annotate_base_pairs_and_NtCs.ipynb

{
  "cells": [
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      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/samuelflores/FreeCAD-ports-cache/blob/master/annotate_base_pairs_and_NtCs.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#!pip install nglview\n",
        "#!jupyter-nbextension enable nglview --py --sys-prefix\n",
        "!pip install -q condacolab\n",
        "import condacolab\n",
        "condacolab.install()\n",
        "!conda --version\n",
        "!conda config --add channels conda-forge\n",
        "!conda install nglview -c bioconda\n",
        "!jupyter-nbextension enable nglview --py --sys-prefix\n"
      ],
      "metadata": {
        "id": "L3J-ZAC7b2_q",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "095242d1-f3fd-4789-b6ee-6f93ca9f9e83"
      },
      "execution_count": 16,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "✨🍰✨ Everything looks OK!\n",
            "conda 4.12.0\n",
            "Warning: 'conda-forge' already in 'channels' list, moving to the top\n",
            "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n",
            "Solving environment: | \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\bdone\n",
            "\n",
            "# All requested packages already installed.\n",
            "\n",
            "Enabling notebook extension nglview-js-widgets/extension...\n",
            "Paths used for configuration of notebook: \n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.d/jupyterlab-plotly.json\n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.d/widgetsnbextension.json\n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.json\n",
            "Paths used for configuration of notebook: \n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.d/jupyterlab-plotly.json\n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.d/widgetsnbextension.json\n",
            "      - Validating: \u001b[32mOK\u001b[0m\n",
            "Paths used for configuration of notebook: \n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.d/jupyterlab-plotly.json\n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.d/widgetsnbextension.json\n",
            "    \t/usr/local/etc/jupyter/nbconfig/notebook.json\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#requires above cell\n",
        "from google.colab import output\n",
        "output.enable_custom_widget_manager()\n",
        "#!pip install -q ase\n",
        "\n",
        "\n",
        "import nglview\n",
        "\n",
        "#view = nglview.show_pdbid(\"3LPO\")  # load \"3pqr\" from RCSB PDB and display viewer widget\n",
        "#view\n",
        "#print (\"hello1\")\n",
        "\n",
        "#view.add_ball_and_stick()\n",
        "#view\n",
        "#3print (\"hello\")\n",
        "#view._display_image()"
      ],
      "metadata": {
        "id": "8qcTUjrkcJgq"
      },
      "execution_count": 18,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas\n",
        "# column Y is 25th letter in alphabet. that column has header \"nearest_class_rotrans\" Other headers are \"nearest_class_proscoH\" and \"nearest_class_prosco\"\n",
        "# chains are in \"chain1\" and \"chain2\", residues are in \"res1\" and \"res2\". insertino codes are \"ins1\" and \"ins2\"\n",
        "#pdbId = \"1gid\"\n",
        "#pdbId = \"3d2g\"\n",
        "#pdbId = \"3rg5\"\n",
        "pdbId = \"6ol3\"\n",
        "\n",
        "\n",
        "basePairingDataFrame = pandas.read_csv(pdbId+\"_zcut2.5_assignment.csv\")\n",
        "print (basePairingDataFrame.columns)\n",
        "basePairingDataFrame = basePairingDataFrame.reset_index()  # make sure indexes pair with number of rows\n",
        "#for index, row in basePairingDataFrame.iterrows():\n",
        "    #print(row['pdbid'], row['nr1'],row['nr2'])\n",
        "\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "X01vSKPst9u3",
        "outputId": "327f4e64-8cad-4e3f-ee65-abc89a00f085"
      },
      "execution_count": 17,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Index(['pdbid', 'model', 'chain1', 'res1', 'nr1', 'ins1', 'atom1', 'alt1',\n",
            "       'chain2', 'res2', 'nr2', 'ins2', 'atom2', 'alt2', 'image', 'dist',\n",
            "       'rmsd', 'proscoH_outlier', 'nearest_class_proscoH', 'max_proscoH',\n",
            "       'prosco_outlier', 'nearest_class_prosco', 'nearest_distance_prosco',\n",
            "       'rotrans_outlier', 'nearest_class_rotrans', 'nearest_distance_rotrans'],\n",
            "      dtype='object')\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 19,
      "metadata": {
        "id": "kMyKWa_ewoOT",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "outputId": "e6c71166-38a8-4409-8f43-dec78e94f330"
      },
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<nglview.component.ComponentViewer at 0x7f687c94ab10>"
            ]
          },
          "metadata": {},
          "execution_count": 19
        }
      ],
      "source": [
        "\n",
        "\n",
        "#view = nglview.show_ase(c60)\n",
        "#view.add_unitcell()\n",
        "#view.add_representation('spacefill', selection='#C', color='blue', radius='1.2')\n",
        "view = nglview.NGLWidget()\n",
        "view.add_pdbid(pdbId)\n",
        "#view.add_representation('licorice', selection='(1-300) ', color='blue', radius='1.2')\n",
        "\n",
        "\n",
        "\n",
        "#!conda install -c acellera -c conda-forge htmd\n",
        "#!htmd_register\n",
        "#from htmd import Molecule\n",
        "#from htmd.ui import *\n",
        "#mol=Molecule('1GID')\n",
        "\n",
        "\n",
        "#mol = view.from_pdb(\"porVO_chain_SH.xyz\")\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "view.clear_representations()\n",
        "view.add_representation('licorice', selection='not backbone', color='element', radius=.2, bondSpacing = 400)\n",
        "view.add_representation('cartoon', selection='backbone', color='element')\n",
        "\n",
        "atomPair = [ [ \"253.P\", \"220.P\" ], [ \"220.P\", \"253.P\" ] ];\n",
        "#atomPair = [  [ \"220.P\", \"253.P\" ] ];\n",
        "\n",
        "#view.add_representation( \"distance\", { atomPair: atomPair } );\n",
        "#print (view.add_representation('licorice', selection='(253 OR 220) and #P', color='element', radius='3.2', bondSpacing = 400)[\"atom1\"][\"x\"])\n",
        "for index, row in basePairingDataFrame.iterrows():\n",
        "    #print(row['pdbid'], row['nr1'],row['nr2'])\n",
        "    atom1String = str(row['nr1']) + \"C1'\"\n",
        "    atom2String = str(row['nr2']) + \"C1'\"\n",
        "    saengerClass = str(row['nearest_class_rotrans']).split(\"_\")[0] # split e.g. 20_A_U_c2_2A on \"_\" and take the zeroth element, in this example 20.\n",
        "    # Saenger classes are listed here http://ndbserver.rutgers.edu/ndbmodule/legends/saenger.html\n",
        "    #print (atom1String, atom2String,saengerClass)\n",
        "    #if (saengerClass == 19) :\n",
        "    if ((saengerClass == \"19\") or (saengerClass == \"20\") or (saengerClass == \"8\")): # WatsonCrick / WatsonCrick / Cis. 19:  purine-pyrimidine, 20 = pyrimidine-purine, 8 = purine-purine.\n",
        "        view.add_distance(atom_pair=[[atom1String, atom2String]], label_color=\"black\", labelType = \"text\", labelText = \"my text\", color = \"blue\")\n",
        "    # for some reaason this does not work:\n",
        "    #if ((saengerClass == \"1\") or (saengerClass == \"3\") or (saengerClass == \"12\") or (saengerClass == \"14\")): # WatsonCrick / WatsonCrick / Trans, offset. \n",
        "    #    view.add_distance(atom_pair=[[atom1String, atom2String]], label_color=\"black\", labelType = \"text\", labelText = \"my text\", color = \"orange\")\n",
        "\n",
        "#view.add_representation('spacefill', selection='61 OR 253', color='blue', radius='1.2', bondSpacing = 40)\n",
        "#view.get_coordinates() # takes an index\n",
        "#view.shape.add_cylinder( [ 0, 2, 7 ], [ 0, 0, 39 ], [ 1, 1, 0 ], 0.5)\n",
        "view"
      ],
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        "outputId": "a68abaaa-6741-49e8-a76a-c1d0c45d3102"
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      "execution_count": 20,
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