ubi_cluster_test.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9c8af0ee",
   "metadata": {},
   "outputs": [],
   "source": [
    "import structuremap.utils"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "8a1b34cf",
   "metadata": {},
   "outputs": [],
   "source": [
    "structuremap.utils.set_logger()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "13c30203",
   "metadata": {},
   "outputs": [],
   "source": [
    "from structuremap.processing import download_alphafold_cif, download_alphafold_pae, format_alphafold_data, annotate_accessibility, get_smooth_score\n",
    "from structuremap.processing import perform_enrichment_analysis, perform_enrichment_analysis_per_protein\n",
    "from structuremap.processing import annotate_proteins_with_idr_pattern, get_extended_flexible_pattern\n",
    "from structuremap.processing import get_avg_3d_dist, get_avg_1d_dist, get_proximity_pvals, evaluate_ptm_colocalization\n",
    "from structuremap.plotting import plot_enrichment, plot_ptm_colocalization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "f10286eb",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import os\n",
    "import re\n",
    "import plotly.express as px\n",
    "import tqdm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "5ca4c1e5",
   "metadata": {},
   "outputs": [],
   "source": [
    "from accessory_functions import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2e52e810",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "4b707cfc",
   "metadata": {},
   "outputs": [],
   "source": [
    "pae_dir = '/Users/isabell/Downloads/alphafold_predicted_aligned_errors'\n",
    "cif_dir = '/Users/isabell/Downloads/alphafold_cifs'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2d1ed0b7",
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   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "be0aa625",
   "metadata": {},
   "outputs": [],
   "source": [
    "alphafold_annotation = pd.read_csv('data/alphafold_data/alphafold_annotation.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e09fa642",
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   "source": []
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   "cell_type": "code",
   "execution_count": 8,
   "id": "fb99d6b6",
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     "name": "stderr",
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     "text": [
      "\r",
      "  0%|                                                                                                                              | 0/7 [00:00<?, ?it/s]"
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ubi_lib_only_treated.csv\n"
     ]
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    {
     "name": "stderr",
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     "text": [
      "\r",
      " 14%|████████████████▊                                                                                                     | 1/7 [00:17<01:43, 17.18s/it]"
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    {
     "name": "stdout",
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     "text": [
      "phosphositeplus_annotation.csv\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 29%|█████████████████████████████████▋                                                                                    | 2/7 [00:42<01:48, 21.74s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "p_ochoa.csv\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 43%|██████████████████████████████████████████████████▌                                                                   | 3/7 [01:08<01:34, 23.66s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ubi_lib_shared.csv\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 57%|███████████████████████████████████████████████████████████████████▍                                                  | 4/7 [01:30<01:09, 23.32s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ubi_lib_only_untreated.csv\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 71%|████████████████████████████████████████████████████████████████████████████████████▎                                 | 5/7 [01:51<00:44, 22.29s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "p_sugiyama.csv\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 86%|█████████████████████████████████████████████████████████████████████████████████████████████████████▏                | 6/7 [02:13<00:22, 22.36s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "p_stukalov.csv\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 7/7 [02:38<00:00, 22.62s/it]\n"
     ]
    }
   ],
   "source": [
    "alphafold_ptms = annotate_ptm_data(alphafold_annotation) "
   ]
  },
  {
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   "id": "2fab404e",
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       " */\n",
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       "  var id = handle.cell.output_area._hv_plot_id;\n",
       "  var server_id = handle.cell.output_area._bokeh_server_id;\n",
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       "  var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n",
       "  if (server_id !== null) {\n",
       "    comm.send({event_type: 'server_delete', 'id': server_id});\n",
       "    return;\n",
       "  } else if (comm !== null) {\n",
       "    comm.send({event_type: 'delete', 'id': id});\n",
       "  }\n",
       "  delete PyViz.plot_index[id];\n",
       "  if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n",
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       " */\n",
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       "  delete PyViz.comms[\"hv-extension-comm\"];\n",
       "  window.PyViz.plot_index = {}\n",
       "}\n",
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       " */\n",
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       "  handle_clear_output(event, {cell: {output_area: handle.output_area}})\n",
       "  handle_add_output(event, handle)\n",
       "}\n",
       "\n",
       "function register_renderer(events, OutputArea) {\n",
       "  function append_mime(data, metadata, element) {\n",
       "    // create a DOM node to render to\n",
       "    var toinsert = this.create_output_subarea(\n",
       "    metadata,\n",
       "    CLASS_NAME,\n",
       "    EXEC_MIME_TYPE\n",
       "    );\n",
       "    this.keyboard_manager.register_events(toinsert);\n",
       "    // Render to node\n",
       "    var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "    render(props, toinsert[0]);\n",
       "    element.append(toinsert);\n",
       "    return toinsert\n",
       "  }\n",
       "\n",
       "  events.on('output_added.OutputArea', handle_add_output);\n",
       "  events.on('output_updated.OutputArea', handle_update_output);\n",
       "  events.on('clear_output.CodeCell', handle_clear_output);\n",
       "  events.on('delete.Cell', handle_clear_output);\n",
       "  events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n",
       "\n",
       "  OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "    safe: true,\n",
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       "  });\n",
       "}\n",
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       "if (window.Jupyter !== undefined) {\n",
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       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  } catch(err) {\n",
       "  }\n",
       "}\n"
      ],
      "application/vnd.holoviews_load.v0+json": "\nif ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n  window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n}\n\n\n    function JupyterCommManager() {\n    }\n\n    JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n      if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n        var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n        comm_manager.register_target(comm_id, function(comm) {\n          comm.on_msg(msg_handler);\n        });\n      } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n        window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n          comm.onMsg = msg_handler;\n        });\n      } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n        google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n          var messages = comm.messages[Symbol.asyncIterator]();\n          function processIteratorResult(result) {\n            var message = result.value;\n            console.log(message)\n            var content = {data: message.data, comm_id};\n            var buffers = []\n            for (var buffer of message.buffers || []) {\n              buffers.push(new DataView(buffer))\n            }\n            var metadata = message.metadata || {};\n            var msg = {content, buffers, metadata}\n            msg_handler(msg);\n            return messages.next().then(processIteratorResult);\n          }\n          return messages.next().then(processIteratorResult);\n        })\n      }\n    }\n\n    JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n      if (comm_id in window.PyViz.comms) {\n        return window.PyViz.comms[comm_id];\n      } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n        var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n        var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n        if (msg_handler) {\n          comm.on_msg(msg_handler);\n        }\n      } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n        var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n        comm.open();\n        if (msg_handler) {\n          comm.onMsg = msg_handler;\n        }\n      } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n        var comm_promise = google.colab.kernel.comms.open(comm_id)\n        comm_promise.then((comm) => {\n          window.PyViz.comms[comm_id] = comm;\n          if (msg_handler) {\n            var messages = comm.messages[Symbol.asyncIterator]();\n            function processIteratorResult(result) {\n              var message = 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the DOM node\n */\nfunction render(props, node) {\n  var div = document.createElement(\"div\");\n  var script = document.createElement(\"script\");\n  node.appendChild(div);\n  node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n  var output_area = handle.output_area;\n  var output = handle.output;\n  if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n    return\n  }\n  var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n  var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n  if (id !== undefined) {\n    var nchildren = toinsert.length;\n    var html_node = toinsert[nchildren-1].children[0];\n    html_node.innerHTML = output.data[HTML_MIME_TYPE];\n    var scripts = [];\n    var nodelist = html_node.querySelectorAll(\"script\");\n    for (var i in nodelist) {\n      if (nodelist.hasOwnProperty(i)) {\n        scripts.push(nodelist[i])\n      }\n    }\n\n    scripts.forEach( function (oldScript) {\n      var newScript = document.createElement(\"script\");\n      var attrs = [];\n      var nodemap = oldScript.attributes;\n      for (var j in nodemap) {\n        if (nodemap.hasOwnProperty(j)) {\n          attrs.push(nodemap[j])\n        }\n      }\n      attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n      newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n      oldScript.parentNode.replaceChild(newScript, oldScript);\n    });\n    if (JS_MIME_TYPE in output.data) {\n      toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n    }\n    output_area._hv_plot_id = id;\n    if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n      window.PyViz.plot_index[id] = Bokeh.index[id];\n    } else {\n      window.PyViz.plot_index[id] = null;\n    }\n  } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n    var bk_div = document.createElement(\"div\");\n    bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n    var script_attrs = bk_div.children[0].attributes;\n    for (var i = 0; i < script_attrs.length; i++) {\n      toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n    }\n    // store reference to server id on output_area\n    output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n  }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n  var id = handle.cell.output_area._hv_plot_id;\n  var server_id = handle.cell.output_area._bokeh_server_id;\n  if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n  var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n  if (server_id !== null) {\n    comm.send({event_type: 'server_delete', 'id': server_id});\n    return;\n  } else if (comm !== null) {\n    comm.send({event_type: 'delete', 'id': id});\n  }\n  delete PyViz.plot_index[id];\n  if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n    var doc = window.Bokeh.index[id].model.document\n    doc.clear();\n    const i = window.Bokeh.documents.indexOf(doc);\n    if (i > -1) {\n      window.Bokeh.documents.splice(i, 1);\n    }\n  }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n  delete PyViz.comms[\"hv-extension-comm\"];\n  window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n  handle_clear_output(event, {cell: {output_area: handle.output_area}})\n  handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n  function append_mime(data, metadata, element) {\n    // create a DOM node to render to\n    var toinsert = this.create_output_subarea(\n    metadata,\n    CLASS_NAME,\n    EXEC_MIME_TYPE\n    );\n    this.keyboard_manager.register_events(toinsert);\n    // Render to node\n    var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n    render(props, toinsert[0]);\n    element.append(toinsert);\n    return toinsert\n  }\n\n  events.on('output_added.OutputArea', handle_add_output);\n  events.on('output_updated.OutputArea', handle_update_output);\n  events.on('clear_output.CodeCell', handle_clear_output);\n  events.on('delete.Cell', handle_clear_output);\n  events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n  OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n    safe: true,\n    index: 0\n  });\n}\n\nif (window.Jupyter !== undefined) {\n  try {\n    var events = require('base/js/events');\n    var OutputArea = require('notebook/js/outputarea').OutputArea;\n    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n      register_renderer(events, OutputArea);\n    }\n  } catch(err) {\n  }\n}\n"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from alphamap.sequenceplot import plot_3d_structuremap, visualize_structure_in_panel"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "a978240e",
   "metadata": {},
   "outputs": [],
   "source": [
    "formatted_data = format_for_3Dviz(df=alphafold_ptms, ptm_dataset=\"ub\") "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "65408f32",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The fasta file for Human is downloaded from github.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00,  2.20it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-04-03 19:08:52> Valid proteins: 1\n",
      "2022-04-03 19:08:52> Invalid proteins: 0\n",
      "2022-04-03 19:08:52> Existing proteins: 0\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 191/191 [00:00<00:00, 1098.33it/s]\n",
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:01<00:00,  1.03s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-04-03 19:08:54> Valid proteins: 1\n",
      "2022-04-03 19:08:54> Invalid proteins: 0\n",
      "2022-04-03 19:08:54> Existing proteins: 0\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:02<00:00,  2.53s/it]\n",
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 56.09it/s]\n",
      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00,  4.98it/s]\n"
     ]
    }
   ],
   "source": [
    "plot3D_html, js_path, cif_path = plot_3d_structuremap(\n",
    "    df=alphafold_ptms,\n",
    "    organism=\"Human\",\n",
    "    protein=\"Q9UN86\", \n",
    "    ptm_type='ub')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "511773b0",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
       "        run_callbacks()\n",
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       "    }\n",
       "\n",
       "    function on_error() {\n",
       "      console.error(\"failed to load \" + url);\n",
       "    }\n",
       "\n",
       "    for (var i = 0; i < css_urls.length; i++) {\n",
       "      var url = css_urls[i];\n",
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       "      element.async = false;\n",
       "      element.src = url;\n",
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       "      document.head.appendChild(element);\n",
       "    }\n",
       "\tif (!js_urls.length) {\n",
       "      on_load()\n",
       "    }\n",
       "  };\n",
       "\n",
       "  function inject_raw_css(css) {\n",
       "    const element = document.createElement(\"style\");\n",
       "    element.appendChild(document.createTextNode(css));\n",
       "    document.body.appendChild(element);\n",
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       "      window.PyViz.plot_index[id] = Bokeh.index[id];\n",
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       "      window.PyViz.plot_index[id] = null;\n",
       "    }\n",
       "  } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
       "    var bk_div = document.createElement(\"div\");\n",
       "    bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "    var script_attrs = bk_div.children[0].attributes;\n",
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       "      toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
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       "  var server_id = handle.cell.output_area._bokeh_server_id;\n",
       "  if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n",
       "  var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n",
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       "  delete PyViz.comms[\"hv-extension-comm\"];\n",
       "  window.PyViz.plot_index = {}\n",
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       "  handle_clear_output(event, {cell: {output_area: handle.output_area}})\n",
       "  handle_add_output(event, handle)\n",
       "}\n",
       "\n",
       "function register_renderer(events, OutputArea) {\n",
       "  function append_mime(data, metadata, element) {\n",
       "    // create a DOM node to render to\n",
       "    var toinsert = this.create_output_subarea(\n",
       "    metadata,\n",
       "    CLASS_NAME,\n",
       "    EXEC_MIME_TYPE\n",
       "    );\n",
       "    this.keyboard_manager.register_events(toinsert);\n",
       "    // Render to node\n",
       "    var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "    render(props, toinsert[0]);\n",
       "    element.append(toinsert);\n",
       "    return toinsert\n",
       "  }\n",
       "\n",
       "  events.on('output_added.OutputArea', handle_add_output);\n",
       "  events.on('output_updated.OutputArea', handle_update_output);\n",
       "  events.on('clear_output.CodeCell', handle_clear_output);\n",
       "  events.on('delete.Cell', handle_clear_output);\n",
       "  events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n",
       "\n",
       "  OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "    safe: true,\n",
       "    index: 0\n",
       "  });\n",
       "}\n",
       "\n",
       "if (window.Jupyter !== undefined) {\n",
       "  try {\n",
       "    var events = require('base/js/events');\n",
       "    var OutputArea = require('notebook/js/outputarea').OutputArea;\n",
       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  } catch(err) {\n",
       "  }\n",
       "}\n"
      ],
      "application/vnd.holoviews_load.v0+json": "\nif ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n  window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n}\n\n\n    function JupyterCommManager() {\n    }\n\n    JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n      if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n        var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n        comm_manager.register_target(comm_id, function(comm) {\n          comm.on_msg(msg_handler);\n        });\n      } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n        window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n          comm.onMsg = msg_handler;\n        });\n      } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n        google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n          var messages = comm.messages[Symbol.asyncIterator]();\n          function processIteratorResult(result) {\n            var message = result.value;\n            console.log(message)\n            var content = {data: message.data, comm_id};\n            var buffers = []\n            for (var buffer of message.buffers || []) {\n              buffers.push(new DataView(buffer))\n            }\n            var metadata = message.metadata || {};\n            var msg = {content, buffers, metadata}\n            msg_handler(msg);\n            return messages.next().then(processIteratorResult);\n          }\n          return messages.next().then(processIteratorResult);\n        })\n      }\n    }\n\n    JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n      if (comm_id in window.PyViz.comms) {\n        return window.PyViz.comms[comm_id];\n      } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n        var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n        var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n        if (msg_handler) {\n          comm.on_msg(msg_handler);\n        }\n      } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n        var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n        comm.open();\n        if (msg_handler) {\n          comm.onMsg = msg_handler;\n        }\n      } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n        var comm_promise = google.colab.kernel.comms.open(comm_id)\n        comm_promise.then((comm) => {\n          window.PyViz.comms[comm_id] = comm;\n          if (msg_handler) {\n            var messages = comm.messages[Symbol.asyncIterator]();\n            function processIteratorResult(result) {\n              var message = 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the DOM node\n */\nfunction render(props, node) {\n  var div = document.createElement(\"div\");\n  var script = document.createElement(\"script\");\n  node.appendChild(div);\n  node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n  var output_area = handle.output_area;\n  var output = handle.output;\n  if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n    return\n  }\n  var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n  var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n  if (id !== undefined) {\n    var nchildren = toinsert.length;\n    var html_node = toinsert[nchildren-1].children[0];\n    html_node.innerHTML = output.data[HTML_MIME_TYPE];\n    var scripts = [];\n    var nodelist = html_node.querySelectorAll(\"script\");\n    for (var i in nodelist) {\n      if (nodelist.hasOwnProperty(i)) {\n        scripts.push(nodelist[i])\n      }\n    }\n\n    scripts.forEach( function (oldScript) {\n      var newScript = document.createElement(\"script\");\n      var attrs = [];\n      var nodemap = oldScript.attributes;\n      for (var j in nodemap) {\n        if (nodemap.hasOwnProperty(j)) {\n          attrs.push(nodemap[j])\n        }\n      }\n      attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n      newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n      oldScript.parentNode.replaceChild(newScript, oldScript);\n    });\n    if (JS_MIME_TYPE in output.data) {\n      toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n    }\n    output_area._hv_plot_id = id;\n    if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n      window.PyViz.plot_index[id] = Bokeh.index[id];\n    } else {\n      window.PyViz.plot_index[id] = null;\n    }\n  } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n    var bk_div = document.createElement(\"div\");\n    bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n    var script_attrs = bk_div.children[0].attributes;\n    for (var i = 0; i < script_attrs.length; i++) {\n      toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n    }\n    // store reference to server id on output_area\n    output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n  }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n  var id = handle.cell.output_area._hv_plot_id;\n  var server_id = handle.cell.output_area._bokeh_server_id;\n  if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n  var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n  if (server_id !== null) {\n    comm.send({event_type: 'server_delete', 'id': server_id});\n    return;\n  } else if (comm !== null) {\n    comm.send({event_type: 'delete', 'id': id});\n  }\n  delete PyViz.plot_index[id];\n  if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n    var doc = window.Bokeh.index[id].model.document\n    doc.clear();\n    const i = window.Bokeh.documents.indexOf(doc);\n    if (i > -1) {\n      window.Bokeh.documents.splice(i, 1);\n    }\n  }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n  delete PyViz.comms[\"hv-extension-comm\"];\n  window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n  handle_clear_output(event, {cell: {output_area: handle.output_area}})\n  handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n  function append_mime(data, metadata, element) {\n    // create a DOM node to render to\n    var toinsert = this.create_output_subarea(\n    metadata,\n    CLASS_NAME,\n    EXEC_MIME_TYPE\n    );\n    this.keyboard_manager.register_events(toinsert);\n    // Render to node\n    var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n    render(props, toinsert[0]);\n    element.append(toinsert);\n    return toinsert\n  }\n\n  events.on('output_added.OutputArea', handle_add_output);\n  events.on('output_updated.OutputArea', handle_update_output);\n  events.on('clear_output.CodeCell', handle_clear_output);\n  events.on('delete.Cell', handle_clear_output);\n  events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n  OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n    safe: true,\n    index: 0\n  });\n}\n\nif (window.Jupyter !== undefined) {\n  try {\n    var events = require('base/js/events');\n    var OutputArea = require('notebook/js/outputarea').OutputArea;\n    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n      register_renderer(events, OutputArea);\n    }\n  } catch(err) {\n  }\n}\n"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-04-03 19:08:57> Starting Bokeh server version 2.2.2 (running on Tornado 6.1)\n",
      "2022-04-03 19:08:57> User authentication hooks NOT provided (default user enabled)\n",
      "2022-04-03 19:08:58> 200 GET / (::1) 290.02ms\n",
      "2022-04-03 19:08:58> 200 GET /js/alphafold-viz.css (::1) 4.15ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/css/alerts.css (::1) 6.91ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/css/card.css (::1) 9.01ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/css/widgets.css (::1) 3.19ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/css/markdown.css (::1) 5.08ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/css/json.css (::1) 7.35ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/css/dataframe.css (::1) 2.24ms\n",
      "2022-04-03 19:08:58> 200 GET /static/js/bokeh.min.js?v=99ecc87bbab1b527ec3485daffb840af9cf81fcc4380b9c622477e33f83db1f623bfa326ad0fdec51658e5a995eb4bf073f2bec7cad0b2c99d4bafb32265316a (::1) 5.50ms\n",
      "2022-04-03 19:08:58> 200 GET /static/js/bokeh-widgets.min.js?v=8d7afc0f68bdd79c70b4ba03e0f6e66f5b01d4422b79a38f9a87c406cda52e0ca0abceaee6da75338360c2107f5c83399461dfd13b7c07c49f4ce82a3db226b1 (::1) 7.44ms\n",
      "2022-04-03 19:08:58> 200 GET /static/js/bokeh-tables.min.js?v=e857b1db3740cfba8b8bbe99e71162ce9362c82d815ed7426df19f556f365f9e85be8753a06207b771ed3da80d09efefef5b11c9cd32941923a79b302f9a8ffe (::1) 4.25ms\n",
      "2022-04-03 19:08:58> 200 GET /static/extensions/panel/panel.min.js (::1) 32.09ms\n",
      "2022-04-03 19:08:58> 200 GET /js/alphafold-viz.js (::1) 118.41ms\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:tornado.access:200 GET / (::1) 290.02ms\n",
      "INFO:tornado.access:200 GET /js/alphafold-viz.css (::1) 4.15ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/css/alerts.css (::1) 6.91ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/css/card.css (::1) 9.01ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/css/widgets.css (::1) 3.19ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/css/markdown.css (::1) 5.08ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/css/json.css (::1) 7.35ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/css/dataframe.css (::1) 2.24ms\n",
      "INFO:tornado.access:200 GET /static/js/bokeh.min.js?v=99ecc87bbab1b527ec3485daffb840af9cf81fcc4380b9c622477e33f83db1f623bfa326ad0fdec51658e5a995eb4bf073f2bec7cad0b2c99d4bafb32265316a (::1) 5.50ms\n",
      "INFO:tornado.access:200 GET /static/js/bokeh-widgets.min.js?v=8d7afc0f68bdd79c70b4ba03e0f6e66f5b01d4422b79a38f9a87c406cda52e0ca0abceaee6da75338360c2107f5c83399461dfd13b7c07c49f4ce82a3db226b1 (::1) 7.44ms\n",
      "INFO:tornado.access:200 GET /static/js/bokeh-tables.min.js?v=e857b1db3740cfba8b8bbe99e71162ce9362c82d815ed7426df19f556f365f9e85be8753a06207b771ed3da80d09efefef5b11c9cd32941923a79b302f9a8ffe (::1) 4.25ms\n",
      "INFO:tornado.access:200 GET /static/extensions/panel/panel.min.js (::1) 32.09ms\n",
      "INFO:tornado.access:200 GET /js/alphafold-viz.js (::1) 118.41ms\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-04-03 19:08:58> 101 GET /ws (::1) 0.85ms\n",
      "2022-04-03 19:08:58> WebSocket connection opened\n",
      "2022-04-03 19:08:58> ServerConnection created\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:tornado.access:101 GET /ws (::1) 0.85ms\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-04-03 19:08:58> 200 GET /cif/Q9UN86_proteome_mod.cif (::1) 3.84ms\n",
      "2022-04-03 19:08:58> 404 GET /favicon.ico (::1) 1.77ms\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:tornado.access:200 GET /cif/Q9UN86_proteome_mod.cif (::1) 3.84ms\n",
      "WARNING:tornado.access:404 GET /favicon.ico (::1) 1.77ms\n"
     ]
    }
   ],
   "source": [
    "visualize_structure_in_panel(plot3D_html, js_path, cif_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e63e7bf1",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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