DataAnalysisExample.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Datamining the Protein Data Bank with mmtf-pyspark"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "mmtf-pyspark is a framework for the interactive mining of the Protein Data Bank (PDB). As an example, this demo analyzes the environment around zinc ions in proteins.\n",
    "\n",
    "This example demonstrates how to:\n",
    "    \n",
    "* Configure pyspark\n",
    "* Read PDB structures in MMTF file format\n",
    "* Create a non-redundant subset of structures\n",
    "* Show results in pandas dataframe\n",
    "* Plot histogram\n",
    "* Visualize structures in 3D\n",
    "\n",
    "For more example notebooks see the [demos folder](./demos) and the\n",
    "[mmtf-workshop2018](https://github.com/sbl-sdsc/mmtf-workshop-2018)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark.sql import SparkSession   \n",
    "from mmtfPyspark.filters import ContainsGroup\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.interactions import InteractionExtractor, InteractionFilter\n",
    "from mmtfPyspark.webfilters import Pisces                        \n",
    "from mmtfPyspark.structureViewer import view_group_interaction\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark\n",
    "Setup pyspark to run locally on 4 cores."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "spark = SparkSession.builder.appName(\"Demo\").getOrCreate()\n",
    "# Enable Arrow-based columnar data transfers to Pandas\n",
    "spark.conf.set(\"spark.sql.execution.arrow.enabled\", \"true\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read PDB structures\n",
    "Read a provided sample (~10,000 structures) of the PDB in MMTF format (https://mmtf.rcsb.org)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = \"./resources/mmtf_full_sample/\"\n",
    "pdb = mmtfReader.read_sequence_file(path)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Create a non-redundant subset\n",
    "Create a Pisces (Protein Sequence Culling Server, http://dunbrack.fccc.edu/PISCES.php) non-redundant subset for this analysis. Select protein chains with less than 20% sequence identity among each other and a resolution of 2.0 A or better."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb = pdb.filter(Pisces(sequenceIdentity = 20, resolution = 2.0))  "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extract Zinc interactions\n",
    "Find polar interactions within 3 A around each zinc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb = pdb.filter(ContainsGroup('ZN'))\n",
    "interaction_filter = InteractionFilter()\n",
    "interaction_filter.set_target_elements(False, ['C','H','P'])  # exclude non-polar elements\n",
    "interaction_filter.set_query_elements(True, ['Zn'])\n",
    "interaction_filter.set_distance_cutoff(3.0)\n",
    "\n",
    "interactions = InteractionExtractor().get_ligand_polymer_interactions(pdb, interaction_filter)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show table of interactions\n",
    "Convert Spark dataframe to a Pandas dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "      <td>19</td>\n",
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       "      <td>RVCPRILLECKKDSDCLAECVCLEHGYCG</td>\n",
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       "      <td>15</td>\n",
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       "      <td>ZN</td>\n",
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       "      <td>A</td>\n",
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       "      <td>ZN</td>\n",
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       "      <td>101</td>\n",
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       "      <td>14</td>\n",
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       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "      <th>19</th>\n",
       "      <td>5WLJ.C</td>\n",
       "      <td>ZN</td>\n",
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       "      <td>101</td>\n",
       "      <td>HIS</td>\n",
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       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "      <th>20</th>\n",
       "      <td>5WLJ.D</td>\n",
       "      <td>ZN</td>\n",
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       "      <td>103</td>\n",
       "      <td>GLU</td>\n",
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       "      <td>12</td>\n",
       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>5WLJ.B</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>104</td>\n",
       "      <td>HIS</td>\n",
       "      <td>B</td>\n",
       "      <td>15</td>\n",
       "      <td>15</td>\n",
       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "      <th>22</th>\n",
       "      <td>5WLJ.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>103</td>\n",
       "      <td>ASP</td>\n",
       "      <td>A</td>\n",
       "      <td>21</td>\n",
       "      <td>21</td>\n",
       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>5WLJ.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>102</td>\n",
       "      <td>ASP</td>\n",
       "      <td>A</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>5WLJ.C</td>\n",
       "      <td>ZN</td>\n",
       "      <td>C</td>\n",
       "      <td>103</td>\n",
       "      <td>GLU</td>\n",
       "      <td>C</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>XIEELLRKILEDEARHVAELEDIEKWLX</td>\n",
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       "      <th>25</th>\n",
       "      <td>1C7K.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>133</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>87</td>\n",
       "      <td>86</td>\n",
       "      <td>TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYE...</td>\n",
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       "      <th>26</th>\n",
       "      <td>1C7K.A</td>\n",
       "      <td>ZN</td>\n",
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       "      <td>133</td>\n",
       "      <td>ASP</td>\n",
       "      <td>A</td>\n",
       "      <td>93</td>\n",
       "      <td>92</td>\n",
       "      <td>TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYE...</td>\n",
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       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>1C7K.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>133</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>83</td>\n",
       "      <td>82</td>\n",
       "      <td>TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYE...</td>\n",
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       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>1F1M.B</td>\n",
       "      <td>ZN</td>\n",
       "      <td>B</td>\n",
       "      <td>802</td>\n",
       "      <td>HIS</td>\n",
       "      <td>B</td>\n",
       "      <td>142</td>\n",
       "      <td>104</td>\n",
       "      <td>KGPNLTEISKKITESNAVVLAVKEVETLLTSIDELAKAIGKKIKSD...</td>\n",
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       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>1F1M.D</td>\n",
       "      <td>ZN</td>\n",
       "      <td>D</td>\n",
       "      <td>806</td>\n",
       "      <td>HIS</td>\n",
       "      <td>D</td>\n",
       "      <td>92</td>\n",
       "      <td>54</td>\n",
       "      <td>KGPNLTEISKKITESNAVVLAVKEVETLLTSIDELAKAIGKKIKSD...</td>\n",
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       "      <th>2819</th>\n",
       "      <td>1VZY.B</td>\n",
       "      <td>ZN</td>\n",
       "      <td>B</td>\n",
       "      <td>1287</td>\n",
       "      <td>CYS</td>\n",
       "      <td>B</td>\n",
       "      <td>268</td>\n",
       "      <td>267</td>\n",
       "      <td>MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2820</th>\n",
       "      <td>1VZY.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1291</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>271</td>\n",
       "      <td>270</td>\n",
       "      <td>MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2821</th>\n",
       "      <td>1VZY.B</td>\n",
       "      <td>ZN</td>\n",
       "      <td>B</td>\n",
       "      <td>1287</td>\n",
       "      <td>CYS</td>\n",
       "      <td>B</td>\n",
       "      <td>271</td>\n",
       "      <td>270</td>\n",
       "      <td>MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2822</th>\n",
       "      <td>1VZY.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1291</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>235</td>\n",
       "      <td>234</td>\n",
       "      <td>MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2823</th>\n",
       "      <td>1VZY.B</td>\n",
       "      <td>ZN</td>\n",
       "      <td>B</td>\n",
       "      <td>1287</td>\n",
       "      <td>CYS</td>\n",
       "      <td>B</td>\n",
       "      <td>235</td>\n",
       "      <td>234</td>\n",
       "      <td>MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2824</th>\n",
       "      <td>1VZY.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1291</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>237</td>\n",
       "      <td>236</td>\n",
       "      <td>MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2825</th>\n",
       "      <td>4UPI.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1576</td>\n",
       "      <td>ASP</td>\n",
       "      <td>A</td>\n",
       "      <td>13</td>\n",
       "      <td>36</td>\n",
       "      <td>MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2826</th>\n",
       "      <td>4UPI.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1576</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>329</td>\n",
       "      <td>352</td>\n",
       "      <td>MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2827</th>\n",
       "      <td>4UPI.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1576</td>\n",
       "      <td>DDZ</td>\n",
       "      <td>A</td>\n",
       "      <td>53</td>\n",
       "      <td>76</td>\n",
       "      <td>MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2828</th>\n",
       "      <td>4UPI.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1576</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>53</td>\n",
       "      <td>-1</td>\n",
       "      <td>MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2829</th>\n",
       "      <td>4UPI.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>1576</td>\n",
       "      <td>ASP</td>\n",
       "      <td>A</td>\n",
       "      <td>328</td>\n",
       "      <td>351</td>\n",
       "      <td>MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2830</th>\n",
       "      <td>4XXF.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>301</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>206</td>\n",
       "      <td>180</td>\n",
       "      <td>GGLAALTKPPTFATVEAERAWLKERLVAAIRIFANEGFDHTVAGHL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2831</th>\n",
       "      <td>4XXF.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>301</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>144</td>\n",
       "      <td>118</td>\n",
       "      <td>GGLAALTKPPTFATVEAERAWLKERLVAAIRIFANEGFDHTVAGHL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2832</th>\n",
       "      <td>4XXF.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>301</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>142</td>\n",
       "      <td>116</td>\n",
       "      <td>GGLAALTKPPTFATVEAERAWLKERLVAAIRIFANEGFDHTVAGHL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2833</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>403</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>238</td>\n",
       "      <td>45</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2834</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>403</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>241</td>\n",
       "      <td>48</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2835</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>401</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>307</td>\n",
       "      <td>114</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2836</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>403</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>212</td>\n",
       "      <td>19</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2837</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>404</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>262</td>\n",
       "      <td>69</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2838</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>404</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>233</td>\n",
       "      <td>40</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2839</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>403</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>209</td>\n",
       "      <td>16</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2840</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>402</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>268</td>\n",
       "      <td>75</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2841</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>404</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>230</td>\n",
       "      <td>37</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2842</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>401</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>284</td>\n",
       "      <td>91</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2843</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>401</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>281</td>\n",
       "      <td>88</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2844</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>404</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>259</td>\n",
       "      <td>66</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2845</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>402</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>265</td>\n",
       "      <td>72</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2846</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>401</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>310</td>\n",
       "      <td>117</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2847</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>402</td>\n",
       "      <td>HIS</td>\n",
       "      <td>A</td>\n",
       "      <td>289</td>\n",
       "      <td>96</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2848</th>\n",
       "      <td>5B78.A</td>\n",
       "      <td>ZN</td>\n",
       "      <td>A</td>\n",
       "      <td>402</td>\n",
       "      <td>CYS</td>\n",
       "      <td>A</td>\n",
       "      <td>292</td>\n",
       "      <td>99</td>\n",
       "      <td>SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2849 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     structureChainId queryGroupId queryChainId queryGroupNumber  \\\n",
       "0              1LFW.A           ZN            A             1002   \n",
       "1              1LFW.A           ZN            A             1001   \n",
       "2              1LFW.A           ZN            A             1001   \n",
       "3              1LFW.A           ZN            A             1001   \n",
       "4              1LFW.A           ZN            A             1002   \n",
       "5              1LFW.A           ZN            A             1002   \n",
       "6              1LU0.A           ZN            A              201   \n",
       "7              1LU0.B           ZN            A              201   \n",
       "8              5WLJ.C           ZN            C              103   \n",
       "9              5WLJ.A           ZN            A              104   \n",
       "10             5WLJ.B           ZN            A              104   \n",
       "11             5WLJ.A           ZN            A              103   \n",
       "12             5WLJ.D           ZN            C              103   \n",
       "13             5WLJ.C           ZN            C              102   \n",
       "14             5WLJ.A           ZN            A              101   \n",
       "15             5WLJ.A           ZN            A              104   \n",
       "16             5WLJ.A           ZN            A              101   \n",
       "17             5WLJ.C           ZN            C              101   \n",
       "18             5WLJ.C           ZN            C              101   \n",
       "19             5WLJ.C           ZN            C              101   \n",
       "20             5WLJ.D           ZN            C              103   \n",
       "21             5WLJ.B           ZN            A              104   \n",
       "22             5WLJ.A           ZN            A              103   \n",
       "23             5WLJ.A           ZN            A              102   \n",
       "24             5WLJ.C           ZN            C              103   \n",
       "25             1C7K.A           ZN            A              133   \n",
       "26             1C7K.A           ZN            A              133   \n",
       "27             1C7K.A           ZN            A              133   \n",
       "28             1F1M.B           ZN            B              802   \n",
       "29             1F1M.D           ZN            D              806   \n",
       "...               ...          ...          ...              ...   \n",
       "2819           1VZY.B           ZN            B             1287   \n",
       "2820           1VZY.A           ZN            A             1291   \n",
       "2821           1VZY.B           ZN            B             1287   \n",
       "2822           1VZY.A           ZN            A             1291   \n",
       "2823           1VZY.B           ZN            B             1287   \n",
       "2824           1VZY.A           ZN            A             1291   \n",
       "2825           4UPI.A           ZN            A             1576   \n",
       "2826           4UPI.A           ZN            A             1576   \n",
       "2827           4UPI.A           ZN            A             1576   \n",
       "2828           4UPI.A           ZN            A             1576   \n",
       "2829           4UPI.A           ZN            A             1576   \n",
       "2830           4XXF.A           ZN            A              301   \n",
       "2831           4XXF.A           ZN            A              301   \n",
       "2832           4XXF.A           ZN            A              301   \n",
       "2833           5B78.A           ZN            A              403   \n",
       "2834           5B78.A           ZN            A              403   \n",
       "2835           5B78.A           ZN            A              401   \n",
       "2836           5B78.A           ZN            A              403   \n",
       "2837           5B78.A           ZN            A              404   \n",
       "2838           5B78.A           ZN            A              404   \n",
       "2839           5B78.A           ZN            A              403   \n",
       "2840           5B78.A           ZN            A              402   \n",
       "2841           5B78.A           ZN            A              404   \n",
       "2842           5B78.A           ZN            A              401   \n",
       "2843           5B78.A           ZN            A              401   \n",
       "2844           5B78.A           ZN            A              404   \n",
       "2845           5B78.A           ZN            A              402   \n",
       "2846           5B78.A           ZN            A              401   \n",
       "2847           5B78.A           ZN            A              402   \n",
       "2848           5B78.A           ZN            A              402   \n",
       "\n",
       "     targetGroupId targetChainId targetGroupNumber  sequenceIndex  \\\n",
       "0              ASP             A               177            176   \n",
       "1              HIS             A               439            438   \n",
       "2              ASP             A               119            118   \n",
       "3              GLU             A               154            153   \n",
       "4              HIS             A                87             86   \n",
       "5              ASP             A               119            118   \n",
       "6              GLU             A                19             18   \n",
       "7              GLU             B                19             18   \n",
       "8              HIS             C                15             15   \n",
       "9              HIS             A                15             15   \n",
       "10             GLU             B                12             12   \n",
       "11             GLU             A                20             20   \n",
       "12             HIS             D                15             15   \n",
       "13             ASP             C                11             11   \n",
       "14             HIS             A                15             15   \n",
       "15             GLU             A                12             12   \n",
       "16             ASP             A                11             11   \n",
       "17             ASP             C                11             11   \n",
       "18             ARG             C                14             14   \n",
       "19             HIS             C                15             15   \n",
       "20             GLU             D                12             12   \n",
       "21             HIS             B                15             15   \n",
       "22             ASP             A                21             21   \n",
       "23             ASP             A                11             11   \n",
       "24             GLU             C                12             12   \n",
       "25             HIS             A                87             86   \n",
       "26             ASP             A                93             92   \n",
       "27             HIS             A                83             82   \n",
       "28             HIS             B               142            104   \n",
       "29             HIS             D                92             54   \n",
       "...            ...           ...               ...            ...   \n",
       "2819           CYS             B               268            267   \n",
       "2820           CYS             A               271            270   \n",
       "2821           CYS             B               271            270   \n",
       "2822           CYS             A               235            234   \n",
       "2823           CYS             B               235            234   \n",
       "2824           CYS             A               237            236   \n",
       "2825           ASP             A                13             36   \n",
       "2826           HIS             A               329            352   \n",
       "2827           DDZ             A                53             76   \n",
       "2828           CYS             A                53             -1   \n",
       "2829           ASP             A               328            351   \n",
       "2830           HIS             A               206            180   \n",
       "2831           HIS             A               144            118   \n",
       "2832           HIS             A               142            116   \n",
       "2833           HIS             A               238             45   \n",
       "2834           CYS             A               241             48   \n",
       "2835           CYS             A               307            114   \n",
       "2836           CYS             A               212             19   \n",
       "2837           CYS             A               262             69   \n",
       "2838           CYS             A               233             40   \n",
       "2839           CYS             A               209             16   \n",
       "2840           CYS             A               268             75   \n",
       "2841           CYS             A               230             37   \n",
       "2842           CYS             A               284             91   \n",
       "2843           CYS             A               281             88   \n",
       "2844           CYS             A               259             66   \n",
       "2845           CYS             A               265             72   \n",
       "2846           CYS             A               310            117   \n",
       "2847           HIS             A               289             96   \n",
       "2848           CYS             A               292             99   \n",
       "\n",
       "                                               sequence  \n",
       "0     MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPV...  \n",
       "1     MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPV...  \n",
       "2     MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPV...  \n",
       "3     MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPV...  \n",
       "4     MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPV...  \n",
       "5     MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPV...  \n",
       "6                         RVCPRILLECKKDSDCLAECVCLEHGYCG  \n",
       "7                         RVCPRILLECKKDSDCLAECVCLEHGYCG  \n",
       "8                          XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "9                          XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "10                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "11                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "12                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "13                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "14                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "15                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "16                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "17                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "18                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "19                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "20                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "21                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "22                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "23                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "24                         XIEELLRKILEDEARHVAELEDIEKWLX  \n",
       "25    TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYE...  \n",
       "26    TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYE...  \n",
       "27    TVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYE...  \n",
       "28    KGPNLTEISKKITESNAVVLAVKEVETLLTSIDELAKAIGKKIKSD...  \n",
       "29    KGPNLTEISKKITESNAVVLAVKEVETLLTSIDELAKAIGKKIKSD...  \n",
       "...                                                 ...  \n",
       "2819  MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...  \n",
       "2820  MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...  \n",
       "2821  MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...  \n",
       "2822  MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...  \n",
       "2823  MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...  \n",
       "2824  MDYLVKALAYDGKVRAYAARTTDMVNEGQRRHGTWPTASAALGRTM...  \n",
       "2825  MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...  \n",
       "2826  MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...  \n",
       "2827  MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...  \n",
       "2828  MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...  \n",
       "2829  MASWSHPQFEKGAETAVPNSSSVPMTQNRNILWIMCDQLRFDYLSC...  \n",
       "2830  GGLAALTKPPTFATVEAERAWLKERLVAAIRIFANEGFDHTVAGHL...  \n",
       "2831  GGLAALTKPPTFATVEAERAWLKERLVAAIRIFANEGFDHTVAGHL...  \n",
       "2832  GGLAALTKPPTFATVEAERAWLKERLVAAIRIFANEGFDHTVAGHL...  \n",
       "2833  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2834  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2835  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2836  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2837  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2838  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2839  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2840  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2841  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2842  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2843  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2844  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2845  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2846  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2847  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "2848  SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGH...  \n",
       "\n",
       "[2849 rows x 9 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = interactions.toPandas()\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Print histogram of the top 10 interacting amino acid groups"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "df.targetGroupId.value_counts().head(10).plot(kind='bar');"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize Structures"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create a list of unique PDB ids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "df['pdbId'] = df.structureChainId.str[:4]\n",
    "pdb_ids = list(df.pdbId.drop_duplicates())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Browse through the list by moving the slider."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f3275c1d70b04da697cd6692d03cff18",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(IntSlider(value=0, continuous_update=False, description='Structure', max=379), Output())…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view_group_interaction(pdb_ids, 'ZN', style = 'cartoon');"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Stop spark\n",
    "Always run the notebook to the end to stop spark!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "spark.stop()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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