hcn.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "rahm_lab.ipynb",
      "provenance": [],
      "authorship_tag": "ABX9TyOMLrOPYR+C3nTxAfsjkbBP",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/ssiddhantsharma/hcn/blob/main/hcn.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "3aM1iARtUNNo",
        "outputId": "344b8af7-8ad1-492e-a204-71162b2e9bbd"
      },
      "source": [
        "!pip install rdkit-pypi mols2grid"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting rdkit-pypi\n",
            "  Downloading rdkit_pypi-2021.3.4-cp37-cp37m-manylinux2014_x86_64.whl (18.6 MB)\n",
            "\u001b[K     |████████████████████████████████| 18.6 MB 155 kB/s \n",
            "\u001b[?25hCollecting mols2grid\n",
            "  Downloading mols2grid-0.0.6-py3-none-any.whl (22 kB)\n",
            "Requirement already satisfied: numpy>=1.19 in /usr/local/lib/python3.7/dist-packages (from rdkit-pypi) (1.19.5)\n",
            "Requirement already satisfied: jinja2 in /usr/local/lib/python3.7/dist-packages (from mols2grid) (2.11.3)\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from mols2grid) (1.1.5)\n",
            "Requirement already satisfied: MarkupSafe>=0.23 in /usr/local/lib/python3.7/dist-packages (from jinja2->mols2grid) (2.0.1)\n",
            "Requirement already satisfied: python-dateutil>=2.7.3 in /usr/local/lib/python3.7/dist-packages (from pandas->mols2grid) (2.8.1)\n",
            "Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->mols2grid) (2018.9)\n",
            "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.7.3->pandas->mols2grid) (1.15.0)\n",
            "Installing collected packages: rdkit-pypi, mols2grid\n",
            "Successfully installed mols2grid-0.0.6 rdkit-pypi-2021.3.4\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "IJAIc3H9ZBjR",
        "outputId": "ec0828c8-0305-4f34-869f-d48e9ed7741c",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 787
        }
      },
      "source": [
        "import mols2grid\n",
        "import pandas as pd\n",
        "url = 'https://raw.githubusercontent.com/ssiddhantsharma/hcn/main/siddhant_chalmers_cassum.csv'\n",
        "df = pd.read_csv(url, sep=',', header=0)  #reading the energy data coming collected over CASSUM\n",
        "ID = df['ID'].tolist()  #number\n",
        "CLASS = df['CLASS'].tolist() #class of molecule: monomer unit or molecule\n",
        "Name = df['Name'].tolist() #according to thermomap\n",
        "smiles = df['smiles'].tolist()\n",
        "ev= df['vac'].tolist() #deltaE for vacuum\n",
        "es= df['solv'].tolist() #deltaE for solvent(H20)\n",
        "gr = df['dG298'].tolist() #delta G for room temp\n",
        "gr_s = df['dGsolv298'].tolist() #delta g for room temp solvent\n",
        "gt = df['dG93.6'].tolist() #delta g for titan temp\n",
        "gt_s = df['dGsolv93.6'].tolist() #delta g for titan temp solvent\n",
        "df = pd.DataFrame({\"id\": ID, \"smiles\": smiles,\"class\": CLASS, \"Name\": Name,\"ΔE-Vac\":ev, \"ΔE-Solv\": es, \"ΔG-298.15 K\": gr, \"ΔG-Solv-298.15 K\": gr_s, \"ΔG-93.6 K\": gt, \"ΔG-Solv-93.6 K\": gt_s})\n",
        "mg = mols2grid.MolGrid(df, smiles_col=\"smiles\", size=(290, 180), useSVG=True, coordGen=True, fixedBondLength=40)\n",
        "mg.display(subset=[\"id\", \"img\", \"class\"], n_cols=3, tooltip=[\"Name\", \"ΔE-Vac\",\"ΔE-Solv\", \"ΔG-298.15 K\", \"ΔG-Solv-298.15 K\", \"ΔG-93.6 K\", \"ΔG-Solv-93.6 K\"], style={\"Name\": lambda x: \"color: red\"}, template=\"pages\",tooltip_placement=\"bottom\", fontsize=\"15pt\", hover_color=\"#f5a841\", n_rows=3, border=\"1px solid #cccccc\", fontfamily = \"roboto, sans-serif\", selection=False)"
      ],
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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fill=&#x27;#0000FF&#x27;/&gt;\\n&lt;/svg&gt;\\n&quot;, &quot;mols2grid-tooltip&quot;: &quot;&lt;strong&gt;Name&lt;/strong&gt;: &lt;span style=\\&quot;color: red\\&quot;&gt;Adenine&lt;/span&gt;&lt;br&gt;&lt;strong&gt;\\u0394E-Vac&lt;/strong&gt;: -17.92 kcal/mol&lt;br&gt;&lt;strong&gt;\\u0394E-Solv&lt;/strong&gt;: -25.77 kcal/mol&lt;br&gt;&lt;strong&gt;\\u0394G-298.15 K&lt;/strong&gt;: -14.86 kcal/mol&lt;br&gt;&lt;strong&gt;\\u0394G-Solv-298.15 K&lt;/strong&gt;: -21.59 kcal/mol&lt;br&gt;&lt;strong&gt;\\u0394G-93.6 K&lt;/strong&gt;: -15.56 kcal/mol&lt;br&gt;&lt;strong&gt;\\u0394G-Solv-93.6 K&lt;/strong&gt;: -22.83 kcal/mol&quot;, &quot;style-Name&quot;: &quot;color: red&quot;}])\n",
              "      \n",
              "      // sort\n",
              "      var sort_field = &quot;mols2grid-id&quot;;\n",
              "      var sort_order = &quot;asc&quot;;\n",
              "      function coerce_type(str) {\n",
              "        if (isNaN(str)) return null;\n",
              "        var num = parseFloat(str)\n",
              "        return isNaN(num) ? str : num;\n",
              "      }\n",
              "      function mols2gridSortFunction(itemA, itemB, options) {\n",
              "        var x = coerce_type(itemA.values()[options.valueName]);\n",
              "        var y = coerce_type(itemB.values()[options.valueName]);\n",
              "        if (x &gt; y) { \n",
              "          return 1;\n",
              "        } else if (x &lt; y) {\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 &quot;+&quot;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",
              "        listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction});\n",
              "      });\n",
              "      // search bar\n",
              "      function SmartsSearch(query, columns) {\n",
              "        query = $(&#x27;#mols2grid #searchbar&#x27;).val();\n",
              "        var smiles = columns[0];\n",
              "        var qmol = RDKitModule.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 mol = RDKitModule.get_mol(item.values()[smiles]);\n",
              "            var results = JSON.parse(mol.get_substruct_match(qmol));\n",
              "            if (results.atoms) {\n",
              "              item.found = true;\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",
              "          listObj.search(query, [&#x27;data-id&#x27;, &#x27;data-class&#x27;, &#x27;mols2grid-tooltip&#x27;]);\n",
              "        } else {\n",
              "          listObj.search(query, [&quot;data-&quot;+&quot;smiles&quot;], SmartsSearch);\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",
              "          });\n",
              "        })\n",
              "      });\n",
              "      \n",
              "      \n",
              "      \n",
              "      listObj.update();\n",
              "      \n",
              "    &lt;/script&gt;\n",
              "  &lt;/body&gt;\n",
              "&lt;/html&gt;\"></iframe>"
            ],
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "808E2wJ7dAA7"
      },
      "source": [
        ""
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}