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   "source": [
    "# Filter By Sequence Regex Demo\n",
    "\n",
    "This example shows how to filter poteins by their sequence regualar expression. \n",
    "\n",
    "[More about regular expression](https://www.regular-expressions.info)\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.filters import ContainsSequenceRegex\n",
    "from mmtfPyspark.structureViewer import view_group_interaction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"FilterBySequenceRegex\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read in MMTF Files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = \"../../resources/mmtf_reduced_sample/\"\n",
    "\n",
    "pdb = mmtfReader.read_sequence_file(path, sc)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Filter by sequence regular expression\n",
    "\n",
    "#### Zinc Finger Motif  regular expression:    C.{2,4}C.{12}H.{3,5}H\n",
    "\n",
    "<img src=\"./figures/ZincFingerMotif.png\" style=\"width: 300px;\"/>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "structures = pdb.filter(ContainsSequenceRegex(\"C.{2,4}C.{12}H.{3,5}H\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Count number of entires"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of entries containing Zinc figure motif is : 16\n"
     ]
    }
   ],
   "source": [
    "count = structures.count()\n",
    "\n",
    "print(f\"Number of entries containing Zinc figure motif is : {count}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize Structure Zinc interactions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
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       "<p>Failed to display Jupyter Widget of type <code>interactive</code>.</p>\n",
       "<p>\n",
       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
       "  that the widgets JavaScript is still loading. If this message persists, it\n",
       "  likely means that the widgets JavaScript library is either not installed or\n",
       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
       "  Widgets Documentation</a> for setup instructions.\n",
       "</p>\n",
       "<p>\n",
       "  If you're reading this message in another frontend (for example, a static\n",
       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
       "  it may mean that your frontend doesn't currently support widgets.\n",
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       "<function mmtfPyspark.structureViewer.view_group_interaction.<locals>.view3d>"
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   "source": [
    "structure_names = structures.keys().collect()\n",
    "view_group_interaction(structure_names, 'ZN', style='line')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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