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   "cell_type": "markdown",
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   "source": [
    "# Map To Protein Dimers Demo\n",
    "\n",
    "Example demonstrating how to extract protein dimers from PDB entries. This example uses a flatMap function to transform a strucure to its dimers.\n",
    "\n",
    "![Protein Dimers](https://upload.wikimedia.org/wikipedia/commons/thumb/c/ce/Galactose-1-phosphate_uridylyltransferase_1GUP.png/220px-Galactose-1-phosphate_uridylyltransferase_1GUP.png)\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.mappers import StructureToProteinDimers, StructureToBioassembly"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                  .setAppName(\"MapToProteinDimersDemo\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Download Protein *1STP* in MMTF format"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "protein = mmtfReader.download_mmtf_files([\"1STP\"], sc)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Map protein structure to Bioassembly, then map to protein dimers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "cutoffDistance = 8.0\n",
    "contacts = 20\n",
    "useAllAtoms = False\n",
    "exclusive = True\n",
    "\n",
    "dimers = protein.flatMap(StructureToBioassembly()) \\\n",
    "                .flatMap(StructureToProteinDimers(cutoffDistance, contacts, useAllAtoms, exclusive))\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Count number of structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of structures : 2\n"
     ]
    }
   ],
   "source": [
    "print(f\"Number of structures : {dimers.count()}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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