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   "source": [
    "# Filter Protein Dna Complexes Demo\n",
    "\n",
    "This example shows how to filter PDB by protein DNA complexes\n",
    "\n",
    "![](./figures/ProteinDnaComplex.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.filters import ContainsDnaChain, ContainsLProteinChain\n",
    "from mmtfPyspark.structureViewer import view_structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"FilterProteinDnaComplexDate\")\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 proteins that cotinas Dna chain and L protein chain\n",
    "\n",
    "1) Retain pdb entires that exclusively contain L-peptide chains\n",
    "2) Retain pdb entries that exclusively contain L-Dna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "structures = pdb.filter(ContainsLProteinChain()) \\\n",
    "         .filter(ContainsDnaChain())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Count number of entires"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of entires that contain L-protein and L-DNA: 124\n"
     ]
    }
   ],
   "source": [
    "count = structures.count()\n",
    "\n",
    "print(f\"Number of entires that contain L-protein and L-DNA: {count}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize Structures"
   ]
  },
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   "cell_type": "code",
   "execution_count": 7,
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    "structure_names = structures.keys().collect()\n",
    "view_structure(structure_names)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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