &lt;button id=&quot;smartsSearch&quot; class=&quot;search-btn dropdown-item&quot;&gt;SMARTS&lt;/button&gt;\n",
              "              &lt;/div&gt;\n",
              "            &lt;/div&gt;\n",
              "          &lt;/div&gt;\n",
              "        &lt;/div&gt;\n",
              "      &lt;/div&gt;\n",
              "    &lt;/div&gt;\n",
              "    &lt;script&gt;\n",
              "    // list.js\n",
              "var listObj = new List(&#x27;mols2grid&#x27;, {\n",
              "    valueNames: [{data: [&#x27;mols2grid-id&#x27;]}, &#x27;data-img&#x27;, &#x27;data-mols2grid-id&#x27;, &#x27;data-ESOL&#x27;, &#x27;data-SMILES&#x27;, &#x27;data-Name&#x27;, &#x27;data-mols2grid-id-copy&#x27;, {attr: &#x27;data-content&#x27;, name: &#x27;mols2grid-tooltip&#x27;}],\n",
              "    item: &#x27;&lt;div class=&quot;cell&quot; data-mols2grid-id=&quot;0&quot;&gt;&lt;input type=&quot;checkbox&quot; class=&quot;position-relative float-left cached_checkbox&quot;&gt;&lt;a tabindex=&quot;0&quot; class=&quot;data data-img mols2grid-tooltip&quot; data-toggle=&quot;popover&quot; data-content=&quot;.&quot;&gt;&lt;/a&gt;&lt;div class=&quot;data data-SMILES&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-Name&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-ESOL&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-mols2grid-id-copy&quot;&gt;&lt;/div&gt;&lt;/div&gt;&#x27;,\n",
              "    page: 9,\n",
              "    pagination: {\n",
              "        name: &quot;pagination&quot;,\n",
              "        item: &#x27;&lt;li class=&quot;page-item&quot;&gt;&lt;a class=&quot;page page-link&quot; href=&quot;#&quot; onclick=&quot;event.preventDefault()&quot;&gt;&lt;/a&gt;&lt;/li&gt;&#x27;,\n",
              "        innerWindow: 1,\n",
              "        outerWindow: 1,\n",
              "    },\n",
              "});\n",
              "listObj.remove(&quot;mols2grid-id&quot;, &quot;0&quot;);\n",
              "listObj.add([{&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 0, &quot;data-ESOL&quot;: -3.9, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Buturon&quot;, &quot;data-mols2grid-id-copy&quot;: 0, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Buturon&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -3.9&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 1, &quot;data-ESOL&quot;: -1.649, &quot;data-SMILES&quot;: &quot;CC(C#C)OCCC(=O)NC1=CC=C([NH])C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 1, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)OCCC(=O)NC1=CC=C([NH])C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -1.649&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 2, &quot;data-ESOL&quot;: -2.576, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)NC1=CC=C(C)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 2, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)NC1=CC=C(C)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.576&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 3, &quot;data-ESOL&quot;: -3.088, &quot;data-SMILES&quot;: &quot;CC(C#C)C(C)C(=O)NC1=CC=C(N)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 3, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)C(C)C(=O)NC1=CC=C(N)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -3.088&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 4, &quot;data-ESOL&quot;: -4.001, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)SC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 4, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)SC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -4.001&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 5, &quot;data-ESOL&quot;: -2.714, &quot;data-SMILES&quot;: &quot;CC(C#C)=C(C)C(=O)NC1=CC=C(F)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 5, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)=C(C)C(=O)NC1=CC=C(F)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.714&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 6, &quot;data-ESOL&quot;: -3.974, &quot;data-SMILES&quot;: &quot;CC(C#C)(CCC)C=O&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 6, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)(CCC)C=O&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -3.974&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 7, &quot;data-ESOL&quot;: -2.576, &quot;data-SMILES&quot;: &quot;CC(C#C)C(C)C(=O)NC1=CC=C(C)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 7, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)C(C)C(=O)NC1=CC=C(C)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -2.576&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 8, &quot;data-ESOL&quot;: -3.032, &quot;data-SMILES&quot;: &quot;CC(C#C)OCCC(=O)OC1=CC=C(F)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 8, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)OCCC(=O)OC1=CC=C(F)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -3.032&quot;}]);\n",
              "// filter\n",
              "if (window.parent.mols2grid_lists === undefined) {\n",
              "    window.parent.mols2grid_lists = {};\n",
              "}\n",
              "window.parent.mols2grid_lists[&quot;Results&quot;] = listObj;\n",
              "\n",
              "\n",
              "// selection\n",
              "class MolStorage extends Map {\n",
              "    multi_set(_id, _smiles) {\n",
              "        for (let i=0; i &lt; _id.length; i++) {\n",
              "            this.set(_id[i], _smiles[i]);\n",
              "        }\n",
              "    }\n",
              "    multi_del(_id) {\n",
              "        for (let i=0; i &lt; _id.length; i++) {\n",
              "            this.delete(_id[i]);\n",
              "        };\n",
              "    }\n",
              "    to_dict() {\n",
              "        var content = &quot;{&quot;;\n",
              "        for (let [key, value] of this) {\n",
              "            content += key + &quot;:&quot; + JSON.stringify(value) + &quot;,&quot;;\n",
              "        }\n",
              "        content = content.length &gt; 1 ? content.slice(0, -1) : content;\n",
              "        content += &quot;}&quot;;\n",
              "        return content\n",
              "    }\n",
              "    download_smi(fileName) {\n",
              "        var content = &quot;SMILES index\\n&quot;;\n",
              "        for (let [key, value] of this) {\n",
              "            content += value + &quot; &quot; + key + &quot;\\n&quot;;\n",
              "        }\n",
              "        var a = document.createElement(&quot;a&quot;);\n",
              "        var file = new Blob([content], {type: &quot;text/plain&quot;});\n",
              "        a.href = URL.createObjectURL(file);\n",
              "        a.download = fileName;\n",
              "        a.click();\n",
              "        a.remove();\n",
              "    }\n",
              "}\n",
              "var SELECTION = new MolStorage();\n",
              "\n",
              "\n",
              "\n",
              "// kernel\n",
              "var kernel_env = null;\n",
              "if (window.parent.IPython !== undefined) {\n",
              "    // Jupyter notebook\n",
              "    kernel_env = &quot;jupyter&quot;;\n",
              "    var kernel = window.parent.IPython.notebook.kernel;\n",
              "    kernel.execute(&#x27;from mols2grid.select import register as _m2g_reg&#x27;)\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "        kernel.execute(&quot;_m2g_reg.add_selection(&#x27;&quot;+grid_id+&quot;&#x27;, &quot;+JSON.stringify(_id)+&quot;,&quot;+JSON.stringify(smiles)+&quot;)&quot;);\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "        kernel.execute(&quot;_m2g_reg.del_selection(&#x27;&quot;+grid_id+&quot;&#x27;, &quot;+JSON.stringify(_id)+&quot;)&quot;);\n",
              "    }\n",
              "} else if (window.parent.google !== undefined) {\n",
              "    // Google colab\n",
              "    kernel_env = &quot;colab&quot;;\n",
              "    var kernel = window.parent.google.colab.kernel;\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "        (async function() {\n",
              "        const result = await kernel.invokeFunction(&#x27;_m2g_reg.add_selection&#x27;,\n",
              "                                                   [grid_id, _id, smiles], {});\n",
              "        })();\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "        (async function() {\n",
              "        const result = await kernel.invokeFunction(&#x27;_m2g_reg.del_selection&#x27;,\n",
              "                                                   [grid_id, _id], {});\n",
              "        })();\n",
              "    }\n",
              "} else {\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "    }\n",
              "}\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// sort\n",
              "var sort_field = &quot;mols2grid-id&quot;;\n",
              "var sort_order = &quot;asc&quot;;\n",
              "function mols2gridSortFunction(itemA, itemB, options) {\n",
              "    var x = itemA.values()[options.valueName];\n",
              "    var y = itemB.values()[options.valueName];\n",
              "    if (typeof x === &quot;number&quot;) {\n",
              "        if (isFinite(x - y)) {\n",
              "            return x - y; \n",
              "        } else {\n",
              "            return isFinite(x) ? -1 : 1;\n",
              "        }\n",
              "    } else {\n",
              "        x = x.toLowerCase();\n",
              "        y = y.toLowerCase();\n",
              "        return (x &lt; y) ? -1: (x &gt; y) ? 1: 0;\n",
              "    }\n",
              "}\n",
              "function checkboxSort(itemA, itemB, options) {\n",
              "    if (itemA.elm !== undefined) {\n",
              "        var checkedA = itemA.elm.firstChild.checked;\n",
              "        if (itemB.elm !== undefined) {\n",
              "            var checkedB = itemB.elm.firstChild.checked;\n",
              "            if (checkedA &amp;&amp; !checkedB) {\n",
              "                return -1;\n",
              "            } else if (!checkedA &amp;&amp; checkedB) {\n",
              "                return 1;\n",
              "            } else {\n",
              "                return 0;\n",
              "            }\n",
              "        } else {\n",
              "            return -1;\n",
              "        }\n",
              "    } else if (itemB.elm !== undefined) {\n",
              "        return 1;\n",
              "    } else {\n",
              "        return 0;\n",
              "    }\n",
              "}\n",
              "$(&#x27;#mols2grid button.sort-btn&#x27;).click(function(e) {\n",
              "    var _field = $(this).attr(&quot;data-name&quot;);\n",
              "    if (_field == sort_field) {\n",
              "        $(this).removeClass(&quot;arrow-&quot; + sort_order)\n",
              "        sort_order = (sort_order === &quot;desc&quot;) ? &quot;asc&quot; : &quot;desc&quot;;\n",
              "    } else {\n",
              "        $(&#x27;#mols2grid button.sort-btn.active&#x27;).removeClass(&quot;active arrow-&quot; + sort_order);\n",
              "        sort_order = &quot;asc&quot;;\n",
              "        sort_field = _field;\n",
              "        $(this).addClass(&quot;active&quot;);\n",
              "    }\n",
              "    $(this).addClass(&quot;arrow-&quot; + sort_order)\n",
              "    if (sort_field == &quot;checkbox&quot;) {\n",
              "        listObj.sort(&quot;mols2grid-id&quot;, {order: sort_order, sortFunction: checkboxSort});\n",
              "    } else {\n",
              "        listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction});\n",
              "    }\n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// tooltips\n",
              "$.fn.tooltip.Constructor.Default.whiteList.span = [&#x27;style&#x27;]\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    $(function () {\n",
              "        // hide previous popovers\n",
              "        $(&#x27;#mols2grid a.page-link&#x27;).click(function(e) {\n",
              "            $(&#x27;.mols2grid-tooltip[data-toggle=&quot;popover&quot;]&#x27;).popover(&#x27;hide&#x27;)\n",
              "        });\n",
              "        // create new popover\n",
              "        $(&#x27;.mols2grid-tooltip[data-toggle=&quot;popover&quot;]&#x27;).popover({\n",
              "            placement: &#x27;bottom&#x27;,\n",
              "            trigger: &#x27;click hover&#x27;,\n",
              "            html: true,\n",
              "            sanitize: false,\n",
              "        });\n",
              "    })\n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "// selection modifyers and export options\n",
              "// check all\n",
              "$(&#x27;#btn-chkbox-all&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id = [];\n",
              "    var _smiles = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox&quot;).each(function() {\n",
              "            this.checked = true;\n",
              "            _id.push(parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;)));\n",
              "            _smiles.push($($(this).siblings(&quot;.data-SMILES&quot;)[0]).text());\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    add_selection(&quot;Results&quot;, _id, _smiles);\n",
              "});\n",
              "// uncheck all\n",
              "$(&#x27;#btn-chkbox-none&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox:checked&quot;).each(function() {\n",
              "            this.checked = false;\n",
              "            _id.push(parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;)));\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    del_selection(&quot;Results&quot;, _id);\n",
              "});\n",
              "// invert\n",
              "$(&#x27;#btn-chkbox-invert&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id_add = [];\n",
              "    var _id_del = [];\n",
              "    var _smiles = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox&quot;).each(function() {\n",
              "            this.checked = !this.checked;\n",
              "            var _id = parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;));\n",
              "            if (this.checked) {\n",
              "                _id_add.push(_id);\n",
              "                _smiles.push($(this).siblings(&quot;.data-SMILES&quot;).first().text());\n",
              "            } else {\n",
              "                _id_del.push(_id);\n",
              "            }\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    del_selection(&quot;Results&quot;, _id_del);\n",
              "    add_selection(&quot;Results&quot;, _id_add, _smiles);\n",
              "});\n",
              "// copy to clipboard\n",
              "$(&quot;#btn-chkbox-copy&quot;).click(function(e) {\n",
              "    navigator.clipboard.writeText(SELECTION.to_dict());\n",
              "});\n",
              "// export smiles\n",
              "$(&quot;#btn-chkbox-dlsmi&quot;).click(function(e) {\n",
              "    SELECTION.download_smi(&quot;selection.smi&quot;);\n",
              "});\n",
              "// export CSV\n",
              "$(&quot;#btn-chkbox-dlcsv&quot;).click(function(e) {\n",
              "    var sep = &quot;\\t&quot;\n",
              "    // same order as subset + tooltip\n",
              "    var columns = Array.from(listObj.items[0].elm.querySelectorAll(&quot;div.data&quot;))\n",
              "                       .map(elm =&gt; elm.classList[1]);\n",
              "    // remove &#x27;data-&#x27;\n",
              "    var header = columns.map(name =&gt; name.slice(5));\n",
              "    // csv content\n",
              "    header = [&quot;index&quot;].concat(header).join(sep);\n",
              "    var content = header + &quot;\\n&quot;;\n",
              "    for (let [index, smiles] of SELECTION.entries()) {\n",
              "        var data = listObj.items[index].values();\n",
              "        content += index;\n",
              "        columns.forEach((key) =&gt; {\n",
              "            content += sep + data[key];\n",
              "        })\n",
              "        content += &quot;\\n&quot;;\n",
              "    }\n",
              "    var a = document.createElement(&quot;a&quot;);\n",
              "    var file = new Blob([content], {type: &quot;text/csv&quot;});\n",
              "    a.href = URL.createObjectURL(file);\n",
              "    a.download = &quot;selection.csv&quot;;\n",
              "    a.click();\n",
              "    a.remove();\n",
              "});\n",
              "// update selection on checkbox click\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    $(&quot;input:checkbox&quot;).change(function() {\n",
              "        var _id = parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;));\n",
              "        if (this.checked) {\n",
              "            var _smiles = $($(this).siblings(&quot;.data-SMILES&quot;)[0]).text();\n",
              "            add_selection(&quot;Results&quot;, [_id], [_smiles]);\n",
              "        } else {\n",
              "            del_selection(&quot;Results&quot;, [_id]);\n",
              "        }\n",
              "    }); \n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// generate images for the currently displayed molecules\n",
              "var draw_opts = {&quot;fixedBondLength&quot;: 25, &quot;width&quot;: 300, &quot;height&quot;: 150};\n",
              "var json_draw_opts = JSON.stringify(draw_opts);\n",
              "\n",
              "var smarts_matches = {};\n",
              "\n",
              "// Load RDKit\n",
              "window\n",
              ".initRDKitModule()\n",
              ".then(function(RDKit) {\n",
              "    console.log(&#x27;RDKit version: &#x27;, RDKit.version());\n",
              "    window.RDKit = RDKit;\n",
              "    window.RDKitModule = RDKit;\n",
              "\n",
              "    // search bar\n",
              "    function SmartsSearch(query, columns) {\n",
              "    var smiles_col = columns[0];\n",
              "    smarts_matches = {};\n",
              "    var query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "    var qmol = RDKit.get_qmol(query);\n",
              "    if (qmol.is_valid()) {\n",
              "        for (var k = 0, kl = listObj.items.length; k &lt; kl; k++) {\n",
              "            var item = listObj.items[k];\n",
              "            var smiles = item.values()[smiles_col]\n",
              "            var mol = RDKit.get_mol(smiles);\n",
              "            if (mol.is_valid()) {\n",
              "                var results = JSON.parse(mol.get_substruct_match(qmol));\n",
              "                if (results.atoms) {\n",
              "                    item.found = true;\n",
              "                    \n",
              "                    smarts_matches[smiles] = results;\n",
              "                    \n",
              "                } else {\n",
              "                    item.found = false;\n",
              "                }\n",
              "            } else {\n",
              "                item.found = false;\n",
              "            }\n",
              "            mol.delete();\n",
              "        }\n",
              "    }\n",
              "    qmol.delete();\n",
              "}\n",
              "var search_type = &quot;Text&quot;;\n",
              "$(&#x27;#mols2grid .search-btn&#x27;).click(function() {\n",
              "    search_type = $(this).text();\n",
              "    $(&#x27;#mols2grid button.search-btn.active&#x27;).removeClass(&quot;active&quot;);\n",
              "    $(this).addClass(&quot;active&quot;);\n",
              "});\n",
              "$(&#x27;#mols2grid #searchbar&#x27;).on(&quot;keyup&quot;, function(e) {\n",
              "    var query = e.target.value;\n",
              "    if (search_type === &quot;Text&quot;) {\n",
              "        smarts_matches = {};\n",
              "        listObj.search(query, [&#x27;data-SMILES&#x27;, &#x27;data-Name&#x27;, &#x27;data-ESOL&#x27;, &#x27;data-mols2grid-id&#x27;, &#x27;mols2grid-tooltip&#x27;]);\n",
              "    } else {\n",
              "        listObj.search(query, [&quot;data-SMILES&quot;], SmartsSearch);\n",
              "    }\n",
              "});\n",
              "\n",
              "    \n",
              "    // generate images for the currently displayed molecules\n",
              "RDKit.prefer_coordgen(true);\n",
              "function draw_mol(smiles) {\n",
              "    var mol = RDKit.get_mol(smiles, &#x27;{&quot;removeHs&quot;: false }&#x27;);\n",
              "    var svg = &quot;&quot;;\n",
              "    if (mol.is_valid()) {\n",
              "        var highlights = smarts_matches[smiles];\n",
              "        if (highlights) {\n",
              "            var details = Object.assign({}, draw_opts, highlights);\n",
              "            details = JSON.stringify(details);\n",
              "        } else {\n",
              "            var details = json_draw_opts;\n",
              "        }\n",
              "        svg = mol.get_svg_with_highlights(details);\n",
              "    }\n",
              "    mol.delete();\n",
              "    if (svg == &quot;&quot;) {\n",
              "        return &#x27;&lt;svg width=&quot;300&quot; height=&quot;150&quot; xmlns=&quot;http://www.w3.org/2000/svg&quot; version=&quot;1.1&quot; viewBox=&quot;0 0 300 150&quot;&gt;&lt;/svg&gt;&#x27;;\n",
              "    }\n",
              "    return svg;\n",
              "}\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    var query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "    if (query === &quot;&quot;) {\n",
              "        smarts_matches = {};\n",
              "    }\n",
              "    $(&#x27;#mols2grid .cell&#x27;).each(function() {\n",
              "        var $t = $(this);\n",
              "        var smiles = $t.children(&quot;.data-SMILES&quot;).first().text()\n",
              "        var svg = draw_mol(smiles);\n",
              "        $t.children(&quot;.data-img&quot;).html(svg);\n",
              "    });\n",
              "});\n",
              "    \n",
              "\n",
              "    // trigger update to activate tooltips, draw images, setup callbacks...\n",
              "    listObj.update();\n",
              "    // resize iframe to fit content\n",
              "    if (window.frameElement) {\n",
              "        window.parent.fit_height(window.frameElement);\n",
              "    }\n",
              "});\n",
              "    &lt;/script&gt;\n",
              "  &lt;/body&gt;\n",
              "&lt;/html&gt;\">\n",
              "</iframe>"
            ],
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ]
          },
          "execution_count": 7,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "smiles = [g[0] for g in generations]\n",
        "esols = [float(g[1].split('>')[-1]) for g in generations]\n",
        "print(\"\\033[1m\" \"\\t\\t\\tButuruon-inspired molecules with a higher solubility score \")\n",
        "result = pd.DataFrame({\n",
        "    \"SMILES\": [smi] + smiles,\n",
        "    \"Name\": [\"Buturon\"] + len(smiles)*[\"Novel (from RT)\"],\n",
        "    \"ESOL\": [true_esol] + [round(e, 3) for e in esols]\n",
        "})\n",
        "mols2grid.display(\n",
        "    result, tooltip=[\"Name\", \"SMILES\", \"ESOL\"], size=(300,150),\n",
        "    fixedBondLength=25, n_cols=3, width=\"100%\", height=None,\n",
        "    name='Results'\n",
        ")"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "fd44be3c",
      "metadata": {
        "id": "fd44be3c"
      },
      "source": [
        "### Or directly tweak the SELFIES and mask specific areas"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "e7e2fdd2",
      "metadata": {
        "id": "e7e2fdd2"
      },
      "outputs": [],
      "source": [
        "config = RegressionTransformerMolecules(algorithm_version=\"solubility\", search=\"sample\", temperature=2, tolerance=5)\n",
        "target = \"<esol>-3.53|[C][C][Branch1_3][Ring1][C][#C][N][Branch1_3][epsilon][C][C][Branch1_3][epsilon][MASK][MASK][MASK][MASK][C][=C][Branch1_3][epsilon][Cl][C][=C][Ring1][Branch1_2]\""
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "3596b2aa",
      "metadata": {
        "id": "3596b2aa",
        "outputId": "36ff2e01-8452-4617-ee43-e51224849c5f"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "[('CC(C#C)N(C)C(C)[NH]ON1C=C(Cl)C=C1', '<esol>-4.0012'),\n",
              " ('CC(C#C)N(C)C(N)C#CC=C(Cl)C=C', '<esol>-5.2467'),\n",
              " ('CC(C#C)N(C)C(=C)OC(C)(Cl)C=C', '<esol>-5.2467'),\n",
              " ('CC(C#C)N(C)C(O)CBr', '<esol>-5.2467'),\n",
              " ('CC(C#C)N(C)C(=C)N=O', '<esol>-5.2467')]"
            ]
          },
          "execution_count": 9,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "esol_generator = RegressionTransformer(\n",
        "    configuration=config, target=target\n",
        ")\n",
        "generations = list(esol_generator.sample(5))\n",
        "generations"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "d106d658",
      "metadata": {
        "id": "d106d658",
        "outputId": "d5627e40-9470-4e66-d145-761689837af8"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "\u001b[1m\t\t\tButuruon-inspired molecules with a higher solubility score \n"
          ]
        },
        {
          "data": {
            "text/html": [
              "<script>\n",
              "    function fit_height(obj) {\n",
              "        obj.style.height = 0;\n",
              "        var height = obj.contentDocument.body.scrollHeight + 18 + 'px';\n",
              "        obj.style.height = height;\n",
              "    }\n",
              "</script>\n",
              "<iframe class=\"mols2grid-iframe\" frameborder=\"0\" width=\"100%\"\n",
              "\n",
              "height=\"200\"\n",
              "\n",
              "\n",
              "allow=\"clipboard-write\"\n",
              "\n",
              "srcdoc=\"&lt;html&gt;\n",
              "  &lt;meta charset=&quot;utf-8&quot;&gt;\n",
              "  &lt;head&gt;\n",
              "    &lt;style&gt;\n",
              "    #mols2grid.gridcontainer {\n",
              "    display: block;\n",
              "    padding-left: 1em;\n",
              "    max-width: 912px;\n",
              "    width: 912px;\n",
              "}\n",
              "#mols2grid .cell {\n",
              "    border: 1px solid #cccccc;\n",
              "    text-align: center;\n",
              "    vertical-align: top;\n",
              "    max-width: 300px;\n",
              "    width: 300px;\n",
              "    font-family: &#x27;DejaVu&#x27;, sans-serif;\n",
              "    font-size: 12pt;\n",
              "    padding: 0;\n",
              "    margin: 0px;\n",
              "    float: left;\n",
              "}\n",
              "#mols2grid .cell:hover {\n",
              "    background-color: #e7e7e7 !important;\n",
              "}\n",
              "#mols2grid .cell .data-img {\n",
              "    padding: 0;\n",
              "    margin: 0;\n",
              "}\n",
              "#mols2grid .cell img, #mols2grid .cell svg {\n",
              "    max-width: 100%;\n",
              "    height: auto;\n",
              "    padding: 0;\n",
              "}\n",
              "#mols2grid .data {\n",
              "    overflow: hidden;\n",
              "    white-space: nowrap;\n",
              "    text-overflow: ellipsis;\n",
              "    display: block;\n",
              "}\n",
              "#mols2grid .arrow-asc:after {\n",
              "    content: &#x27;↑&#x27;;\n",
              "    text-align: right;\n",
              "    float:right;\n",
              "}\n",
              "#mols2grid .arrow-desc:after {\n",
              "    content: &#x27;↓&#x27;;\n",
              "    text-align: right;\n",
              "    float:right;\n",
              "}\n",
              "    /* custom CSS */\n",
              "    \n",
              "    &lt;/style&gt;\n",
              "    &lt;script src=&quot;https://cdnjs.cloudflare.com/ajax/libs/list.js/2.3.1/list.min.js&quot;&gt;&lt;/script&gt;\n",
              "&lt;link rel=&quot;stylesheet&quot; href=&quot;https://cdn.jsdelivr.net/npm/bootstrap@4.6.0/dist/css/bootstrap.min.css&quot; integrity=&quot;sha384-B0vP5xmATw1+K9KRQjQERJvTumQW0nPEzvF6L/Z6nronJ3oUOFUFpCjEUQouq2+l&quot; crossorigin=&quot;anonymous&quot;&gt;\n",
              "&lt;script src=&quot;https://code.jquery.com/jquery-3.5.1.slim.min.js&quot; integrity=&quot;sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj&quot; crossorigin=&quot;anonymous&quot;&gt;&lt;/script&gt;\n",
              "&lt;script src=&quot;https://cdn.jsdelivr.net/npm/bootstrap@4.6.0/dist/js/bootstrap.bundle.min.js&quot; integrity=&quot;sha384-Piv4xVNRyMGpqkS2by6br4gNJ7DXjqk09RmUpJ8jgGtD7zP9yug3goQfGII0yAns&quot; crossorigin=&quot;anonymous&quot;&gt;&lt;/script&gt;\n",
              "&lt;script src=&quot;https://unpkg.com/@rdkit/rdkit@2021.9.4/Code/MinimalLib/dist/RDKit_minimal.js&quot;&gt;&lt;/script&gt;\n",
              "    &lt;!-- custom header --&gt;\n",
              "    \n",
              "  &lt;/head&gt;\n",
              "  &lt;body&gt;\n",
              "    &lt;div id=&quot;mols2grid&quot; class=&quot;gridcontainer grid-Results&quot;&gt;\n",
              "      &lt;div class=&quot;row mb-3&quot;&gt;\n",
              "        &lt;div class=&quot;list&quot;&gt;&lt;div class=&quot;cell&quot; data-mols2grid-id=&quot;0&quot;&gt;&lt;input type=&quot;checkbox&quot; class=&quot;position-relative float-left cached_checkbox&quot;&gt;&lt;a tabindex=&quot;0&quot; class=&quot;data data-img mols2grid-tooltip&quot; data-toggle=&quot;popover&quot; data-content=&quot;.&quot;&gt;&lt;/a&gt;&lt;div class=&quot;data data-SMILES&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-Name&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-ESOL&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-mols2grid-id-copy&quot;&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;\n",
              "      &lt;/div&gt;\n",
              "      &lt;div class=&quot;d-inline&quot;&gt;\n",
              "        &lt;ul class=&quot;pagination float-left&quot;&gt;&lt;/ul&gt;\n",
              "        &lt;div id=&quot;controls&quot; class=&quot;d-flex flex-row float-right&quot;&gt;\n",
              "          \n",
              "          &lt;div id=&quot;chkbox-dropdown&quot; class=&quot;dropdown&quot;&gt;\n",
              "    &lt;button class=&quot;btn btn-light dropdown-toggle&quot; type=&quot;button&quot; id=&quot;chkboxDropdown&quot; data-toggle=&quot;dropdown&quot; aria-haspopup=&quot;true&quot; aria-expanded=&quot;false&quot;&gt;☑&lt;/button&gt;\n",
              "    &lt;div class=&quot;dropdown-menu&quot; aria-labelledby=&quot;checkboxDropdownMenu&quot;&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-all&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Check all&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-none&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Uncheck all&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-invert&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Invert&lt;/button&gt;\n",
              "        &lt;div class=&quot;dropdown-divider&quot;&gt;&lt;/div&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-copy&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Copy to clipboard&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-dlsmi&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Save SMILES&lt;/button&gt;\n",
              "        &lt;button id=&quot;btn-chkbox-dlcsv&quot; class=&quot;dropdown-item&quot; type=&quot;button&quot;&gt;Save CSV&lt;/button&gt;\n",
              "    &lt;/div&gt;\n",
              "&lt;/div&gt;\n",
              "          \n",
              "          &lt;div id=&quot;sort-dropdown&quot; class=&quot;dropdown pl-2&quot;&gt;\n",
              "            &lt;button class=&quot;btn btn-light dropdown-toggle&quot; type=&quot;button&quot; id=&quot;sortDropdown&quot; data-toggle=&quot;dropdown&quot; aria-haspopup=&quot;true&quot; aria-expanded=&quot;false&quot;&gt;\n",
              "              Sort by\n",
              "            &lt;/button&gt;\n",
              "            &lt;div class=&quot;dropdown-menu&quot; aria-labelledby=&quot;sortDropdownMenu&quot;&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn arrow-asc active&quot; type=&quot;button&quot; data-name=&quot;mols2grid-id&quot;&gt;Index&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn &quot; type=&quot;button&quot; data-name=&quot;data-SMILES&quot;&gt;SMILES&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn &quot; type=&quot;button&quot; data-name=&quot;data-Name&quot;&gt;Name&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn &quot; type=&quot;button&quot; data-name=&quot;data-ESOL&quot;&gt;ESOL&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn arrow-asc active&quot; type=&quot;button&quot; data-name=&quot;data-mols2grid-id&quot;&gt;mols2grid-id&lt;/button&gt;\n",
              "              \n",
              "              \n",
              "              \n",
              "              &lt;button class=&quot;dropdown-item sort-btn&quot; type=&quot;button&quot; data-name=&quot;checkbox&quot;&gt;Selected&lt;/button&gt;\n",
              "              \n",
              "            &lt;/div&gt;\n",
              "          &lt;/div&gt;\n",
              "          &lt;div class=&quot;input-group row pl-4&quot;&gt;\n",
              "            &lt;input type=&quot;text&quot; id=&quot;searchbar&quot; class=&quot;form-control&quot; placeholder=&quot;Search&quot; aria-label=&quot;Search&quot; aria-describedby=&quot;basic-addon1&quot;&gt;\n",
              "            &lt;div class=&quot;input-group-append&quot;&gt;\n",
              "              &lt;button id=&quot;searchBtn&quot; class=&quot;btn btn-light dropdown-toggle&quot; type=&quot;button&quot; data-toggle=&quot;dropdown&quot; aria-haspopup=&quot;true&quot; aria-expanded=&quot;false&quot;&gt;🔎&lt;/button&gt;\n",
              "              &lt;div class=&quot;dropdown-menu dropdown-menu-right&quot;&gt;\n",
              "                &lt;button id=&quot;txtSearch&quot; class=&quot;search-btn dropdown-item active&quot;&gt;Text&lt;/button&gt;\n",
              "                &lt;button id=&quot;smartsSearch&quot; class=&quot;search-btn dropdown-item&quot;&gt;SMARTS&lt;/button&gt;\n",
              "              &lt;/div&gt;\n",
              "            &lt;/div&gt;\n",
              "          &lt;/div&gt;\n",
              "        &lt;/div&gt;\n",
              "      &lt;/div&gt;\n",
              "    &lt;/div&gt;\n",
              "    &lt;script&gt;\n",
              "    // list.js\n",
              "var listObj = new List(&#x27;mols2grid&#x27;, {\n",
              "    valueNames: [{data: [&#x27;mols2grid-id&#x27;]}, &#x27;data-img&#x27;, &#x27;data-mols2grid-id&#x27;, &#x27;data-ESOL&#x27;, &#x27;data-SMILES&#x27;, &#x27;data-Name&#x27;, &#x27;data-mols2grid-id-copy&#x27;, {attr: &#x27;data-content&#x27;, name: &#x27;mols2grid-tooltip&#x27;}],\n",
              "    item: &#x27;&lt;div class=&quot;cell&quot; data-mols2grid-id=&quot;0&quot;&gt;&lt;input type=&quot;checkbox&quot; class=&quot;position-relative float-left cached_checkbox&quot;&gt;&lt;a tabindex=&quot;0&quot; class=&quot;data data-img mols2grid-tooltip&quot; data-toggle=&quot;popover&quot; data-content=&quot;.&quot;&gt;&lt;/a&gt;&lt;div class=&quot;data data-SMILES&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-Name&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-ESOL&quot;&gt;&lt;/div&gt;&lt;div class=&quot;data data-mols2grid-id-copy&quot;&gt;&lt;/div&gt;&lt;/div&gt;&#x27;,\n",
              "    page: 9,\n",
              "    pagination: {\n",
              "        name: &quot;pagination&quot;,\n",
              "        item: &#x27;&lt;li class=&quot;page-item&quot;&gt;&lt;a class=&quot;page page-link&quot; href=&quot;#&quot; onclick=&quot;event.preventDefault()&quot;&gt;&lt;/a&gt;&lt;/li&gt;&#x27;,\n",
              "        innerWindow: 1,\n",
              "        outerWindow: 1,\n",
              "    },\n",
              "});\n",
              "listObj.remove(&quot;mols2grid-id&quot;, &quot;0&quot;);\n",
              "listObj.add([{&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 0, &quot;data-ESOL&quot;: -3.9, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Buturon&quot;, &quot;data-mols2grid-id-copy&quot;: 0, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Buturon&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -3.9&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 1, &quot;data-ESOL&quot;: -4.001, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(C)[NH]ON1C=C(Cl)C=C1&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 1, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(C)[NH]ON1C=C(Cl)C=C1&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -4.001&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 2, &quot;data-ESOL&quot;: -5.247, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(N)C#CC=C(Cl)C=C&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 2, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(N)C#CC=C(Cl)C=C&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -5.247&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 3, &quot;data-ESOL&quot;: -5.247, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=C)OC(C)(Cl)C=C&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 3, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=C)OC(C)(Cl)C=C&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -5.247&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 4, &quot;data-ESOL&quot;: -5.247, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(O)CBr&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 4, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(O)CBr&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -5.247&quot;}, {&quot;data-img&quot;: null, &quot;mols2grid-id&quot;: 5, &quot;data-ESOL&quot;: -5.247, &quot;data-SMILES&quot;: &quot;CC(C#C)N(C)C(=C)N=O&quot;, &quot;data-Name&quot;: &quot;Novel (from RT)&quot;, &quot;data-mols2grid-id-copy&quot;: 5, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: Novel (from RT)&lt;br&gt;&lt;strong&gt;SMILES&lt;/strong&gt;: CC(C#C)N(C)C(=C)N=O&lt;br&gt;&lt;strong&gt;ESOL&lt;/strong&gt;: -5.247&quot;}]);\n",
              "// filter\n",
              "if (window.parent.mols2grid_lists === undefined) {\n",
              "    window.parent.mols2grid_lists = {};\n",
              "}\n",
              "window.parent.mols2grid_lists[&quot;Results&quot;] = listObj;\n",
              "\n",
              "\n",
              "// selection\n",
              "class MolStorage extends Map {\n",
              "    multi_set(_id, _smiles) {\n",
              "        for (let i=0; i &lt; _id.length; i++) {\n",
              "            this.set(_id[i], _smiles[i]);\n",
              "        }\n",
              "    }\n",
              "    multi_del(_id) {\n",
              "        for (let i=0; i &lt; _id.length; i++) {\n",
              "            this.delete(_id[i]);\n",
              "        };\n",
              "    }\n",
              "    to_dict() {\n",
              "        var content = &quot;{&quot;;\n",
              "        for (let [key, value] of this) {\n",
              "            content += key + &quot;:&quot; + JSON.stringify(value) + &quot;,&quot;;\n",
              "        }\n",
              "        content = content.length &gt; 1 ? content.slice(0, -1) : content;\n",
              "        content += &quot;}&quot;;\n",
              "        return content\n",
              "    }\n",
              "    download_smi(fileName) {\n",
              "        var content = &quot;SMILES index\\n&quot;;\n",
              "        for (let [key, value] of this) {\n",
              "            content += value + &quot; &quot; + key + &quot;\\n&quot;;\n",
              "        }\n",
              "        var a = document.createElement(&quot;a&quot;);\n",
              "        var file = new Blob([content], {type: &quot;text/plain&quot;});\n",
              "        a.href = URL.createObjectURL(file);\n",
              "        a.download = fileName;\n",
              "        a.click();\n",
              "        a.remove();\n",
              "    }\n",
              "}\n",
              "var SELECTION = new MolStorage();\n",
              "\n",
              "\n",
              "\n",
              "// kernel\n",
              "var kernel_env = null;\n",
              "if (window.parent.IPython !== undefined) {\n",
              "    // Jupyter notebook\n",
              "    kernel_env = &quot;jupyter&quot;;\n",
              "    var kernel = window.parent.IPython.notebook.kernel;\n",
              "    kernel.execute(&#x27;from mols2grid.select import register as _m2g_reg&#x27;)\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "        kernel.execute(&quot;_m2g_reg.add_selection(&#x27;&quot;+grid_id+&quot;&#x27;, &quot;+JSON.stringify(_id)+&quot;,&quot;+JSON.stringify(smiles)+&quot;)&quot;);\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "        kernel.execute(&quot;_m2g_reg.del_selection(&#x27;&quot;+grid_id+&quot;&#x27;, &quot;+JSON.stringify(_id)+&quot;)&quot;);\n",
              "    }\n",
              "} else if (window.parent.google !== undefined) {\n",
              "    // Google colab\n",
              "    kernel_env = &quot;colab&quot;;\n",
              "    var kernel = window.parent.google.colab.kernel;\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "        (async function() {\n",
              "        const result = await kernel.invokeFunction(&#x27;_m2g_reg.add_selection&#x27;,\n",
              "                                                   [grid_id, _id, smiles], {});\n",
              "        })();\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "        (async function() {\n",
              "        const result = await kernel.invokeFunction(&#x27;_m2g_reg.del_selection&#x27;,\n",
              "                                                   [grid_id, _id], {});\n",
              "        })();\n",
              "    }\n",
              "} else {\n",
              "    function add_selection(grid_id, _id, smiles) {\n",
              "        SELECTION.multi_set(_id, smiles);\n",
              "    }\n",
              "    function del_selection(grid_id, _id) {\n",
              "        SELECTION.multi_del(_id);\n",
              "    }\n",
              "}\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// sort\n",
              "var sort_field = &quot;mols2grid-id&quot;;\n",
              "var sort_order = &quot;asc&quot;;\n",
              "function mols2gridSortFunction(itemA, itemB, options) {\n",
              "    var x = itemA.values()[options.valueName];\n",
              "    var y = itemB.values()[options.valueName];\n",
              "    if (typeof x === &quot;number&quot;) {\n",
              "        if (isFinite(x - y)) {\n",
              "            return x - y; \n",
              "        } else {\n",
              "            return isFinite(x) ? -1 : 1;\n",
              "        }\n",
              "    } else {\n",
              "        x = x.toLowerCase();\n",
              "        y = y.toLowerCase();\n",
              "        return (x &lt; y) ? -1: (x &gt; y) ? 1: 0;\n",
              "    }\n",
              "}\n",
              "function checkboxSort(itemA, itemB, options) {\n",
              "    if (itemA.elm !== undefined) {\n",
              "        var checkedA = itemA.elm.firstChild.checked;\n",
              "        if (itemB.elm !== undefined) {\n",
              "            var checkedB = itemB.elm.firstChild.checked;\n",
              "            if (checkedA &amp;&amp; !checkedB) {\n",
              "                return -1;\n",
              "            } else if (!checkedA &amp;&amp; checkedB) {\n",
              "                return 1;\n",
              "            } else {\n",
              "                return 0;\n",
              "            }\n",
              "        } else {\n",
              "            return -1;\n",
              "        }\n",
              "    } else if (itemB.elm !== undefined) {\n",
              "        return 1;\n",
              "    } else {\n",
              "        return 0;\n",
              "    }\n",
              "}\n",
              "$(&#x27;#mols2grid button.sort-btn&#x27;).click(function(e) {\n",
              "    var _field = $(this).attr(&quot;data-name&quot;);\n",
              "    if (_field == sort_field) {\n",
              "        $(this).removeClass(&quot;arrow-&quot; + sort_order)\n",
              "        sort_order = (sort_order === &quot;desc&quot;) ? &quot;asc&quot; : &quot;desc&quot;;\n",
              "    } else {\n",
              "        $(&#x27;#mols2grid button.sort-btn.active&#x27;).removeClass(&quot;active arrow-&quot; + sort_order);\n",
              "        sort_order = &quot;asc&quot;;\n",
              "        sort_field = _field;\n",
              "        $(this).addClass(&quot;active&quot;);\n",
              "    }\n",
              "    $(this).addClass(&quot;arrow-&quot; + sort_order)\n",
              "    if (sort_field == &quot;checkbox&quot;) {\n",
              "        listObj.sort(&quot;mols2grid-id&quot;, {order: sort_order, sortFunction: checkboxSort});\n",
              "    } else {\n",
              "        listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction});\n",
              "    }\n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// tooltips\n",
              "$.fn.tooltip.Constructor.Default.whiteList.span = [&#x27;style&#x27;]\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    $(function () {\n",
              "        // hide previous popovers\n",
              "        $(&#x27;#mols2grid a.page-link&#x27;).click(function(e) {\n",
              "            $(&#x27;.mols2grid-tooltip[data-toggle=&quot;popover&quot;]&#x27;).popover(&#x27;hide&#x27;)\n",
              "        });\n",
              "        // create new popover\n",
              "        $(&#x27;.mols2grid-tooltip[data-toggle=&quot;popover&quot;]&#x27;).popover({\n",
              "            placement: &#x27;bottom&#x27;,\n",
              "            trigger: &#x27;click hover&#x27;,\n",
              "            html: true,\n",
              "            sanitize: false,\n",
              "        });\n",
              "    })\n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "// selection modifyers and export options\n",
              "// check all\n",
              "$(&#x27;#btn-chkbox-all&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id = [];\n",
              "    var _smiles = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox&quot;).each(function() {\n",
              "            this.checked = true;\n",
              "            _id.push(parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;)));\n",
              "            _smiles.push($($(this).siblings(&quot;.data-SMILES&quot;)[0]).text());\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    add_selection(&quot;Results&quot;, _id, _smiles);\n",
              "});\n",
              "// uncheck all\n",
              "$(&#x27;#btn-chkbox-none&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox:checked&quot;).each(function() {\n",
              "            this.checked = false;\n",
              "            _id.push(parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;)));\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    del_selection(&quot;Results&quot;, _id);\n",
              "});\n",
              "// invert\n",
              "$(&#x27;#btn-chkbox-invert&#x27;).click(function (e) {\n",
              "    var current_page = parseInt($(&quot;li.page-item.active &gt; a&quot;).text());\n",
              "    var n_items = 9;\n",
              "    var last_page = parseInt($(&quot;li.page-item &gt; a&quot;).last().text());\n",
              "    var _id_add = [];\n",
              "    var _id_del = [];\n",
              "    var _smiles = [];\n",
              "    for (let i = 0; i &lt; last_page; i++) {\n",
              "        listObj.show(i * n_items + 1, n_items);\n",
              "        $(&quot;input:checkbox&quot;).each(function() {\n",
              "            this.checked = !this.checked;\n",
              "            var _id = parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;));\n",
              "            if (this.checked) {\n",
              "                _id_add.push(_id);\n",
              "                _smiles.push($(this).siblings(&quot;.data-SMILES&quot;).first().text());\n",
              "            } else {\n",
              "                _id_del.push(_id);\n",
              "            }\n",
              "        });\n",
              "    }\n",
              "    listObj.show((current_page - 1) * n_items + 1, n_items);\n",
              "    del_selection(&quot;Results&quot;, _id_del);\n",
              "    add_selection(&quot;Results&quot;, _id_add, _smiles);\n",
              "});\n",
              "// copy to clipboard\n",
              "$(&quot;#btn-chkbox-copy&quot;).click(function(e) {\n",
              "    navigator.clipboard.writeText(SELECTION.to_dict());\n",
              "});\n",
              "// export smiles\n",
              "$(&quot;#btn-chkbox-dlsmi&quot;).click(function(e) {\n",
              "    SELECTION.download_smi(&quot;selection.smi&quot;);\n",
              "});\n",
              "// export CSV\n",
              "$(&quot;#btn-chkbox-dlcsv&quot;).click(function(e) {\n",
              "    var sep = &quot;\\t&quot;\n",
              "    // same order as subset + tooltip\n",
              "    var columns = Array.from(listObj.items[0].elm.querySelectorAll(&quot;div.data&quot;))\n",
              "                       .map(elm =&gt; elm.classList[1]);\n",
              "    // remove &#x27;data-&#x27;\n",
              "    var header = columns.map(name =&gt; name.slice(5));\n",
              "    // csv content\n",
              "    header = [&quot;index&quot;].concat(header).join(sep);\n",
              "    var content = header + &quot;\\n&quot;;\n",
              "    for (let [index, smiles] of SELECTION.entries()) {\n",
              "        var data = listObj.items[index].values();\n",
              "        content += index;\n",
              "        columns.forEach((key) =&gt; {\n",
              "            content += sep + data[key];\n",
              "        })\n",
              "        content += &quot;\\n&quot;;\n",
              "    }\n",
              "    var a = document.createElement(&quot;a&quot;);\n",
              "    var file = new Blob([content], {type: &quot;text/csv&quot;});\n",
              "    a.href = URL.createObjectURL(file);\n",
              "    a.download = &quot;selection.csv&quot;;\n",
              "    a.click();\n",
              "    a.remove();\n",
              "});\n",
              "// update selection on checkbox click\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    $(&quot;input:checkbox&quot;).change(function() {\n",
              "        var _id = parseInt($(this).closest(&quot;.cell&quot;).attr(&quot;data-mols2grid-id&quot;));\n",
              "        if (this.checked) {\n",
              "            var _smiles = $($(this).siblings(&quot;.data-SMILES&quot;)[0]).text();\n",
              "            add_selection(&quot;Results&quot;, [_id], [_smiles]);\n",
              "        } else {\n",
              "            del_selection(&quot;Results&quot;, [_id]);\n",
              "        }\n",
              "    }); \n",
              "});\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "\n",
              "// generate images for the currently displayed molecules\n",
              "var draw_opts = {&quot;fixedBondLength&quot;: 25, &quot;width&quot;: 300, &quot;height&quot;: 150};\n",
              "var json_draw_opts = JSON.stringify(draw_opts);\n",
              "\n",
              "var smarts_matches = {};\n",
              "\n",
              "// Load RDKit\n",
              "window\n",
              ".initRDKitModule()\n",
              ".then(function(RDKit) {\n",
              "    console.log(&#x27;RDKit version: &#x27;, RDKit.version());\n",
              "    window.RDKit = RDKit;\n",
              "    window.RDKitModule = RDKit;\n",
              "\n",
              "    // search bar\n",
              "    function SmartsSearch(query, columns) {\n",
              "    var smiles_col = columns[0];\n",
              "    smarts_matches = {};\n",
              "    var query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "    var qmol = RDKit.get_qmol(query);\n",
              "    if (qmol.is_valid()) {\n",
              "        for (var k = 0, kl = listObj.items.length; k &lt; kl; k++) {\n",
              "            var item = listObj.items[k];\n",
              "            var smiles = item.values()[smiles_col]\n",
              "            var mol = RDKit.get_mol(smiles);\n",
              "            if (mol.is_valid()) {\n",
              "                var results = JSON.parse(mol.get_substruct_match(qmol));\n",
              "                if (results.atoms) {\n",
              "                    item.found = true;\n",
              "                    \n",
              "                    smarts_matches[smiles] = results;\n",
              "                    \n",
              "                } else {\n",
              "                    item.found = false;\n",
              "                }\n",
              "            } else {\n",
              "                item.found = false;\n",
              "            }\n",
              "            mol.delete();\n",
              "        }\n",
              "    }\n",
              "    qmol.delete();\n",
              "}\n",
              "var search_type = &quot;Text&quot;;\n",
              "$(&#x27;#mols2grid .search-btn&#x27;).click(function() {\n",
              "    search_type = $(this).text();\n",
              "    $(&#x27;#mols2grid button.search-btn.active&#x27;).removeClass(&quot;active&quot;);\n",
              "    $(this).addClass(&quot;active&quot;);\n",
              "});\n",
              "$(&#x27;#mols2grid #searchbar&#x27;).on(&quot;keyup&quot;, function(e) {\n",
              "    var query = e.target.value;\n",
              "    if (search_type === &quot;Text&quot;) {\n",
              "        smarts_matches = {};\n",
              "        listObj.search(query, [&#x27;data-SMILES&#x27;, &#x27;data-Name&#x27;, &#x27;data-ESOL&#x27;, &#x27;data-mols2grid-id&#x27;, &#x27;mols2grid-tooltip&#x27;]);\n",
              "    } else {\n",
              "        listObj.search(query, [&quot;data-SMILES&quot;], SmartsSearch);\n",
              "    }\n",
              "});\n",
              "\n",
              "    \n",
              "    // generate images for the currently displayed molecules\n",
              "RDKit.prefer_coordgen(true);\n",
              "function draw_mol(smiles) {\n",
              "    var mol = RDKit.get_mol(smiles, &#x27;{&quot;removeHs&quot;: false }&#x27;);\n",
              "    var svg = &quot;&quot;;\n",
              "    if (mol.is_valid()) {\n",
              "        var highlights = smarts_matches[smiles];\n",
              "        if (highlights) {\n",
              "            var details = Object.assign({}, draw_opts, highlights);\n",
              "            details = JSON.stringify(details);\n",
              "        } else {\n",
              "            var details = json_draw_opts;\n",
              "        }\n",
              "        svg = mol.get_svg_with_highlights(details);\n",
              "    }\n",
              "    mol.delete();\n",
              "    if (svg == &quot;&quot;) {\n",
              "        return &#x27;&lt;svg width=&quot;300&quot; height=&quot;150&quot; xmlns=&quot;http://www.w3.org/2000/svg&quot; version=&quot;1.1&quot; viewBox=&quot;0 0 300 150&quot;&gt;&lt;/svg&gt;&#x27;;\n",
              "    }\n",
              "    return svg;\n",
              "}\n",
              "listObj.on(&quot;updated&quot;, function (list) {\n",
              "    var query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "    if (query === &quot;&quot;) {\n",
              "        smarts_matches = {};\n",
              "    }\n",
              "    $(&#x27;#mols2grid .cell&#x27;).each(function() {\n",
              "        var $t = $(this);\n",
              "        var smiles = $t.children(&quot;.data-SMILES&quot;).first().text()\n",
              "        var svg = draw_mol(smiles);\n",
              "        $t.children(&quot;.data-img&quot;).html(svg);\n",
              "    });\n",
              "});\n",
              "    \n",
              "\n",
              "    // trigger update to activate tooltips, draw images, setup callbacks...\n",
              "    listObj.update();\n",
              "    // resize iframe to fit content\n",
              "    if (window.frameElement) {\n",
              "        window.parent.fit_height(window.frameElement);\n",
              "    }\n",
              "});\n",
              "    &lt;/script&gt;\n",
              "  &lt;/body&gt;\n",
              "&lt;/html&gt;\">\n",
              "</iframe>"
            ],
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ]
          },
          "execution_count": 10,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "smiles = [g[0] for g in generations]\n",
        "esols = [float(g[1].split('>')[-1]) for g in generations]\n",
        "print(\"\\033[1m\" \"\\t\\t\\tButuruon-inspired molecules with a higher solubility score \")\n",
        "result = pd.DataFrame({\n",
        "    \"SMILES\": [smi] + smiles,\n",
        "    \"Name\": [\"Buturon\"] + 5*[\"Novel (from RT)\"],\n",
        "    \"ESOL\": [true_esol] + [round(e, 3) for e in esols]\n",
        "})\n",
        "mols2grid.display(\n",
        "    result, tooltip=[\"Name\", \"SMILES\", \"ESOL\"], size=(300,150),\n",
        "    fixedBondLength=25, n_cols=3, width=\"100%\", height=None,\n",
        "    name='Results'\n",
        ")"
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3 (ipykernel)",
      "language": "python",
      "name": "python3"
    },
    "language_info": {
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.7.12"
    },
    "colab": {
      "provenance": []
    }
  },
  "nbformat": 4,
  "nbformat_minor": 5
}