{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Secondary Structure Property Encoder Demo\n",
    "\n",
    "This demo creates a dataset of sequence segments dericed from a non-redundant set. The dataset contains the sequence segment, the DSSP Q8 and DSSP Q3 code of the center residue in a seuqnce segment, and a property encoding of the sequence segment.\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext, SQLContext\n",
    "from mmtfPyspark.ml import ProteinSequenceEncoder\n",
    "from mmtfPyspark.mappers import StructureToPolymerChains\n",
    "from mmtfPyspark.filters import ContainsLProteinChain\n",
    "from mmtfPyspark.datasets import secondaryStructureSegmentExtractor\n",
    "from mmtfPyspark.webfilters import Pisces\n",
    "from mmtfPyspark.io import mmtfReader"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark Context"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf() \\\n",
    "            .setMaster(\"local[*]\") \\\n",
    "            .setAppName(\"SecondaryStructurePropertyEncoderDemo\")\n",
    "\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " ## Read MMTF Hadoop sequence file and \n",
    " \n",
    " Create a non-redundant set(<=20% seq. identity) of L-protein chains"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = \"../../resources/mmtf_reduced_sample/\"\n",
    "sequenceIdentity = 20\n",
    "resolution = 2.0\n",
    "fraction = 0.1\n",
    "seed = 123\n",
    "\n",
    "pdb = mmtfReader \\\n",
    "        .read_sequence_file(path, sc) \\\n",
    "        .flatMap(StructureToPolymerChains()) \\\n",
    "        .filter(Pisces(sequenceIdentity, resolution)) \\\n",
    "        .filter(ContainsLProteinChain()) \\\n",
    "        .sample(False, fraction, seed)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get content"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "original data   : 2149\n"
     ]
    }
   ],
   "source": [
    "segmentLength = 11\n",
    "data = secondaryStructureSegmentExtractor.get_dataset(pdb, segmentLength).cache()\n",
    "print(f\"original data   : {data.count()}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Drop Q3 and sequence duplicates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "- duplicate Q3/seq  : 2149\n"
     ]
    }
   ],
   "source": [
    "data = data.dropDuplicates([\"labelQ3\", \"sequence\"]).cache()\n",
    "print(f\"- duplicate Q3/seq  : {data.count()}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Drop sequence duplicates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "- duplicate seq  : 2149\n"
     ]
    }
   ],
   "source": [
    "data = data.dropDuplicates([\"sequence\"])\n",
    "print(f\"- duplicate seq  : {data.count()}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Property Encoding"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "root\n",
      " |-- structureChainId: string (nullable = true)\n",
      " |-- sequence: string (nullable = false)\n",
      " |-- labelQ8: string (nullable = true)\n",
      " |-- labelQ3: string (nullable = true)\n",
      " |-- features: vector (nullable = true)\n",
      "\n",
      "+----------------+-----------+-------+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "|structureChainId|sequence   |labelQ8|labelQ3|features                                                                                                                                                                                                                                                                                                                                                                                     |\n",
      "+----------------+-----------+-------+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "|1A9X.F          |DIDTRKLTRLL|H      |H      |[1.6,0.11,2.78,-0.77,2.95,0.25,0.2,4.19,0.19,4.0,1.8,6.04,0.3,0.45,1.6,0.11,2.78,-0.77,2.95,0.25,0.2,3.03,0.11,2.6,0.26,5.6,0.21,0.36,1.89,0.22,4.77,-0.99,9.99,0.32,0.27,2.59,0.19,4.0,1.7,6.04,0.39,0.31,3.03,0.11,2.6,0.26,5.6,0.21,0.36,2.59,0.19,4.0,1.7,6.04,0.39,0.31,2.59,0.19,4.0,1.7,6.04,0.39,0.31]                                                                               |\n",
      "|1FO8.A          |DLEVAPDFFEY|T      |C      |[1.6,0.11,2.78,-0.77,2.95,0.25,0.2,2.59,0.19,4.0,1.7,6.04,0.39,0.31,1.56,0.15,3.78,-0.64,3.09,0.42,0.21,3.67,0.14,3.0,1.22,6.02,0.27,0.49,2.34,0.29,6.13,-1.01,10.74,0.36,0.25,2.67,0.0,2.72,0.72,6.8,0.13,0.34,1.6,0.11,2.78,-0.77,2.95,0.25,0.2,2.94,0.29,5.89,1.79,5.67,0.3,0.38,2.94,0.29,5.89,1.79,5.67,0.3,0.38,1.56,0.15,3.78,-0.64,3.09,0.42,0.21,2.94,0.3,6.47,0.96,5.66,0.25,0.41] |\n",
      "|1A9X.F          |EDLSSYLKRHN|H      |H      |[1.56,0.15,3.78,-0.64,3.09,0.42,0.21,1.6,0.11,2.78,-0.77,2.95,0.25,0.2,2.59,0.19,4.0,1.7,6.04,0.39,0.31,1.31,0.06,1.6,-0.04,5.7,0.2,0.28,1.31,0.06,1.6,-0.04,5.7,0.2,0.28,2.94,0.3,6.47,0.96,5.66,0.25,0.41,2.59,0.19,4.0,1.7,6.04,0.39,0.31,1.89,0.22,4.77,-0.99,9.99,0.32,0.27,2.99,0.23,4.66,0.13,7.69,0.27,0.3,1.6,0.13,2.95,-0.6,6.52,0.21,0.22]                                        |\n",
      "|1EB6.A          |GDESKFEEYFK|H      |H      |[0.0,0.0,0.0,0.0,6.07,0.13,0.15,1.6,0.11,2.78,-0.77,2.95,0.25,0.2,1.56,0.15,3.78,-0.64,3.09,0.42,0.21,1.31,0.06,1.6,-0.04,5.7,0.2,0.28,1.89,0.22,4.77,-0.99,9.99,0.32,0.27,2.94,0.29,5.89,1.79,5.67,0.3,0.38,1.56,0.15,3.78,-0.64,3.09,0.42,0.21,1.56,0.15,3.78,-0.64,3.09,0.42,0.21,2.94,0.3,6.47,0.96,5.66,0.25,0.41,2.94,0.29,5.89,1.79,5.67,0.3,0.38,1.89,0.22,4.77,-0.99,9.99,0.32,0.27]|\n",
      "|1C1K.A          |IISFETFILLD|H      |H      |[4.19,0.19,4.0,1.8,6.04,0.3,0.45,4.19,0.19,4.0,1.8,6.04,0.3,0.45,1.31,0.06,1.6,-0.04,5.7,0.2,0.28,2.94,0.29,5.89,1.79,5.67,0.3,0.38,1.56,0.15,3.78,-0.64,3.09,0.42,0.21,3.03,0.11,2.6,0.26,5.6,0.21,0.36,2.94,0.29,5.89,1.79,5.67,0.3,0.38,4.19,0.19,4.0,1.8,6.04,0.3,0.45,2.59,0.19,4.0,1.7,6.04,0.39,0.31,2.59,0.19,4.0,1.7,6.04,0.39,0.31,1.6,0.11,2.78,-0.77,2.95,0.25,0.2]              |\n",
      "+----------------+-----------+-------+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "only showing top 5 rows\n",
      "\n"
     ]
    }
   ],
   "source": [
    "encoder = ProteinSequenceEncoder(data)\n",
    "data = encoder.property_encode()\n",
    "\n",
    "data.printSchema()\n",
    "data.show(5, False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark Context"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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