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   "source": [
    "# Flat Map Chains Demo\n",
    "\n",
    "Example demonstrateing how to extract protein chains from PDB entries. This example uses a flatMap function to transform a structure to its polymer chains.\n",
    "\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext\n",
    "from mmtfPyspark.filters import PolymerComposition\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.mappers import StructureToPolymerChains"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                  .setAppName(\"FlatMapChainsDemo\")\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": [
    "## flat map structure to polymer chains, filter by polymer composition and count\n",
    "\n",
    "### Supported polymer composition type:\n",
    "\n",
    "** polymerComposition.AMINO_ACIDS_20  **= [\"ALA\",\"ARG\",\"ASN\",\"ASP\",\"CYS\",\"GLN\",\"GLU\",\"GLY\",\"HIS\",\"ILE\",\"LEU\",\"LYS\",\"MET\",\"PHE\",\"PRO\",\"SER\",\"THR\",\"TRP\",\"TYR\",\"VAL\"]\n",
    "\n",
    "** polymerComposition.AMINO_ACIDS_22 **= [\"ALA\",\"ARG\",\"ASN\",\"ASP\",\"CYS\",\"GLN\",\"GLU\",\"GLY\",\"HIS\",\"ILE\",\"LEU\",\"LYS\",\"MET\",\"PHE\",\"PRO\",\"SER\",\"THR\",\"TRP\",\"TYR\",\"VAL\",\"SEC\",\"PYL\"]\n",
    "\n",
    "** polymerComposition.DNA_STD_NUCLEOTIDES **= [\"DA\",\"DC\",\"DG\",\"DT\"]\n",
    "\n",
    "** polymerComposition.RNA_STD_NUCLEOTIDES **= [\"A\",\"C\",\"G\",\"U\"]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Chains with standard amino acids: 9386\n"
     ]
    }
   ],
   "source": [
    "count = pdb.flatMap(StructureToPolymerChains(False, True)) \\\n",
    "           .filter(PolymerComposition(PolymerComposition.AMINO_ACIDS_20)) \\\n",
    "           .count()\n",
    "        \n",
    "print(f\"Chains with standard amino acids: {count}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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