Structures_available_Variant_Course_May2024.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/glevans/PDBe_Notebooks/blob/main/Structures_available_Variant_Course_May2024.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "**<H1>Structures available</H1>**\n",
        "**Using PDBe-KB & 3D-Beacons to gain understanding on genetic variants**\n",
        "<img src=\"https://www.ebi.ac.uk/pdbe/docs_dev/logos/images/RGB/PDBe-logo-RGB_2013.png\" height=\"300\" align=\"right\">\n",
        "\n",
        "#Welcome to this notebook!\n",
        "\n",
        "To use this notebook in Colab (link at top of the page):\n",
        "\n",
        "*   you will need to have a Google account\n",
        "*   be logged in to Google Colab (by being logged into Google account)\n",
        "\n",
        "<br>\n",
        "\n",
        "You can also download this notebook and view it *via* a local installation of [Jupyter](https://jupyter.org/) (*i.e.* latest Jupyterlab or original Juptyer Notebook).\n",
        "\n",
        "Alternatively, the file can be downloaded and uploaded into a browser instance of [JupyterLab](https://jupyter.org/try-jupyter/lab/).\n",
        "\n",
        "<br>\n"
      ],
      "metadata": {
        "id": "QXp8HG3aOXzS"
      },
      "id": "QXp8HG3aOXzS"
    },
    {
      "cell_type": "markdown",
      "source": [
        "\n",
        "\n",
        "---\n",
        "\n",
        "  ## How to use this notebook:\n",
        "1. To run a code cell, click on the cell to select it. You will notice a play button (▶️) on the left side of the cell. Click on the play button or **press Shift+Enter** to run the code in the selected cell.\n",
        "2. The code will start executing, and you will see the output, if any, displayed below the code cell.\n",
        "3. Move to the next code cell and repeat steps 2 and 3 until you have executed all the desired code cells in sequence.\n",
        "4. The currently running step is indicated by a circle with a stop sign next to it.\n",
        "If you need to stop or interrupt the execution of a code cell, you can click on the stop button (■) located next to the play button.\n",
        "\n",
        "*Remember to run the code cells in the correct order, as their execution might depend on variables or functions defined in previous cells. You can modify the code in a code cell and re-run it to see updated results.*\n",
        "\n",
        "<br>\n",
        "\n",
        "---\n",
        "\n",
        "## Contact us\n",
        "\n",
        "If you experience any bugs please contact pdbehelp@ebi.ac.uk and put \"Help with\" and the title of the notebook in the subject line of the message.\n"
      ],
      "metadata": {
        "id": "6Mg5aemEWkiz"
      },
      "id": "6Mg5aemEWkiz"
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "# Why use this notebook:\n",
        "\n",
        "<img src=\"https://github.com/glevans/7ADD-workshop-2024/blob/main/Images/API_image.png?raw=true\" height=\"300\" align=\"right\">\n",
        "\n",
        "This interactive Python notebook demonstrates accessing **Protein Data Bank**,\n",
        "\n",
        "using some tools developed by the **Protein Data Bank in Europe (PDBe)**:\n",
        "\n",
        "<br>\n",
        "\n",
        "- [PDBe Knowledge Base -> pdbe-kb.org](https://www.ebi.ac.uk/pdbe/pdbe-kb/)\n",
        "\n",
        "- [3D Beacons -> 3d-beacons.org](https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/)\n",
        "\n",
        "<br>\n",
        "\n",
        "<p>An API (Application Programming Interface) is a programmatic way to obtain information.</p>\n",
        "\n",
        "<p>Virtually every webpage you visit is using one or more APIs.</p>\n",
        "\n",
        "<p>We will be tapping into the potential of APIs to more quickly access and assess information.</p>\n",
        "\n",
        "<p> </p>"
      ],
      "metadata": {
        "id": "OVmjjknE0Ntq"
      },
      "id": "OVmjjknE0Ntq"
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "*We will very briefly touch on:*\n",
        "### **3D-Beacons**\n",
        "\n",
        "The main purpose of 3D-Beacons is to provide programmatic access to **BOTH** experimentally determined and theoretical structures from one web location.\n",
        "\n",
        "Some example theoretical model providers:\n",
        "* SWISS-MODEL\n",
        "* AlphaFold DB\n",
        "* AlphaFill\n",
        "* ModelArchive\n",
        "* isoform.io\n",
        "* levylab\n",
        "\n",
        "A more comprehensive list is available here: [Data providers](https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/guidelines)\n",
        "\n",
        "For direct link to 3D-Beacons API interface, visit [3D-Beacons API page](https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/)\n",
        "\n",
        "A link to main webpage:\n",
        "[3D Beacons -> 3d-beacons.org](https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/)\n",
        "<br>"
      ],
      "metadata": {
        "id": "g3VQfvEXI3F7"
      },
      "id": "g3VQfvEXI3F7"
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "*We will focus more on:*\n",
        "### **Protein Data Bank in Europe Knowledge Base (PDBe-KB)**\n",
        "\n",
        "**PDBe-KB** provides more information and analysis specifically for experimentally-determined structures.\n",
        "\n",
        "**3D Beacons** is being used <i>'behind-the-scenes'</i> on the **PDBe-KB** pages to enable theoretical macromolecule models to be displayed alongside experimental models.\n",
        "\n",
        "**PDBe-KB** provides information on 3D macromolecular structures in the context of other macromolecular structures.\n",
        "\n",
        "With **PDBe-KB** webpages and its APIs, the following information can be accessed:\n",
        "\n",
        "* Identify PDB ids (aka multiple structures) known to contain related data due to one or more chains being associated with the same UniProt ID.\n",
        "* Insight on compounds & residues from considering these in the context with each other.\n",
        "* Mappings to CATH, EC, GO, InterPro, Pfam, SCOP, etc\n",
        "* and more...\n",
        "\n",
        "For direct link to PDBe-KB's Aggregated API, visit [PDBe-KB Aggregated API page](https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/)\n",
        "\n",
        "A link to main webpage:\n",
        "[PDBe Knowledge Base -> pdbe-kb.org](https://www.ebi.ac.uk/pdbe/pdbe-kb/)\n",
        "<br>\n"
      ],
      "metadata": {
        "id": "zdgXov-aJNYi"
      },
      "id": "zdgXov-aJNYi"
    },
    {
      "cell_type": "markdown",
      "source": [
        "# 1)  Setting up"
      ],
      "metadata": {
        "id": "cLqmWcyS6tRl"
      },
      "id": "cLqmWcyS6tRl"
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "R7fad_36A4PL",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "d639021c-202e-49a0-e7b2-b587488ca1b1",
        "cellView": "form"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Succesfully installed!\n"
          ]
        }
      ],
      "source": [
        "#@title Press shift+enter to start\n",
        "\n",
        "# @markdown <br>\n",
        "# @markdown This section installs libraries and sets up Python code to extract information from PDBe-KB's APIs.\n",
        "# @markdown <br>\n",
        "# @markdown <br>\n",
        "# @markdown After running this cell, this Notebook will be able to connect 3D-Beacons and PDBe-KB's APIs.\n",
        "# @markdown <br>\n",
        "# @markdown It will create summary tables for some information about the structures associated with a UniProt ID.\n",
        "# @markdown <br>\n",
        "# @markdown <br>\n",
        "# @markdown The information listed below can also be found either on PDBe-KB pages and/or utilizing 3D Beacons.\n",
        "# @markdown <br>\n",
        "\n",
        "\n",
        "######## LIBRARIES\n",
        "\n",
        "import requests, sys, json\n",
        "import pandas as pd\n",
        "from pprint import pprint\n",
        "\n",
        "print(\"Succesfully installed!\")\n",
        "\n",
        "####### 3D BEACONS FUNCTIONS\n",
        "#defining functions for search and summary\n",
        "\n",
        "def _search_3DBeacons(UniProt_ID):\n",
        "    try:\n",
        "        api_url = f\"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/v2/uniprot/summary/{UniProt_ID}.json\"\n",
        "        response = requests.get(api_url)\n",
        "        response.raise_for_status()\n",
        "        return response.json().get(\"structures\", [])\n",
        "    except requests.exceptions.RequestException as err:\n",
        "        print(\"Double check if the UniProt id is correct.\")\n",
        "        print()\n",
        "        raise Exception(f\"Error fetching data: {err}\")\n",
        "\n",
        "def _create_structure_dataframe(structures):\n",
        "    if structures:\n",
        "        details_list = [\n",
        "            [\n",
        "                s[\"summary\"][\"model_identifier\"],\n",
        "                s[\"summary\"][\"model_category\"],\n",
        "                s[\"summary\"][\"provider\"],\n",
        "                s[\"summary\"][\"uniprot_start\"],\n",
        "                s[\"summary\"][\"uniprot_end\"],\n",
        "            ]\n",
        "            for s in structures\n",
        "        ]\n",
        "        columns = [\"ID\", \"Type\", \"Provider\", \"UniProt start\", \"UniProt end\"]\n",
        "        df = pd.DataFrame(details_list, columns=columns)\n",
        "        return df\n",
        "    else:\n",
        "        raise Exception(\"No structures found for the given UniProt ID.\")\n",
        "\n",
        "def all_structure_data(UniProt_ID):\n",
        "    try:\n",
        "        structures = _search_3DBeacons(UniProt_ID)\n",
        "        return _create_structure_dataframe(structures)\n",
        "    except Exception as e:\n",
        "        return f\"Error: {e}\"\n",
        "\n",
        "def displaying_3dbeacon_summary(UniProt_ID):\n",
        "    df_3D_beacons = all_structure_data(UniProt_ID)\n",
        "    if type(df_3D_beacons) == str:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "    elif df_3D_beacons is not None:\n",
        "        num_rows = df_3D_beacons.shape[0]\n",
        "        print(f\"There are {num_rows} structures available associated with UniProt ID {UniProt_ID}\")\n",
        "        print()\n",
        "        return df_3D_beacons.head(num_rows)\n",
        "    else:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "\n",
        "def displaying_3dbeacon_exp_summary(UniProt_ID):\n",
        "    df_3D_beacons = all_structure_data(UniProt_ID)\n",
        "    if type(df_3D_beacons) == str:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "    elif df_3D_beacons is not None:\n",
        "        df_3D_beacons2 = df_3D_beacons.drop(df_3D_beacons[df_3D_beacons['Type'] == 'TEMPLATE-BASED'].index)\n",
        "        df_3D_beacons3 = df_3D_beacons2.drop(df_3D_beacons[df_3D_beacons['Type'] == 'CONFORMATIONAL ENSEMBLE'].index)\n",
        "        df_3D_beacons4 = df_3D_beacons3.drop(df_3D_beacons[df_3D_beacons['Type'] == 'AB-INITIO'].index)\n",
        "        num_rows = df_3D_beacons4.shape[0]\n",
        "        print(f\"There are {num_rows} different structures, where experimental data was used for the structure, associated with UniProt ID {UniProt_ID}\")\n",
        "        print()\n",
        "        return df_3D_beacons4.head(num_rows)\n",
        "    else:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "\n",
        "####### 3D BEACONS FUNCTIONS\n",
        "#defining functions for reporting urls\n",
        "\n",
        "def links_for_structures(UniProt_ID):\n",
        "    try:\n",
        "        structures = _search_3DBeacons(UniProt_ID)\n",
        "        print(f\"There are {len(structures)} listed associated with UniProt id {UniProt_ID}\")\n",
        "        list_of_lists =[]\n",
        "        for index in range(0, len(structures)):\n",
        "            structure_details = structures[index]['summary']\n",
        "            model_identifier = structure_details['model_identifier']\n",
        "            model_catergory = structure_details['model_category']\n",
        "            provider = structure_details['provider']\n",
        "            model_url = structure_details['model_url']\n",
        "            model_format = structure_details['model_format']\n",
        "            label = f\"Click on url to download the coordinate file - {model_format} format:\"\n",
        "            details_list = {model_identifier : [label, model_url]}\n",
        "            print()\n",
        "            pprint(details_list)\n",
        "            print()\n",
        "    except Exception as e:\n",
        "        return f\"Error: {e}\"\n",
        "\n",
        "def display_urls_for_structures(UniProt_ID):\n",
        "    try:\n",
        "        link_list = links_for_structures(UniProt_ID)\n",
        "    except Exception as e:\n",
        "        return f\"An error occurred: {e}\"\n",
        "\n",
        "######## PDBe-KB FUNCTIONS\n",
        "#defining functions for search and summary for variants\n",
        "\n",
        "def api_structure_PDBeKB(UniProt_ID):\n",
        "    try:\n",
        "        requestURL = f\"https://www.ebi.ac.uk/pdbe/graph-api/uniprot/unipdb/{UniProt_ID}\"\n",
        "        response = requests.get(requestURL)\n",
        "        response.raise_for_status()\n",
        "        return json.loads(response.text)\n",
        "    except requests.exceptions.RequestException as err:\n",
        "        print(f\"Request Error: {err}\")\n",
        "        return None\n",
        "\n",
        "def _parse_variant_data(structure_data, UniProt_ID):\n",
        "\n",
        "    if type(structure_data) == dict:\n",
        "        structure_details = structure_data[UniProt_ID]['data']\n",
        "        amount = len(structure_details)\n",
        "        UniProt_ID = UniProt_ID\n",
        "        UniProt_summary = []\n",
        "        UniProt_summary_list = []\n",
        "        row_list = []\n",
        "\n",
        "        for index in range(0, amount): # PDB ids\n",
        "\n",
        "            pdb_id = structure_details[index]['accession']\n",
        "            accession_item = structure_details[index]\n",
        "\n",
        "            modified_residues = _modified_list(accession_item['residues'])\n",
        "            mutated_residues = _mutated_list(accession_item['residues'])\n",
        "\n",
        "            if modified_residues == None and mutated_residues == None:\n",
        "                pass\n",
        "            elif modified_residues == None and mutated_residues != None:\n",
        "                row_list = []\n",
        "                for index in range(0, len(mutated_residues)):\n",
        "                    mutated_residues[index].update({\"PDB_ID\" : pdb_id})\n",
        "                row_list.append(mutated_residues)\n",
        "            elif modified_residues != None and mutated_residues == None:\n",
        "                row_list = []\n",
        "                for index in range(0, len(modified_residues)):\n",
        "                    modified_residues[index].update({\"PDB_ID\" : pdb_id})\n",
        "                row_list.append(modified_residues)\n",
        "            elif modified_residues != None and mutated_residues != None:\n",
        "                row_list = []\n",
        "                for index in range(0, len(modified_residues)):\n",
        "                    modified_residues[index].update({\"PDB_ID\" : pdb_id})\n",
        "                row_list.append(modified_residues)\n",
        "                for index in range(0, len(mutated_residues)):\n",
        "                    mutated_residues[index].update({\"PDB_ID\" : pdb_id})\n",
        "                row_list.append(mutated_residues)\n",
        "            UniProt_summary_list.extend(row_list)\n",
        "\n",
        "        for number in range(0,len(UniProt_summary_list)):\n",
        "            UniProt_summary += UniProt_summary_list[number]\n",
        "        return UniProt_summary\n",
        "\n",
        "def _modified_list(residues):\n",
        "    modified_list = []  # Initialize the list outside of the loop\n",
        "    for residue_info in residues:\n",
        "        if 'modification' in residue_info:\n",
        "            modified = _modification_info(residue_info)\n",
        "            modified_list.append(modified)  # Append the mutation to the list\n",
        "    if modified_list == []:\n",
        "        return None\n",
        "    else:\n",
        "        return modified_list  # Return the list\n",
        "\n",
        "def _mutated_list(residues):\n",
        "    mutated_list = []  # Initialize the list outside of the loop\n",
        "    for residue_info in residues:\n",
        "        if 'mutation' in residue_info:\n",
        "            mutation = _mutation_info(residue_info)\n",
        "            mutated_list.append(mutation)  # Append the mutation to the list\n",
        "    if mutated_list == []:\n",
        "        return None\n",
        "    else:\n",
        "        return mutated_list  # Return the list\n",
        "\n",
        "def _mutation_info(residue_info):\n",
        "    if residue_info['startIndex'] == residue_info['endIndex']:\n",
        "        residue_position = residue_info['startIndex']\n",
        "        UniProt_amino_acid = residue_info['startCode']\n",
        "        coordinate_amino_acid = residue_info['pdbCode']\n",
        "        change = residue_info['mutationType']\n",
        "        mutated_residue = {'change': change, 'position' : residue_position, 'from_aa' : UniProt_amino_acid, 'to_aa' : coordinate_amino_acid}\n",
        "        return mutated_residue\n",
        "\n",
        "def _modification_info(residue_info):\n",
        "    if residue_info['startIndex'] == residue_info['endIndex']:\n",
        "        residue_position = residue_info['startIndex']\n",
        "        UniProt_amino_acid = residue_info['startCode']\n",
        "        coordinate_amino_acid = residue_info['pdbCode']\n",
        "        change = \"Modification\"\n",
        "        modified_residue = {'change': change, 'position' : residue_position, 'from_aa' : UniProt_amino_acid, 'to_aa' : coordinate_amino_acid}\n",
        "        return modified_residue\n",
        "\n",
        "def variant_summary(UniProt_ID):\n",
        "    try:\n",
        "        structure_data = api_structure_PDBeKB(UniProt_ID)\n",
        "        UniProt_info = _parse_variant_data(structure_data, UniProt_ID)\n",
        "        return UniProt_info\n",
        "    except Exception as e:\n",
        "        print(\"Double check if the UniProt id is correct.\")\n",
        "        print()\n",
        "        return f\"Error: {e}\"\n",
        "\n",
        "def displaying_variant_summary(UniProt_ID):\n",
        "    list_of_dict = variant_summary(UniProt_ID)\n",
        "    if type(list_of_dict) == str:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "    elif list_of_dict== []:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "    elif list_of_dict is not None:\n",
        "        print(f\"This is the output from entering the UniProt ID {UniProt_ID}.\")\n",
        "        df_variants = pd.DataFrame.from_dict(list_of_dict)\n",
        "        df_variants2 = df_variants.sort_values(['position'], na_position='first', ascending=True, key=pd.to_numeric)\n",
        "        df_variants3 = df_variants2.drop_duplicates() # Remove duplicate instance of same conflicts for same PDB ids\n",
        "        df_variants4 = df_variants3.reset_index()\n",
        "        df_variants5 = df_variants4.drop(['index'], axis=1)\n",
        "        num_rows = df_variants5.shape[0]\n",
        "        print()\n",
        "        return df_variants5.head(num_rows)\n",
        "    else:\n",
        "        print(\"Something went wrong. Check the UniProt ID.\")\n",
        "\n",
        "######## PDBe-KB FUNCTIONS\n",
        "#defining functions for search and summary\n",
        "\n",
        "def parse_general_structure_data(structure_data, UniProt_ID):\n",
        "    structure_details = structure_data[UniProt_ID]['data']\n",
        "\n",
        "    accession_id_list = []\n",
        "    UniProt_summary = {}\n",
        "    print(f\"There are {len(structure_details)} experimentally-determined structures associated with UniProt id {UniProt_ID}.\")\n",
        "    print()\n",
        "\n",
        "    for number in range(0,len(structure_details)):\n",
        "        accession_item = structure_details[number]\n",
        "        accession_id = accession_item['accession']\n",
        "        accession_id_list.append(accession_id)\n",
        "\n",
        "        additionalData = accession_item['additionalData']\n",
        "        resolution = additionalData['resolution']\n",
        "        resolution = round(resolution,3)\n",
        "        experiment = additionalData['experiment']\n",
        "\n",
        "        if experiment == 'X-ray diffraction':\n",
        "            concatenated_list = [experiment,resolution]\n",
        "            UniProt_row = {accession_item['accession'] : concatenated_list}\n",
        "        elif experiment == 'Electron Microscopy':\n",
        "            concatenated_list = [experiment,resolution]\n",
        "            UniProt_row = {accession_item['accession'] : concatenated_list}\n",
        "        elif experiment == 'Solution NMR':\n",
        "            concatenated_list = [experiment,None]\n",
        "            UniProt_row = {accession_item['accession'] : concatenated_list}\n",
        "        else:\n",
        "            concatenated_list = [experiment,resolution]\n",
        "            UniProt_row = {accession_item['accession'] : concatenated_list}\n",
        "        UniProt_summary.update(UniProt_row)\n",
        "    return UniProt_summary\n",
        "\n",
        "def general_summary(UniProt_ID):\n",
        "  try:\n",
        "    structure_data = api_structure_PDBeKB(UniProt_ID)\n",
        "    UniProt_info = parse_general_structure_data(structure_data, UniProt_ID)\n",
        "    return(UniProt_info)\n",
        "  except Exception as e:\n",
        "    print(\"Double check if the UniProt id is correct.\")\n",
        "    print()\n",
        "    return f\"Error: {e}\"\n",
        "\n",
        "def display_exp_structure_summary(UniProt_ID):\n",
        "    try:\n",
        "        data = general_summary(UniProt_ID)\n",
        "        if type(data) == str:\n",
        "            print()\n",
        "            print(\"Something has gone wrong. Double-check if the UniProt ID is okay.\")\n",
        "        else:\n",
        "            df1 = pd.DataFrame.from_dict(data, orient=\"index\", columns=['Experimental Method', 'Resolution (in Angstroms)'])\n",
        "            num_rows = df1.shape[0]\n",
        "            return df1.head(num_rows)\n",
        "    except Exception as e:\n",
        "        print(f\"An error occurred: {e}\")\n",
        "\n",
        "def comma_pdb_id_list(UniProt_ID):\n",
        "    try:\n",
        "        data = general_summary(UniProt_ID)\n",
        "        if type(data) == str:\n",
        "            print()\n",
        "            print(\"Something has gone wrong. Double-check if the UniProt ID is okay.\")\n",
        "        else:\n",
        "            df1 = pd.DataFrame.from_dict(data, orient=\"index\", columns=['Experimental Method', 'Resolution (in Angstroms)'])\n",
        "            index_as_list = df1.index.tolist()\n",
        "            print(', '.join(map(str, index_as_list)))\n",
        "    except Exception as e:\n",
        "        print(f\"An error occurred: {e}\")\n",
        "\n",
        "######## PDBe-KB FUNCTION\n",
        "#converting a json into a comma-delimited list\n",
        "\n",
        "def getting_list_of_PDB_ids(load):\n",
        "    PDB_ID_list = []\n",
        "    for item in range (0, len(load)):\n",
        "        PDBid = load[item][\"PDB_ID\"]\n",
        "        PDB_ID_list.append(PDBid)\n",
        "    str_PDB_ID_list = [str(item) for item in PDB_ID_list]\n",
        "    delimiter_comma = \", \"\n",
        "    print(delimiter_comma.join(str_PDB_ID_list))\n",
        "\n",
        "######## PDBe-KB FUNCTION\n",
        "#generate comma-delimited list of nonmodified PDB IDs\n",
        "\n",
        "def nonmodified_PDB_IDs(UniProt_ID):\n",
        "    general = general_summary(UniProt_ID)\n",
        "    variant = variant_summary(UniProt_ID)\n",
        "\n",
        "    PDB_ID_list = []\n",
        "    for item in range (0, len(variant)):\n",
        "        PDBid = variant[item][\"PDB_ID\"]\n",
        "        PDB_ID_list.append(PDBid)\n",
        "    PDB_IDs_with_variant_list = list(dict.fromkeys(PDB_ID_list))\n",
        "    all_PDB_ID = list(general.keys())\n",
        "\n",
        "    s = set(PDB_IDs_with_variant_list)\n",
        "    PDB_IDs_without_variant_list = [x for x in all_PDB_ID if x not in s]\n",
        "    print(f\"Of these there are {len(PDB_IDs_without_variant_list)} experimentally-determined structures without any modifications or discrepancies with UniProt id {UniProt_ID}.\")\n",
        "\n",
        "    print()\n",
        "\n",
        "    PDB_ID_list = []\n",
        "    for item in range (0, len(PDB_IDs_without_variant_list)):\n",
        "        PDBid = PDB_IDs_without_variant_list[item]\n",
        "        PDB_ID_list.append(PDBid)\n",
        "    str_PDB_ID_list = [str(item) for item in PDB_ID_list]\n",
        "    delimiter_comma = \", \"\n",
        "    print(delimiter_comma.join(str_PDB_ID_list))\n",
        "\n",
        "######## PDBe-KB and 3D Beacon FUNCTION\n",
        "#converting a json into a comma-delimited list\n",
        "\n",
        "def diff_btwn_PDBeKB_3DBeacons(UniProt_ID):\n",
        "    print(\"Output from PDBe-KB:\")\n",
        "    general = general_summary(UniProt_ID)\n",
        "    all_PDB_IDs = list(general.keys())\n",
        "\n",
        "    print(\"Output from 3D-Beacons for experimentally-determined structures:\")\n",
        "    df_all_expdata = displaying_3dbeacon_exp_summary(UniProt_ID)\n",
        "    all_expdata_list = df_all_expdata [\"ID\"].tolist()\n",
        "\n",
        "    s = set(all_expdata_list)\n",
        "    PDB_ids_not_in_3Dbeacons = [x for x in all_PDB_IDs if x not in s]\n",
        "    print(PDB_ids_not_in_3Dbeacons)"
      ],
      "id": "R7fad_36A4PL"
    },
    {
      "cell_type": "markdown",
      "source": [
        "# 2)  Structures available using **3D-Beacons**\n",
        "This section reports on predicted and experimentally-determined structures structures for a UniProt ID that are available *via* **3D-Beacons**."
      ],
      "metadata": {
        "id": "ZGUCKZwiNXhn"
      },
      "id": "ZGUCKZwiNXhn"
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "These structures/models have a *'type'* assigned such as:\n",
        "\n",
        "* EXPERIMENTALLY DETERMINED\n",
        "* CONFORMATIONAL ENSEMBLE\n",
        "* TEMPLATE-BASED\n",
        "* AB-INITIO\n",
        "\n",
        "If the *'Type'* is not 'EXPERIMENTALLY DETERMINED' then it is a predicted structure."
      ],
      "metadata": {
        "id": "V4nFBuNEQ7LA"
      },
      "id": "V4nFBuNEQ7LA"
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 2.1.  Get predicted structures, as well as experimentally determined structures associated with a UniProt ID\n",
        "#@markdown  In this sub-section you will be able to retrieve BOTH predicted structures, as well as experimentally determined structures associated with an Uniprot accession ID.\n",
        "#@markdown  <br>\n",
        "#@markdown  <br>\n",
        "#@markdown  With 3D-Beacons there are options to search based on sequence and Ensembl id as well.\n",
        "#@markdown  <br>\n",
        "#@markdown  <br>\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#Run this code to perform a API call and load result into a DataFrame\n",
        "displaying_3dbeacon_summary(UniProt_ID)\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "15665318-242f-495f-c291-2911e1f21e4e",
        "cellView": "form",
        "id": "Md-cOAlsHtpx"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "There are 54 structures available associated with UniProt ID P13569\n",
            "\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "                         ID                       Type      Provider  \\\n",
              "0                      2pze  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "1                      7qi1  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "2                      2pzg  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "3                      5tfj  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "4                      6wbs  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "5                      6hep  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "6                      5tf8  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "7                      5tfa  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "8                      5tfb  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "9                      5tfd  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "10                     5tff  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "11                     5tfi  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "12                     5tfg  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "13                     5tgk  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "14                     5tfc  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "15                     5tf7  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "16                     6gjs  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "17                     2pzf  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "18                     2bbs  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "19                     4wz6  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "20                     5d2d  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "21                     6rqr  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "22                     1xmi  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "23                     1xmj  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "24                     2bbt  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "25                     6gjq  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "26                     2bbo  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "27                     6gju  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "28                     6uk1  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "29                     7svd  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "30                     8ubr  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "31                     6ze1  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "32                     5d3f  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "33                     5d3e  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "34                     8eio  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "35                     3isw  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "36                     6gk4  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "37                     6gkd  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "38                     8eiq  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "39                     6msm  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "40                     6o1v  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "41                     6o2p  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "42                     8eig  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "43                     7sv7  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "44                     5uak  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "45                     7svr  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "46                     8fzq  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "47                     8ej1  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "48                     2lob  EXPERIMENTALLY DETERMINED          PDBe   \n",
              "49   P13569_1-1451:8eio.1.A             TEMPLATE-BASED   SWISS-MODEL   \n",
              "50  P13569_42-1439:6d3r.1.A             TEMPLATE-BASED   SWISS-MODEL   \n",
              "51   P13569_3-1436:7svr.1.A             TEMPLATE-BASED   SWISS-MODEL   \n",
              "52             AF-P13569-F1                  AB-INITIO  AlphaFold DB   \n",
              "53                   P13569             TEMPLATE-BASED     AlphaFill   \n",
              "\n",
              "    UniProt start  UniProt end  \n",
              "0             387          646  \n",
              "1             747          774  \n",
              "2             375          646  \n",
              "3             387          646  \n",
              "4             388          646  \n",
              "5             747          774  \n",
              "6             387          646  \n",
              "7             387          646  \n",
              "8             387          646  \n",
              "9             387          646  \n",
              "10            387          646  \n",
              "11            387          646  \n",
              "12            387          646  \n",
              "13            387          646  \n",
              "14            387          646  \n",
              "15            387          646  \n",
              "16            387          646  \n",
              "17            387          646  \n",
              "18            388          678  \n",
              "19            389          678  \n",
              "20            747          774  \n",
              "21           1101         1101  \n",
              "22            388          678  \n",
              "23            388          678  \n",
              "24            388          678  \n",
              "25            387          646  \n",
              "26            388          678  \n",
              "27            387          646  \n",
              "28           1202         1430  \n",
              "29              1         1480  \n",
              "30              1         1480  \n",
              "31            387          646  \n",
              "32            747          774  \n",
              "33            762          801  \n",
              "34              1         1480  \n",
              "35              5           22  \n",
              "36            387          646  \n",
              "37            387          646  \n",
              "38              1         1480  \n",
              "39              1         1480  \n",
              "40              1         1480  \n",
              "41              1         1480  \n",
              "42              1         1480  \n",
              "43              1         1480  \n",
              "44              1         1480  \n",
              "45              1         1480  \n",
              "46              1         1480  \n",
              "47              1         1480  \n",
              "48           1473         1480  \n",
              "49              1         1451  \n",
              "50             42         1439  \n",
              "51              3         1436  \n",
              "52              1         1480  \n",
              "53              1         1480  "
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-08dec5da-4f4f-4361-8833-83827db7d627\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>ID</th>\n",
              "      <th>Type</th>\n",
              "      <th>Provider</th>\n",
              "      <th>UniProt start</th>\n",
              "      <th>UniProt end</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>2pze</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>7qi1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>2pzg</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>375</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>5tfj</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>6wbs</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>6hep</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>5tf8</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>5tfa</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>5tfb</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>5tfd</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>10</th>\n",
              "      <td>5tff</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>11</th>\n",
              "      <td>5tfi</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>12</th>\n",
              "      <td>5tfg</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>13</th>\n",
              "      <td>5tgk</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>14</th>\n",
              "      <td>5tfc</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>15</th>\n",
              "      <td>5tf7</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>16</th>\n",
              "      <td>6gjs</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>17</th>\n",
              "      <td>2pzf</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18</th>\n",
              "      <td>2bbs</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>19</th>\n",
              "      <td>4wz6</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>389</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>20</th>\n",
              "      <td>5d2d</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>21</th>\n",
              "      <td>6rqr</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1101</td>\n",
              "      <td>1101</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>22</th>\n",
              "      <td>1xmi</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>23</th>\n",
              "      <td>1xmj</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>24</th>\n",
              "      <td>2bbt</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>25</th>\n",
              "      <td>6gjq</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>26</th>\n",
              "      <td>2bbo</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>27</th>\n",
              "      <td>6gju</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>28</th>\n",
              "      <td>6uk1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1202</td>\n",
              "      <td>1430</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>29</th>\n",
              "      <td>7svd</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>30</th>\n",
              "      <td>8ubr</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>31</th>\n",
              "      <td>6ze1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>32</th>\n",
              "      <td>5d3f</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>33</th>\n",
              "      <td>5d3e</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>762</td>\n",
              "      <td>801</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>34</th>\n",
              "      <td>8eio</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>35</th>\n",
              "      <td>3isw</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>5</td>\n",
              "      <td>22</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>36</th>\n",
              "      <td>6gk4</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>37</th>\n",
              "      <td>6gkd</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>38</th>\n",
              "      <td>8eiq</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>39</th>\n",
              "      <td>6msm</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>40</th>\n",
              "      <td>6o1v</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>41</th>\n",
              "      <td>6o2p</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>42</th>\n",
              "      <td>8eig</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>43</th>\n",
              "      <td>7sv7</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>44</th>\n",
              "      <td>5uak</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>45</th>\n",
              "      <td>7svr</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>46</th>\n",
              "      <td>8fzq</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>47</th>\n",
              "      <td>8ej1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>48</th>\n",
              "      <td>2lob</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1473</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>49</th>\n",
              "      <td>P13569_1-1451:8eio.1.A</td>\n",
              "      <td>TEMPLATE-BASED</td>\n",
              "      <td>SWISS-MODEL</td>\n",
              "      <td>1</td>\n",
              "      <td>1451</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>50</th>\n",
              "      <td>P13569_42-1439:6d3r.1.A</td>\n",
              "      <td>TEMPLATE-BASED</td>\n",
              "      <td>SWISS-MODEL</td>\n",
              "      <td>42</td>\n",
              "      <td>1439</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>51</th>\n",
              "      <td>P13569_3-1436:7svr.1.A</td>\n",
              "      <td>TEMPLATE-BASED</td>\n",
              "      <td>SWISS-MODEL</td>\n",
              "      <td>3</td>\n",
              "      <td>1436</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>52</th>\n",
              "      <td>AF-P13569-F1</td>\n",
              "      <td>AB-INITIO</td>\n",
              "      <td>AlphaFold DB</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>53</th>\n",
              "      <td>P13569</td>\n",
              "      <td>TEMPLATE-BASED</td>\n",
              "      <td>AlphaFill</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
              "\n",
              "  <div class=\"colab-df-container\">\n",
              "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-08dec5da-4f4f-4361-8833-83827db7d627')\"\n",
              "            title=\"Convert this dataframe to an interactive table.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
              "    <path d=\"M120-120v-720h720v720H120Zm60-500h600v-160H180v160Zm220 220h160v-160H400v160Zm0 220h160v-160H400v160ZM180-400h160v-160H180v160Zm440 0h160v-160H620v160ZM180-180h160v-160H180v160Zm440 0h160v-160H620v160Z\"/>\n",
              "  </svg>\n",
              "    </button>\n",
              "\n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    .colab-df-buttons div {\n",
              "      margin-bottom: 4px;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "    <script>\n",
              "      const buttonEl =\n",
              "        document.querySelector('#df-08dec5da-4f4f-4361-8833-83827db7d627 button.colab-df-convert');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      async function convertToInteractive(key) {\n",
              "        const element = document.querySelector('#df-08dec5da-4f4f-4361-8833-83827db7d627');\n",
              "        const dataTable =\n",
              "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "          + ' to learn more about interactive tables.';\n",
              "        element.innerHTML = '';\n",
              "        dataTable['output_type'] = 'display_data';\n",
              "        await google.colab.output.renderOutput(dataTable, element);\n",
              "        const docLink = document.createElement('div');\n",
              "        docLink.innerHTML = docLinkHtml;\n",
              "        element.appendChild(docLink);\n",
              "      }\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "\n",
              "<div id=\"df-0c0d10ca-4ab6-4dc4-bccb-17713893fef9\">\n",
              "  <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-0c0d10ca-4ab6-4dc4-bccb-17713893fef9')\"\n",
              "            title=\"Suggest charts\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "     width=\"24px\">\n",
              "    <g>\n",
              "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
              "    </g>\n",
              "</svg>\n",
              "  </button>\n",
              "\n",
              "<style>\n",
              "  .colab-df-quickchart {\n",
              "      --bg-color: #E8F0FE;\n",
              "      --fill-color: #1967D2;\n",
              "      --hover-bg-color: #E2EBFA;\n",
              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
              "      --disabled-bg-color: #DDD;\n",
              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
              "      --hover-fill-color: #FFFFFF;\n",
              "      --disabled-bg-color: #3B4455;\n",
              "      --disabled-fill-color: #666;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart {\n",
              "    background-color: var(--bg-color);\n",
              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
              "    fill: var(--fill-color);\n",
              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "    fill: var(--button-hover-fill-color);\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
              "    }\n",
              "    20% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    30% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-0c0d10ca-4ab6-4dc4-bccb-17713893fef9 button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "summary": "{\n  \"name\": \"displaying_3dbeacon_summary(UniProt_ID)\",\n  \"rows\": 54,\n  \"fields\": [\n    {\n      \"column\": \"ID\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 54,\n        \"samples\": [\n          \"4wz6\",\n          \"P13569_1-1451:8eio.1.A\",\n          \"2lob\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"Type\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"EXPERIMENTALLY DETERMINED\",\n          \"TEMPLATE-BASED\",\n          \"AB-INITIO\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"Provider\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 4,\n        \"samples\": [\n          \"SWISS-MODEL\",\n          \"AlphaFill\",\n          \"PDBe\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"UniProt start\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 326,\n        \"min\": 1,\n        \"max\": 1473,\n        \"num_unique_values\": 13,\n        \"samples\": [\n          42,\n          5,\n          387\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"UniProt end\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 408,\n        \"min\": 22,\n        \"max\": 1480,\n        \"num_unique_values\": 11,\n        \"samples\": [\n          1480,\n          646,\n          1439\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 2
        }
      ],
      "id": "Md-cOAlsHtpx"
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 2.2. Get experimentally-determined structural data associated with a UniProt ID\n",
        "#@markdown  In this sub-section you will be able to retrieve experimentally determined data (including the wwPDB and a curated repository of small angle scattering data and models) associated with an Uniprot accession ID.\n",
        "#@markdown  <br>\n",
        "#@markdown  <br>\n",
        "#@markdown  <br>\n",
        "\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#Run this code to perform a API call and load result into a DataFrame\n",
        "displaying_3dbeacon_exp_summary(UniProt_ID)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "cellView": "form",
        "id": "Q62C_xQt3ZJe",
        "outputId": "85424199-a91f-4c4f-e96a-ad4505471419"
      },
      "id": "Q62C_xQt3ZJe",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "There are 49 different structures, where experimental data was used for the structure, associated with UniProt ID P13569\n",
            "\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "      ID                       Type Provider  UniProt start  UniProt end\n",
              "0   2pze  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "1   7qi1  EXPERIMENTALLY DETERMINED     PDBe            747          774\n",
              "2   2pzg  EXPERIMENTALLY DETERMINED     PDBe            375          646\n",
              "3   5tfj  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "4   6wbs  EXPERIMENTALLY DETERMINED     PDBe            388          646\n",
              "5   6hep  EXPERIMENTALLY DETERMINED     PDBe            747          774\n",
              "6   5tf8  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "7   5tfa  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "8   5tfb  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "9   5tfd  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "10  5tff  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "11  5tfi  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "12  5tfg  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "13  5tgk  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "14  5tfc  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "15  5tf7  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "16  6gjs  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "17  2pzf  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "18  2bbs  EXPERIMENTALLY DETERMINED     PDBe            388          678\n",
              "19  4wz6  EXPERIMENTALLY DETERMINED     PDBe            389          678\n",
              "20  5d2d  EXPERIMENTALLY DETERMINED     PDBe            747          774\n",
              "21  6rqr  EXPERIMENTALLY DETERMINED     PDBe           1101         1101\n",
              "22  1xmi  EXPERIMENTALLY DETERMINED     PDBe            388          678\n",
              "23  1xmj  EXPERIMENTALLY DETERMINED     PDBe            388          678\n",
              "24  2bbt  EXPERIMENTALLY DETERMINED     PDBe            388          678\n",
              "25  6gjq  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "26  2bbo  EXPERIMENTALLY DETERMINED     PDBe            388          678\n",
              "27  6gju  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "28  6uk1  EXPERIMENTALLY DETERMINED     PDBe           1202         1430\n",
              "29  7svd  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "30  8ubr  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "31  6ze1  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "32  5d3f  EXPERIMENTALLY DETERMINED     PDBe            747          774\n",
              "33  5d3e  EXPERIMENTALLY DETERMINED     PDBe            762          801\n",
              "34  8eio  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "35  3isw  EXPERIMENTALLY DETERMINED     PDBe              5           22\n",
              "36  6gk4  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "37  6gkd  EXPERIMENTALLY DETERMINED     PDBe            387          646\n",
              "38  8eiq  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "39  6msm  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "40  6o1v  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "41  6o2p  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "42  8eig  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "43  7sv7  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "44  5uak  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "45  7svr  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "46  8fzq  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "47  8ej1  EXPERIMENTALLY DETERMINED     PDBe              1         1480\n",
              "48  2lob  EXPERIMENTALLY DETERMINED     PDBe           1473         1480"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-cb1e0da2-5739-4fa0-9c90-3d967eb85ab6\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>ID</th>\n",
              "      <th>Type</th>\n",
              "      <th>Provider</th>\n",
              "      <th>UniProt start</th>\n",
              "      <th>UniProt end</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>2pze</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>7qi1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>2pzg</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>375</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>5tfj</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>6wbs</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>6hep</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>5tf8</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>5tfa</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>5tfb</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>5tfd</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>10</th>\n",
              "      <td>5tff</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>11</th>\n",
              "      <td>5tfi</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>12</th>\n",
              "      <td>5tfg</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>13</th>\n",
              "      <td>5tgk</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>14</th>\n",
              "      <td>5tfc</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>15</th>\n",
              "      <td>5tf7</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>16</th>\n",
              "      <td>6gjs</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>17</th>\n",
              "      <td>2pzf</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18</th>\n",
              "      <td>2bbs</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>19</th>\n",
              "      <td>4wz6</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>389</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>20</th>\n",
              "      <td>5d2d</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>21</th>\n",
              "      <td>6rqr</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1101</td>\n",
              "      <td>1101</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>22</th>\n",
              "      <td>1xmi</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>23</th>\n",
              "      <td>1xmj</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>24</th>\n",
              "      <td>2bbt</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>25</th>\n",
              "      <td>6gjq</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>26</th>\n",
              "      <td>2bbo</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>388</td>\n",
              "      <td>678</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>27</th>\n",
              "      <td>6gju</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>28</th>\n",
              "      <td>6uk1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1202</td>\n",
              "      <td>1430</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>29</th>\n",
              "      <td>7svd</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>30</th>\n",
              "      <td>8ubr</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>31</th>\n",
              "      <td>6ze1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>32</th>\n",
              "      <td>5d3f</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>747</td>\n",
              "      <td>774</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>33</th>\n",
              "      <td>5d3e</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>762</td>\n",
              "      <td>801</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>34</th>\n",
              "      <td>8eio</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>35</th>\n",
              "      <td>3isw</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>5</td>\n",
              "      <td>22</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>36</th>\n",
              "      <td>6gk4</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>37</th>\n",
              "      <td>6gkd</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>387</td>\n",
              "      <td>646</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>38</th>\n",
              "      <td>8eiq</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>39</th>\n",
              "      <td>6msm</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>40</th>\n",
              "      <td>6o1v</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>41</th>\n",
              "      <td>6o2p</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>42</th>\n",
              "      <td>8eig</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>43</th>\n",
              "      <td>7sv7</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>44</th>\n",
              "      <td>5uak</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>45</th>\n",
              "      <td>7svr</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>46</th>\n",
              "      <td>8fzq</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>47</th>\n",
              "      <td>8ej1</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>48</th>\n",
              "      <td>2lob</td>\n",
              "      <td>EXPERIMENTALLY DETERMINED</td>\n",
              "      <td>PDBe</td>\n",
              "      <td>1473</td>\n",
              "      <td>1480</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
              "\n",
              "  <div class=\"colab-df-container\">\n",
              "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-cb1e0da2-5739-4fa0-9c90-3d967eb85ab6')\"\n",
              "            title=\"Convert this dataframe to an interactive table.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
              "    <path d=\"M120-120v-720h720v720H120Zm60-500h600v-160H180v160Zm220 220h160v-160H400v160Zm0 220h160v-160H400v160ZM180-400h160v-160H180v160Zm440 0h160v-160H620v160ZM180-180h160v-160H180v160Zm440 0h160v-160H620v160Z\"/>\n",
              "  </svg>\n",
              "    </button>\n",
              "\n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    .colab-df-buttons div {\n",
              "      margin-bottom: 4px;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "    <script>\n",
              "      const buttonEl =\n",
              "        document.querySelector('#df-cb1e0da2-5739-4fa0-9c90-3d967eb85ab6 button.colab-df-convert');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      async function convertToInteractive(key) {\n",
              "        const element = document.querySelector('#df-cb1e0da2-5739-4fa0-9c90-3d967eb85ab6');\n",
              "        const dataTable =\n",
              "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "          + ' to learn more about interactive tables.';\n",
              "        element.innerHTML = '';\n",
              "        dataTable['output_type'] = 'display_data';\n",
              "        await google.colab.output.renderOutput(dataTable, element);\n",
              "        const docLink = document.createElement('div');\n",
              "        docLink.innerHTML = docLinkHtml;\n",
              "        element.appendChild(docLink);\n",
              "      }\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "\n",
              "<div id=\"df-2491121a-f75b-4a6f-9645-b03d053d15bf\">\n",
              "  <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-2491121a-f75b-4a6f-9645-b03d053d15bf')\"\n",
              "            title=\"Suggest charts\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "     width=\"24px\">\n",
              "    <g>\n",
              "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
              "    </g>\n",
              "</svg>\n",
              "  </button>\n",
              "\n",
              "<style>\n",
              "  .colab-df-quickchart {\n",
              "      --bg-color: #E8F0FE;\n",
              "      --fill-color: #1967D2;\n",
              "      --hover-bg-color: #E2EBFA;\n",
              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
              "      --disabled-bg-color: #DDD;\n",
              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
              "      --hover-fill-color: #FFFFFF;\n",
              "      --disabled-bg-color: #3B4455;\n",
              "      --disabled-fill-color: #666;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart {\n",
              "    background-color: var(--bg-color);\n",
              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
              "    fill: var(--fill-color);\n",
              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "    fill: var(--button-hover-fill-color);\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
              "    }\n",
              "    20% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    30% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-2491121a-f75b-4a6f-9645-b03d053d15bf button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "summary": "{\n  \"name\": \"displaying_3dbeacon_exp_summary(UniProt_ID)\",\n  \"rows\": 49,\n  \"fields\": [\n    {\n      \"column\": \"ID\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 49,\n        \"samples\": [\n          \"5tgk\",\n          \"7svr\",\n          \"8ej1\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"Type\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"EXPERIMENTALLY DETERMINED\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"Provider\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"PDBe\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"UniProt start\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 325,\n        \"min\": 1,\n        \"max\": 1473,\n        \"num_unique_values\": 11,\n        \"samples\": [\n          1101\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"UniProt end\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 395,\n        \"min\": 22,\n        \"max\": 1480,\n        \"num_unique_values\": 8,\n        \"samples\": [\n          774\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 3
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 2.3.  Get clickable links to download coordinates\n",
        "#@markdown  In this sub-section you will be able to retrieve urls for predicted and experimentally-determined structures associated with a UniProt ID.\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#Run this code to perform a API call and gets urls and display the urls\n",
        "display_urls_for_structures(UniProt_ID)\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "cellView": "form",
        "id": "NiVRjOsYIwDC",
        "outputId": "35b5ad0c-988e-4575-95fb-15d37bc46c53"
      },
      "id": "NiVRjOsYIwDC",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "There are 54 listed associated with UniProt id P13569\n",
            "\n",
            "{'2pze': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2pze_updated.cif']}\n",
            "\n",
            "\n",
            "{'7qi1': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/7qi1_updated.cif']}\n",
            "\n",
            "\n",
            "{'2pzg': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2pzg_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfj': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfj_updated.cif']}\n",
            "\n",
            "\n",
            "{'6wbs': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6wbs_updated.cif']}\n",
            "\n",
            "\n",
            "{'6hep': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6hep_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tf8': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tf8_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfa': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfa_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfb': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfb_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfd': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfd_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tff': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tff_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfi': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfi_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfg': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfg_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tgk': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tgk_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tfc': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tfc_updated.cif']}\n",
            "\n",
            "\n",
            "{'5tf7': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5tf7_updated.cif']}\n",
            "\n",
            "\n",
            "{'6gjs': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6gjs_updated.cif']}\n",
            "\n",
            "\n",
            "{'2pzf': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2pzf_updated.cif']}\n",
            "\n",
            "\n",
            "{'2bbs': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2bbs_updated.cif']}\n",
            "\n",
            "\n",
            "{'4wz6': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/4wz6_updated.cif']}\n",
            "\n",
            "\n",
            "{'5d2d': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5d2d_updated.cif']}\n",
            "\n",
            "\n",
            "{'6rqr': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6rqr_updated.cif']}\n",
            "\n",
            "\n",
            "{'1xmi': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/1xmi_updated.cif']}\n",
            "\n",
            "\n",
            "{'1xmj': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/1xmj_updated.cif']}\n",
            "\n",
            "\n",
            "{'2bbt': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2bbt_updated.cif']}\n",
            "\n",
            "\n",
            "{'6gjq': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6gjq_updated.cif']}\n",
            "\n",
            "\n",
            "{'2bbo': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2bbo_updated.cif']}\n",
            "\n",
            "\n",
            "{'6gju': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6gju_updated.cif']}\n",
            "\n",
            "\n",
            "{'6uk1': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6uk1_updated.cif']}\n",
            "\n",
            "\n",
            "{'7svd': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/7svd_updated.cif']}\n",
            "\n",
            "\n",
            "{'8ubr': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/8ubr_updated.cif']}\n",
            "\n",
            "\n",
            "{'6ze1': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6ze1_updated.cif']}\n",
            "\n",
            "\n",
            "{'5d3f': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5d3f_updated.cif']}\n",
            "\n",
            "\n",
            "{'5d3e': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5d3e_updated.cif']}\n",
            "\n",
            "\n",
            "{'8eio': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/8eio_updated.cif']}\n",
            "\n",
            "\n",
            "{'3isw': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/3isw_updated.cif']}\n",
            "\n",
            "\n",
            "{'6gk4': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6gk4_updated.cif']}\n",
            "\n",
            "\n",
            "{'6gkd': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6gkd_updated.cif']}\n",
            "\n",
            "\n",
            "{'8eiq': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/8eiq_updated.cif']}\n",
            "\n",
            "\n",
            "{'6msm': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6msm_updated.cif']}\n",
            "\n",
            "\n",
            "{'6o1v': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6o1v_updated.cif']}\n",
            "\n",
            "\n",
            "{'6o2p': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/6o2p_updated.cif']}\n",
            "\n",
            "\n",
            "{'8eig': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/8eig_updated.cif']}\n",
            "\n",
            "\n",
            "{'7sv7': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/7sv7_updated.cif']}\n",
            "\n",
            "\n",
            "{'5uak': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/5uak_updated.cif']}\n",
            "\n",
            "\n",
            "{'7svr': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/7svr_updated.cif']}\n",
            "\n",
            "\n",
            "{'8fzq': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/8fzq_updated.cif']}\n",
            "\n",
            "\n",
            "{'8ej1': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/8ej1_updated.cif']}\n",
            "\n",
            "\n",
            "{'2lob': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "          'https://www.ebi.ac.uk/pdbe/static/entry/2lob_updated.cif']}\n",
            "\n",
            "\n",
            "{'P13569_1-1451:8eio.1.A': ['Click on url to download the coordinate file - '\n",
            "                            'PDB format:',\n",
            "                            'https://swissmodel.expasy.org/3d-beacons/uniprot/P13569.pdb?range=1-1451&template=8eio.1.A&provider=swissmodel']}\n",
            "\n",
            "\n",
            "{'P13569_42-1439:6d3r.1.A': ['Click on url to download the coordinate file - '\n",
            "                             'PDB format:',\n",
            "                             'https://swissmodel.expasy.org/3d-beacons/uniprot/P13569.pdb?range=42-1439&template=6d3r.1.A&provider=swissmodel']}\n",
            "\n",
            "\n",
            "{'P13569_3-1436:7svr.1.A': ['Click on url to download the coordinate file - '\n",
            "                            'PDB format:',\n",
            "                            'https://swissmodel.expasy.org/3d-beacons/uniprot/P13569.pdb?range=3-1436&template=7svr.1.A&provider=swissmodel']}\n",
            "\n",
            "\n",
            "{'AF-P13569-F1': ['Click on url to download the coordinate file - MMCIF '\n",
            "                  'format:',\n",
            "                  'https://alphafold.ebi.ac.uk/files/AF-P13569-F1-model_v4.cif']}\n",
            "\n",
            "\n",
            "{'P13569': ['Click on url to download the coordinate file - MMCIF format:',\n",
            "            'https://alphafill.eu/v1/aff/P13569']}\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#3)  Structures available using **PDBe-KB**\n",
        "\n",
        "This section reports on the PDB ids for the experimentally-determined structures where at least one of the protein chains in the structure is associated with a UniProt ID.\n",
        "\n",
        "The identity of these structures as well as more analysis of structures are available *via* **PDBe-KB**.\n",
        "\n",
        "Structures of variants / engineered mutations of proteins are some times part of research studies. This section provides options to explores whether these exist and what they are."
      ],
      "metadata": {
        "id": "qncyCaFMOzsb"
      },
      "id": "qncyCaFMOzsb"
    },
    {
      "cell_type": "markdown",
      "source": [
        "---\n",
        "*More details:*\n",
        "<p>The experimentaly-determined structures/data available <i>via</i> <strong>PDBe-KB</strong> are associated with UniProt IDs are due to both manual and semi-automated curation.</p>\n",
        "<p>That is a scientific curator is checking sequence alignments, with a feedback loop with the scientist(s) depositing the data confirming the right UniProt IDs are assigned before the data is made public.</p>\n",
        "<p>This means that if there are structures where there was a lot of engineered mutations or where two or more proteins were engineered to make a new polymer chain to gain scientific insight -- these may not be as findable with certain sequence-based search approaches but will be found listed on <strong>PDBe-KB</strong> pages.</p>\n",
        "<p>If the appropriate UniProt IDs are not available at the time of publishing, then after the structures are published, and there is a semi-automated process to assign unmapped structures to the appropriate UniProt ID. There is a synching process that means ultimately all structures associated with a UniProt ID end up listed on both <strong>PDBe-KB</strong> and UniProt pages</p>"
      ],
      "metadata": {
        "id": "SY6enheJGCjj"
      },
      "id": "SY6enheJGCjj"
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 3.1. Get experimentally-determined coordinates associated with a UniProt ID\n",
        "#@markdown  In this sub-section you will be able to retrieve experimentally-determined coordinates where based on sequence and reported taxonomy there is one or more chains associated with the same specified Uniprot accession ID.\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#Run this code to perform a API call and load result into a DataFrame\n",
        "display_exp_structure_summary(UniProt_ID)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "id": "8jmeuVCnQGGB",
        "outputId": "cab778fa-cc52-42b3-bef5-c02a641c5f0d",
        "cellView": "form"
      },
      "id": "8jmeuVCnQGGB",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "There are 50 experimentally-determined structures associated with UniProt id P13569.\n",
            "\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "      Experimental Method  Resolution (in Angstroms)\n",
              "5tfb    X-ray diffraction                       1.87\n",
              "5tf7    X-ray diffraction                       1.93\n",
              "5tgk    X-ray diffraction                       1.91\n",
              "5tf8    X-ray diffraction                       1.86\n",
              "5tff    X-ray diffraction                       1.89\n",
              "5tfa    X-ray diffraction                       1.87\n",
              "5tfc    X-ray diffraction                       1.92\n",
              "5tfj    X-ray diffraction                       1.85\n",
              "5tfg    X-ray diffraction                       1.91\n",
              "6wbs    X-ray diffraction                       1.86\n",
              "5tfd    X-ray diffraction                       1.89\n",
              "6gjs    X-ray diffraction                       1.95\n",
              "2pzf    X-ray diffraction                       2.00\n",
              "8ubr  Electron Microscopy                       2.70\n",
              "7svd  Electron Microscopy                       2.70\n",
              "5tfi    X-ray diffraction                       1.89\n",
              "2pzg    X-ray diffraction                       1.80\n",
              "6gjq    X-ray diffraction                       2.49\n",
              "5d2d    X-ray diffraction                       2.10\n",
              "7qi1    X-ray diffraction                       1.76\n",
              "6hep    X-ray diffraction                       1.86\n",
              "6rqr    X-ray diffraction                       2.20\n",
              "5d3e    X-ray diffraction                       2.75\n",
              "5d3f    X-ray diffraction                       2.74\n",
              "6uk1    X-ray diffraction                       2.69\n",
              "2pze    X-ray diffraction                       1.70\n",
              "3isw    X-ray diffraction                       2.80\n",
              "4wz6    X-ray diffraction                       2.05\n",
              "2lob         Solution NMR                        NaN\n",
              "8eiq  Electron Microscopy                       3.00\n",
              "6gju    X-ray diffraction                       2.60\n",
              "2bbt    X-ray diffraction                       2.30\n",
              "6ze1    X-ray diffraction                       2.71\n",
              "6gkd    X-ray diffraction                       2.99\n",
              "6o2p  Electron Microscopy                       3.30\n",
              "2bbs    X-ray diffraction                       2.05\n",
              "8eio  Electron Microscopy                       2.80\n",
              "2bbo    X-ray diffraction                       2.55\n",
              "6gk4    X-ray diffraction                       2.91\n",
              "3gd7    X-ray diffraction                       2.70\n",
              "1xmi    X-ray diffraction                       2.25\n",
              "1xmj    X-ray diffraction                       2.30\n",
              "5uak  Electron Microscopy                       3.87\n",
              "6o1v  Electron Microscopy                       3.20\n",
              "7sv7  Electron Microscopy                       3.80\n",
              "6msm  Electron Microscopy                       3.20\n",
              "8eig  Electron Microscopy                       3.60\n",
              "7svr  Electron Microscopy                       3.90\n",
              "8fzq  Electron Microscopy                       4.30\n",
              "8ej1  Electron Microscopy                       6.90"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-de0d4e38-1c1f-45c6-b24f-a014406c83d9\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Experimental Method</th>\n",
              "      <th>Resolution (in Angstroms)</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>5tfb</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.87</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tf7</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.93</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tgk</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.91</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tf8</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.86</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tff</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.89</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tfa</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.87</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tfc</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.92</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tfj</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.85</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tfg</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.91</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6wbs</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.86</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tfd</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.89</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6gjs</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.95</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2pzf</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8ubr</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>2.70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7svd</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>2.70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5tfi</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.89</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2pzg</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.80</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6gjq</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.49</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5d2d</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.10</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7qi1</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.76</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6hep</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.86</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6rqr</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.20</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5d3e</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.75</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5d3f</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.74</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6uk1</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.69</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2pze</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>1.70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3isw</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.80</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4wz6</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.05</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2lob</th>\n",
              "      <td>Solution NMR</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8eiq</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6gju</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.60</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2bbt</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.30</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6ze1</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.71</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6gkd</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.99</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6o2p</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.30</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2bbs</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.05</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8eio</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>2.80</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2bbo</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.55</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6gk4</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.91</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3gd7</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.70</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1xmi</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.25</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1xmj</th>\n",
              "      <td>X-ray diffraction</td>\n",
              "      <td>2.30</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5uak</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.87</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6o1v</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.20</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7sv7</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.80</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6msm</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.20</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8eig</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.60</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7svr</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>3.90</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8fzq</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>4.30</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8ej1</th>\n",
              "      <td>Electron Microscopy</td>\n",
              "      <td>6.90</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
              "\n",
              "  <div class=\"colab-df-container\">\n",
              "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-de0d4e38-1c1f-45c6-b24f-a014406c83d9')\"\n",
              "            title=\"Convert this dataframe to an interactive table.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
              "    <path d=\"M120-120v-720h720v720H120Zm60-500h600v-160H180v160Zm220 220h160v-160H400v160Zm0 220h160v-160H400v160ZM180-400h160v-160H180v160Zm440 0h160v-160H620v160ZM180-180h160v-160H180v160Zm440 0h160v-160H620v160Z\"/>\n",
              "  </svg>\n",
              "    </button>\n",
              "\n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    .colab-df-buttons div {\n",
              "      margin-bottom: 4px;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "    <script>\n",
              "      const buttonEl =\n",
              "        document.querySelector('#df-de0d4e38-1c1f-45c6-b24f-a014406c83d9 button.colab-df-convert');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      async function convertToInteractive(key) {\n",
              "        const element = document.querySelector('#df-de0d4e38-1c1f-45c6-b24f-a014406c83d9');\n",
              "        const dataTable =\n",
              "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "          + ' to learn more about interactive tables.';\n",
              "        element.innerHTML = '';\n",
              "        dataTable['output_type'] = 'display_data';\n",
              "        await google.colab.output.renderOutput(dataTable, element);\n",
              "        const docLink = document.createElement('div');\n",
              "        docLink.innerHTML = docLinkHtml;\n",
              "        element.appendChild(docLink);\n",
              "      }\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "\n",
              "<div id=\"df-e683d8f3-75ae-474e-9dac-c148555c3288\">\n",
              "  <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-e683d8f3-75ae-474e-9dac-c148555c3288')\"\n",
              "            title=\"Suggest charts\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "     width=\"24px\">\n",
              "    <g>\n",
              "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
              "    </g>\n",
              "</svg>\n",
              "  </button>\n",
              "\n",
              "<style>\n",
              "  .colab-df-quickchart {\n",
              "      --bg-color: #E8F0FE;\n",
              "      --fill-color: #1967D2;\n",
              "      --hover-bg-color: #E2EBFA;\n",
              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
              "      --disabled-bg-color: #DDD;\n",
              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
              "      --hover-fill-color: #FFFFFF;\n",
              "      --disabled-bg-color: #3B4455;\n",
              "      --disabled-fill-color: #666;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart {\n",
              "    background-color: var(--bg-color);\n",
              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
              "    fill: var(--fill-color);\n",
              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "    fill: var(--button-hover-fill-color);\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
              "    }\n",
              "    20% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    30% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-e683d8f3-75ae-474e-9dac-c148555c3288 button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "summary": "{\n  \"name\": \"display_exp_structure_summary(UniProt_ID)\",\n  \"rows\": 50,\n  \"fields\": [\n    {\n      \"column\": \"Experimental Method\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"X-ray diffraction\",\n          \"Electron Microscopy\",\n          \"Solution NMR\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"Resolution (in Angstroms)\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 0.9105815963094219,\n        \"min\": 1.7,\n        \"max\": 6.9,\n        \"num_unique_values\": 37,\n        \"samples\": [\n          2.69,\n          1.76,\n          1.89\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 3.2. Press shift+enter to generate a list for copying-and-pasting\n",
        "#@markdown Here is a copy-and-paste comma list of all the PDB ids for one UniProt id.\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#Run this code to perform a API call and shows results as comma-delimited list\n",
        "comma_pdb_id_list(UniProt_ID)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "cellView": "form",
        "id": "v-t0VJIugq_q",
        "outputId": "36dbc9e5-1897-4b76-dfea-c616d256e04e"
      },
      "id": "v-t0VJIugq_q",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "There are 50 experimentally-determined structures associated with UniProt id P13569.\n",
            "\n",
            "5tfb, 5tf7, 5tgk, 5tf8, 5tff, 5tfa, 5tfc, 5tfj, 5tfg, 6wbs, 5tfd, 6gjs, 2pzf, 8ubr, 7svd, 5tfi, 2pzg, 6gjq, 5d2d, 7qi1, 6hep, 6rqr, 5d3e, 5d3f, 6uk1, 2pze, 3isw, 4wz6, 2lob, 8eiq, 6gju, 2bbt, 6ze1, 6gkd, 6o2p, 2bbs, 8eio, 2bbo, 6gk4, 3gd7, 1xmi, 1xmj, 5uak, 6o1v, 7sv7, 6msm, 8eig, 7svr, 8fzq, 8ej1\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "<img src=\"https://github.com/glevans/7ADD-workshop-2024/blob/main/Images/Mol_Viewer_Loading_Multiples.png?raw=true\" align=\"right\">\n",
        "\n",
        "The above list can be pasted into the [Molstar viewer](https://molstar.org/viewer/) and upon *'Apply'* all the coordinates will be loaded into the viewer."
      ],
      "metadata": {
        "id": "9uSjq-AMmAoT"
      },
      "id": "9uSjq-AMmAoT"
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 3.3. Press shift+enter to generate a list for copying-and-pasting\n",
        "#@markdown Here is a copy-and-paste comma list of the PDB ids with no modifications or discrepancy compared UniProt id.\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#Run this code to perform a API call and shows results as comma-delimited list\n",
        "nonmodified_PDB_IDs(UniProt_ID)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "cellView": "form",
        "id": "se_9EEpn7uH4",
        "outputId": "e14b551a-fb5e-4fb1-c9a4-0da1efdb01a6"
      },
      "id": "se_9EEpn7uH4",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "There are 50 experimentally-determined structures associated with UniProt id P13569.\n",
            "\n",
            "Of these there are 35 experimentally-determined structures without any modifications or discrepancies with UniProt id P13569.\n",
            "\n",
            "5tfb, 5tf7, 5tgk, 5tf8, 5tff, 5tfa, 5tfc, 5tfj, 5tfg, 5tfd, 6gjs, 8ubr, 7svd, 5tfi, 6gjq, 3isw, 4wz6, 2lob, 8eiq, 6gju, 6ze1, 6gkd, 6o2p, 8eio, 2bbo, 6gk4, 1xmj, 5uak, 6o1v, 7sv7, 6msm, 8eig, 7svr, 8fzq, 8ej1\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 3.4. Get summary of sequence discrepancy (*e.g.* variants) compared to the UniProt sequence\n",
        "#@markdown In this sub-section the variants, engineered mutations, modified residues, etc for experimental structures will be reported.\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "#@markdown These have been identified as positions that are in conflict with the UniProt sequence.\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P00519\" #@param {type:\"string\"}\n",
        "\n",
        "#@markdown <br>\n",
        "#@markdown Use filter button and imput the residue number to see if there is an experimental structure for a particular genetic variant.\n",
        "#@markdown\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "\n",
        "displaying_variant_summary(UniProt_ID)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 437
        },
        "outputId": "ed3a3295-8fa1-416d-ed65-fa16af5503d4",
        "id": "UIbBveXuS2Go",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "This is the output from entering the UniProt ID P00519.\n",
            "\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "                  change  position from_aa to_aa PDB_ID\n",
              "0               Conflict         6     LEU   ILE   1opl\n",
              "1               Conflict         6     LEU   ILE   6amv\n",
              "2               Conflict         6     LEU   ILE   6amw\n",
              "3               Conflict         8     LEU   GLY   1opl\n",
              "4               Conflict         8     LEU   GLY   6amv\n",
              "..                   ...       ...     ...   ...    ...\n",
              "133  Engineered mutation       396     HIS   PRO   2f4j\n",
              "134  Engineered mutation       396     HIS   PRO   2g2f\n",
              "135  Engineered mutation       396     HIS   PRO   2g2h\n",
              "136             Conflict       445     LEU   PRO   6bl8\n",
              "137              Variant      1065     THR   SER   1zzp\n",
              "\n",
              "[138 rows x 5 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-1ee40705-eee3-4afe-adb0-2acf9bfd12f3\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>change</th>\n",
              "      <th>position</th>\n",
              "      <th>from_aa</th>\n",
              "      <th>to_aa</th>\n",
              "      <th>PDB_ID</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>Conflict</td>\n",
              "      <td>6</td>\n",
              "      <td>LEU</td>\n",
              "      <td>ILE</td>\n",
              "      <td>1opl</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>Conflict</td>\n",
              "      <td>6</td>\n",
              "      <td>LEU</td>\n",
              "      <td>ILE</td>\n",
              "      <td>6amv</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>Conflict</td>\n",
              "      <td>6</td>\n",
              "      <td>LEU</td>\n",
              "      <td>ILE</td>\n",
              "      <td>6amw</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>Conflict</td>\n",
              "      <td>8</td>\n",
              "      <td>LEU</td>\n",
              "      <td>GLY</td>\n",
              "      <td>1opl</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>Conflict</td>\n",
              "      <td>8</td>\n",
              "      <td>LEU</td>\n",
              "      <td>GLY</td>\n",
              "      <td>6amv</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>133</th>\n",
              "      <td>Engineered mutation</td>\n",
              "      <td>396</td>\n",
              "      <td>HIS</td>\n",
              "      <td>PRO</td>\n",
              "      <td>2f4j</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>134</th>\n",
              "      <td>Engineered mutation</td>\n",
              "      <td>396</td>\n",
              "      <td>HIS</td>\n",
              "      <td>PRO</td>\n",
              "      <td>2g2f</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>135</th>\n",
              "      <td>Engineered mutation</td>\n",
              "      <td>396</td>\n",
              "      <td>HIS</td>\n",
              "      <td>PRO</td>\n",
              "      <td>2g2h</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>136</th>\n",
              "      <td>Conflict</td>\n",
              "      <td>445</td>\n",
              "      <td>LEU</td>\n",
              "      <td>PRO</td>\n",
              "      <td>6bl8</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>137</th>\n",
              "      <td>Variant</td>\n",
              "      <td>1065</td>\n",
              "      <td>THR</td>\n",
              "      <td>SER</td>\n",
              "      <td>1zzp</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>138 rows × 5 columns</p>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
              "\n",
              "  <div class=\"colab-df-container\">\n",
              "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-1ee40705-eee3-4afe-adb0-2acf9bfd12f3')\"\n",
              "            title=\"Convert this dataframe to an interactive table.\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
              "    <path d=\"M120-120v-720h720v720H120Zm60-500h600v-160H180v160Zm220 220h160v-160H400v160Zm0 220h160v-160H400v160ZM180-400h160v-160H180v160Zm440 0h160v-160H620v160ZM180-180h160v-160H180v160Zm440 0h160v-160H620v160Z\"/>\n",
              "  </svg>\n",
              "    </button>\n",
              "\n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    .colab-df-buttons div {\n",
              "      margin-bottom: 4px;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "    <script>\n",
              "      const buttonEl =\n",
              "        document.querySelector('#df-1ee40705-eee3-4afe-adb0-2acf9bfd12f3 button.colab-df-convert');\n",
              "      buttonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "      async function convertToInteractive(key) {\n",
              "        const element = document.querySelector('#df-1ee40705-eee3-4afe-adb0-2acf9bfd12f3');\n",
              "        const dataTable =\n",
              "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                    [key], {});\n",
              "        if (!dataTable) return;\n",
              "\n",
              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "          + ' to learn more about interactive tables.';\n",
              "        element.innerHTML = '';\n",
              "        dataTable['output_type'] = 'display_data';\n",
              "        await google.colab.output.renderOutput(dataTable, element);\n",
              "        const docLink = document.createElement('div');\n",
              "        docLink.innerHTML = docLinkHtml;\n",
              "        element.appendChild(docLink);\n",
              "      }\n",
              "    </script>\n",
              "  </div>\n",
              "\n",
              "\n",
              "<div id=\"df-24f1aa3f-e41a-4a56-afd4-af17c736469b\">\n",
              "  <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-24f1aa3f-e41a-4a56-afd4-af17c736469b')\"\n",
              "            title=\"Suggest charts\"\n",
              "            style=\"display:none;\">\n",
              "\n",
              "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "     width=\"24px\">\n",
              "    <g>\n",
              "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
              "    </g>\n",
              "</svg>\n",
              "  </button>\n",
              "\n",
              "<style>\n",
              "  .colab-df-quickchart {\n",
              "      --bg-color: #E8F0FE;\n",
              "      --fill-color: #1967D2;\n",
              "      --hover-bg-color: #E2EBFA;\n",
              "      --hover-fill-color: #174EA6;\n",
              "      --disabled-fill-color: #AAA;\n",
              "      --disabled-bg-color: #DDD;\n",
              "  }\n",
              "\n",
              "  [theme=dark] .colab-df-quickchart {\n",
              "      --bg-color: #3B4455;\n",
              "      --fill-color: #D2E3FC;\n",
              "      --hover-bg-color: #434B5C;\n",
              "      --hover-fill-color: #FFFFFF;\n",
              "      --disabled-bg-color: #3B4455;\n",
              "      --disabled-fill-color: #666;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart {\n",
              "    background-color: var(--bg-color);\n",
              "    border: none;\n",
              "    border-radius: 50%;\n",
              "    cursor: pointer;\n",
              "    display: none;\n",
              "    fill: var(--fill-color);\n",
              "    height: 32px;\n",
              "    padding: 0;\n",
              "    width: 32px;\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart:hover {\n",
              "    background-color: var(--hover-bg-color);\n",
              "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "    fill: var(--button-hover-fill-color);\n",
              "  }\n",
              "\n",
              "  .colab-df-quickchart-complete:disabled,\n",
              "  .colab-df-quickchart-complete:disabled:hover {\n",
              "    background-color: var(--disabled-bg-color);\n",
              "    fill: var(--disabled-fill-color);\n",
              "    box-shadow: none;\n",
              "  }\n",
              "\n",
              "  .colab-df-spinner {\n",
              "    border: 2px solid var(--fill-color);\n",
              "    border-color: transparent;\n",
              "    border-bottom-color: var(--fill-color);\n",
              "    animation:\n",
              "      spin 1s steps(1) infinite;\n",
              "  }\n",
              "\n",
              "  @keyframes spin {\n",
              "    0% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
              "    }\n",
              "    20% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    30% {\n",
              "      border-color: transparent;\n",
              "      border-left-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    40% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-top-color: var(--fill-color);\n",
              "    }\n",
              "    60% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "    }\n",
              "    80% {\n",
              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "    90% {\n",
              "      border-color: transparent;\n",
              "      border-bottom-color: var(--fill-color);\n",
              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
              "    }\n",
              "    (() => {\n",
              "      let quickchartButtonEl =\n",
              "        document.querySelector('#df-24f1aa3f-e41a-4a56-afd4-af17c736469b button');\n",
              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "    })();\n",
              "  </script>\n",
              "</div>\n",
              "    </div>\n",
              "  </div>\n"
            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "summary": "{\n  \"name\": \"displaying_variant_summary(UniProt_ID)\",\n  \"rows\": 138,\n  \"fields\": [\n    {\n      \"column\": \"change\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"Engineered mutation\",\n          \"Variant\",\n          \"Modification\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"position\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 147,\n        \"min\": 6,\n        \"max\": 1065,\n        \"num_unique_values\": 50,\n        \"samples\": [\n          23,\n          228,\n          92\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"from_aa\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 15,\n        \"samples\": [\n          \"PRO\",\n          \"GLY\",\n          \"LEU\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"to_aa\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 20,\n        \"samples\": [\n          \"ILE\",\n          \"MET\",\n          \"THR\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"PDB_ID\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 38,\n        \"samples\": [\n          \"7w7x\",\n          \"2g2h\",\n          \"1awo\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 8
        }
      ],
      "id": "UIbBveXuS2Go"
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 3.5. Convert specific set of sequence discrepancy (*e.g.* variants) to a comma-delimited list\n",
        "#@markdown In this sub-section the PDB ids with a specific variant / engineered mutation / modified residues / etc for experimental structures will be converted into a comma-delimited list.\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "\n",
        "#Run this code to display the widget\n",
        "JSON = [{\"index\":79,\"change\":\"Engineered mutation\",\"position\":92,\"from_aa\":\"GLY\",\"to_aa\":\"ASN\",\"PDB_ID\":\"7pvr\"},{\"index\":80,\"change\":\"Engineered mutation\",\"position\":92,\"from_aa\":\"GLY\",\"to_aa\":\"ASN\",\"PDB_ID\":\"7pvv\"},{\"index\":81,\"change\":\"Engineered mutation\",\"position\":92,\"from_aa\":\"GLY\",\"to_aa\":\"ASN\",\"PDB_ID\":\"7pvs\"},{\"index\":82,\"change\":\"Engineered mutation\",\"position\":92,\"from_aa\":\"GLY\",\"to_aa\":\"ASN\",\"PDB_ID\":\"7pvq\"}] #@param {type:\"raw\"}\n",
        "\n",
        "getting_list_of_PDB_ids(JSON)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "cellView": "form",
        "id": "XEqMMvtIzD2y",
        "outputId": "d0b7ca93-807b-4117-8b2f-d5d480a16dd8"
      },
      "id": "XEqMMvtIzD2y",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "7pvr, 7pvv, 7pvs, 7pvq\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# 4) Comparing results from **3D Beacons** and **PDBe-KB**\n",
        "\n",
        "On relatively rare occasions more experimentally-determined PDB structures will be listed associated with a UniProt id from a **PDBe-KB** API compared to a **3D Beacons** API.\n",
        "\n",
        "The below does a comparison and reports the PDB ids listed from **PDBe-KB** but not from **3D-Beacons** for a UniProt id.\n",
        "\n",
        "On the rare occasions that there are more PDB ids listed from **PDBe-KB** APIs compared to **3D Beacons** APIs, these proteins typically have multiple engineered mutations. Thus from a sequence point of view appear to be quite different from the wild-type protein, however by structure, can be overall similar with subtle differences."
      ],
      "metadata": {
        "id": "xuDgLnj6ayzy"
      },
      "id": "xuDgLnj6ayzy"
    },
    {
      "cell_type": "markdown",
      "source": [
        "It should be also noted that there are some Cryo Electron Microscopy (CryoEM) maps, where coordinates/models are NOT built, due to limitations of resolution or other reasons. These are not findable using **PDBe-KB** or **3D Beacons** APIs. These Cryo EM maps where coordinates are NOT built often do not have protein sequences listed (so generally less findable from a protein sequence point of view). However, these CryoEM maps may provide insight -- in particular for protein systems where there is lots of flexibility / dynamics and/or few to no experimentally-determined coordinates available.\n",
        "\n",
        "To find information on CryoEM Maps without coordinates please visit:\n",
        "<br>\n",
        "[Electron Microscopy Data Bank (EMDB)](https://www.ebi.ac.uk/emdb/)"
      ],
      "metadata": {
        "id": "ioUfDNoKjypD"
      },
      "id": "ioUfDNoKjypD"
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 4.1. List PDB ids found *via* **PDBe-KB** but not *via* **3D Beacons**\n",
        "#@markdown In this sub-section any experimentally-determined structures found *via* **PDBe-KB** but not found *via* **3D Beacons** will be reported.\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "\n",
        "#Run this code to display the widget\n",
        "UniProt_ID = \"P13569\" #@param {type:\"string\"}\n",
        "\n",
        "#@markdown <br>\n",
        "#@markdown Use filter button and imput the residue number to see if there is an experimental structure for a particular genetic variant.\n",
        "#@markdown\n",
        "#@markdown <br>\n",
        "#@markdown <br>\n",
        "\n",
        "diff_btwn_PDBeKB_3DBeacons(UniProt_ID)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "cellView": "form",
        "id": "yDio2cg8iZGC",
        "outputId": "ce269176-cfdc-40e3-dfef-159f3313174d"
      },
      "id": "yDio2cg8iZGC",
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Output from PDBe-KB:\n",
            "There are 50 experimentally-determined structures associated with UniProt id P13569.\n",
            "\n",
            "Output from 3D-Beacons for experimentally-determined structures:\n",
            "There are 49 different structures, where experimental data was used for the structure, associated with UniProt ID P13569\n",
            "\n",
            "['3gd7']\n"
          ]
        }
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    },
    "colab": {
      "provenance": [],
      "collapsed_sections": [
        "QXp8HG3aOXzS",
        "OVmjjknE0Ntq",
        "ZGUCKZwiNXhn",
        "qncyCaFMOzsb",
        "xuDgLnj6ayzy"
      ],
      "include_colab_link": true
    }
  },
  "nbformat": 4,
  "nbformat_minor": 5
}