{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Secondary Structure Blosum62 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 Blosum62 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(\"SecondaryStructureBlosumEncoderDemo\")\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": [
    "## Blosum62 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",
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      "+----------------+-----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "only showing top 5 rows\n",
      "\n"
     ]
    }
   ],
   "source": [
    "encoder = ProteinSequenceEncoder(data)\n",
    "data = encoder.blosum62_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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