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    "# Filter By RFree Demo\n",
    "\n",
    "Example of reading an MMTF Hadoop Sequence file, filtering the entries by resolution, and counting the number of entries. This example shows how methods can be chained together.\n",
    "\n",
    "[R Free](http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/r-value-and-r-free)\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.filters import RFree\n",
    "from mmtfPyspark.structureViewer import view_structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"FilterByRFreeDate\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read in MMTF Files, filter by RFree and count"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of structures : 1397\n"
     ]
    }
   ],
   "source": [
    "path = \"../../resources/mmtf_reduced_sample/\"\n",
    "\n",
    "structures = mmtfReader.read_sequence_file(path, sc) \\\n",
    "                       .filter(RFree(0.15,0.25))\n",
    "        \n",
    "print(f\"Number of structures : {structures.count()}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize Structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
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    "structure_names = structures.keys().collect()\n",
    "view_structure(structure_names, style='stick')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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