3-mmtf-pyspark/Solution-1.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Solution-1\n",
    "Apply your skills to filter structures and visualize the hits.\n",
    "\n",
    "For details see [filters](https://github.com/sbl-sdsc/mmtf-pyspark/tree/master/mmtfPyspark/filters) and [demos](https://github.com/sbl-sdsc/mmtf-pyspark/tree/master/demos/filters)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Import pyspark and mmtfPyspark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark.sql import SparkSession\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.filters import ContainsDnaChain, ContainsLProteinChain, ContainsSequenceRegex, RFree\n",
    "from mmtfPyspark.structureViewer import view_structure, view_group_interaction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "spark = SparkSession.builder.appName(\"Solution-1\").getOrCreate()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Read PDB structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = \"../resources/mmtf_reduced_sample/\"\n",
    "pdb = mmtfReader.read_sequence_file(path).cache()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### TODO-1: Filter structures by R-free in the range [0, 0.2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb = pdb.filter(RFree(0, 0.2))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### TODO-2: Find the protein-DNA complexes in this dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb = pdb.filter(ContainsLProteinChain()).filter(ContainsDnaChain())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### TODO-3: Create a of list the PDB IDs of the protein-DNA complexes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "complexes = pdb.keys().collect()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Visualize the protein-DNA complexes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "6d49f36a76fb49fd8062c591e180025a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(IntSlider(value=0, continuous_update=False, description='Structure', max=27), Output()),…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view_structure(complexes);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### TODO-4: Find complexes with a Zinc finger motif\n",
    "Zinc finger have the following sequence motif (regular expression): \"C.{2,4}C.{12}H.{3,5}H\"."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb = pdb.filter(ContainsSequenceRegex(\"C.{2,4}C.{12}H.{3,5}H\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "652b13469a604badba47a5b622e14524",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(IntSlider(value=0, continuous_update=False, description='Structure', max=1), Output()), …"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view_group_interaction(pdb.keys().collect(),\"ZN\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "spark.stop()"
   ]
  }
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