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   "source": [
    "# Custom Report Demo\n",
    "\n",
    "This demo shows how to create and query a dataset. The dataset in this case is generated by running an RCSB PDB web service to create a custom report of PDB annotations.\n",
    "\n",
    "[PDB custom report](http://www.rcsb.org/pdb/results/reportField.do)\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext, SQLContext\n",
    "from mmtfPyspark.datasets import customReportService\n",
    "import time"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"secondaryStructureSegmentDemo\")\n",
    "sc = SparkContext(conf = conf)\n",
    "sqlContext = SQLContext(sc)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Retrieve PDB annotation:\n",
    "Binding addinities (Ki, Kd), group name of the ligand (hetId), and the Enzyme Classification number (ecNo)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "ds = customReportService.get_dataset([\"Ki\",\"Kd\",\"hetId\",\"ecNo\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show the schema of this dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "root\n",
      " |-- structureChainId: string (nullable = true)\n",
      " |-- structureId: string (nullable = true)\n",
      " |-- chainId: string (nullable = true)\n",
      " |-- Ki: string (nullable = true)\n",
      " |-- Kd: string (nullable = true)\n",
      " |-- hetId: string (nullable = true)\n",
      " |-- ecNo: string (nullable = true)\n",
      "\n"
     ]
    }
   ],
   "source": [
    "ds.printSchema()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Filtering\n",
    "\n",
    "### Select structures that either have Ki or Kd values(s) and are protein-serine/threonine kinases (EC 2.7.1.*)\n",
    "\n",
    "\n",
    "#### A. By using dataset operations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "+----------------+-----------+-------+--------------------+------------+-----+---------+\n",
      "|structureChainId|structureId|chainId|                  Ki|          Kd|hetId|     ecNo|\n",
      "+----------------+-----------+-------+--------------------+------------+-----+---------+\n",
      "|          2CLQ.A|       2CLQ|      A|                null|11-120 (BDB)|  STU|2.7.11.25|\n",
      "|          2CLQ.B|       2CLQ|      B|                null|11-120 (BDB)|  STU|2.7.11.25|\n",
      "|          2E9N.A|       2E9N|      A|           6.3 (BDB)|        null|  76A| 2.7.11.1|\n",
      "|          2E9O.A|       2E9O|      A|            20 (BDB)|        null|  A58| 2.7.11.1|\n",
      "|          2E9P.A|       2E9P|      A|            20 (BDB)|        null|  77A| 2.7.11.1|\n",
      "|          2E9U.A|       2E9U|      A|7.94 (PDBbind)#7....|        null|  A25| 2.7.11.1|\n",
      "|          2E9V.A|       2E9V|      A|12.59 (PDBbind)#1...|        null|  85A| 2.7.11.1|\n",
      "|          2E9V.B|       2E9V|      B|12.59 (PDBbind)#1...|        null|  85A| 2.7.11.1|\n",
      "|          2GNF.A|       2GNF|      A|6000 (BMOAD_9806)...|        null|  Y27|2.7.11.11|\n",
      "|          2GNH.A|       2GNH|      A|149 (BMOAD_9880)#...|        null|  H52|2.7.11.11|\n",
      "+----------------+-----------+-------+--------------------+------------+-----+---------+\n",
      "only showing top 10 rows\n",
      "\n"
     ]
    }
   ],
   "source": [
    "ds = ds.filter(\"(Ki IS NOT NULL OR Kd IS NOT NULL) AND ecNo LIKE '2.7.11.%'\")\n",
    "\n",
    "ds.show(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### B. By creating a temporary query and running SQL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "+----------------+-----------+-------+--------------------+------------+-----+---------+\n",
      "|structureChainId|structureId|chainId|                  Ki|          Kd|hetId|     ecNo|\n",
      "+----------------+-----------+-------+--------------------+------------+-----+---------+\n",
      "|          2CLQ.A|       2CLQ|      A|                null|11-120 (BDB)|  STU|2.7.11.25|\n",
      "|          2CLQ.B|       2CLQ|      B|                null|11-120 (BDB)|  STU|2.7.11.25|\n",
      "|          2E9N.A|       2E9N|      A|           6.3 (BDB)|        null|  76A| 2.7.11.1|\n",
      "|          2E9O.A|       2E9O|      A|            20 (BDB)|        null|  A58| 2.7.11.1|\n",
      "|          2E9P.A|       2E9P|      A|            20 (BDB)|        null|  77A| 2.7.11.1|\n",
      "|          2E9U.A|       2E9U|      A|7.94 (PDBbind)#7....|        null|  A25| 2.7.11.1|\n",
      "|          2E9V.A|       2E9V|      A|12.59 (PDBbind)#1...|        null|  85A| 2.7.11.1|\n",
      "|          2E9V.B|       2E9V|      B|12.59 (PDBbind)#1...|        null|  85A| 2.7.11.1|\n",
      "|          2GNF.A|       2GNF|      A|6000 (BMOAD_9806)...|        null|  Y27|2.7.11.11|\n",
      "|          2GNH.A|       2GNH|      A|149 (BMOAD_9880)#...|        null|  H52|2.7.11.11|\n",
      "+----------------+-----------+-------+--------------------+------------+-----+---------+\n",
      "only showing top 10 rows\n",
      "\n"
     ]
    }
   ],
   "source": [
    "ds.createOrReplaceTempView(\"table\")\n",
    "\n",
    "ds = sqlContext.sql(\"SELECT * from table WHERE (Ki IS NOT NULL OR Kd IS NOT NULL) AND ecNo LIKE '2.7.11.%'\")\n",
    "\n",
    "ds.show(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Terminate Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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