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   "source": [
    "# DSSP Demo\n",
    "\n",
    "This demo shows how to create and query a dssp dataset.\n",
    "\n",
    "DSSP is a database of secondary structure assigmnets for all protein entries in the Protein Data Bank (PDB).\n",
    "\n",
    "[DSSP Website](http://swift.cmbi.ru.nl/gv/dssp/)\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext, SQLContext\n",
    "from mmtfPyspark.datasets import secondaryStructureExtractor\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.mappers import StructureToPolymerChains\n",
    "import time"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"DSSPDemo\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Download single protein (1STP)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdbIds = [\"1STP\"]\n",
    "\n",
    "pdb = mmtfReader.download_mmtf_files(pdbIds, sc).cache()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Flatmap to polymer chains"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb = pdb.flatMap(StructureToPolymerChains())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extract Secondary Structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "root\n",
      " |-- structureChainId: string (nullable = false)\n",
      " |-- sequence: string (nullable = false)\n",
      " |-- alpha: float (nullable = false)\n",
      " |-- beta: float (nullable = false)\n",
      " |-- coil: float (nullable = false)\n",
      " |-- dsspQ8Code: string (nullable = false)\n",
      " |-- dsspQ3Code: string (nullable = false)\n",
      "\n",
      "+----------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+--------+----------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "|structureChainId|sequence                                                                                                                                                       |alpha     |beta    |coil      |dsspQ8Code                                                                                                                                                     |dsspQ3Code                                                                                                                                                     |\n",
      "+----------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+--------+----------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "|1STP.A          |DPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ|0.08264463|0.553719|0.36363637|XXXXXXXXXXXXCHHHHCEEEEETTCCEEEEEECTTSEEEEEEECSSSSCCSCEEEEEEECSSCCSSSCCEEEEEEEEEECSSCEEEEEEEEEEEEECSTTCEEEEEEEEEECCCGGGGGGCEEEEEEEEECCXXXXXXXXXXXXXXXXXXXXXXXXXX|XXXXXXXXXXXXCHHHHCEEEEECCCCEEEEEECCCCEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEEEEECCCCCEEEEEEEEEECCCHHHHHHCEEEEEEEEECCXXXXXXXXXXXXXXXXXXXXXXXXXX|\n",
      "+----------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+--------+----------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "\n"
     ]
    }
   ],
   "source": [
    "ds = secondaryStructureExtractor.get_dataset(pdb)\n",
    "\n",
    "ds.printSchema()\n",
    "ds.show(2, False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Terminate Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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