notebooks/dataprep/01f-PDBStructure.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Downloads PDB Structure Information\n",
    "**[Work in progress]**\n",
    "\n",
    "This notebook downloads 3D-structure information from the Worldwide Protein Data Bank.\n",
    "\n",
    "Data sources: \n",
    "[Protein Data Bank Japan](https://pdbj.org/), \n",
    "[PDBe Protein Data Bank Europe](https://www.ebi.ac.uk/pdbe/)\n",
    "\n",
    "Author: Peter Rose (pwrose@ucsd.edu)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import re\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import dateutil\n",
    "import urllib\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.options.display.max_rows = None  # display all rows\n",
    "pd.options.display.max_columns = None  # display all columsns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/peter/Library/Application Support/com.Neo4j.Relate/data/dbmss/dbms-8bf637fc-0d20-4d9f-9c6f-f7e72e92a4da/import\n"
     ]
    }
   ],
   "source": [
    "NEO4J_IMPORT = Path(os.getenv('NEO4J_IMPORT'))\n",
    "print(NEO4J_IMPORT)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get PDB summary data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "URL = 'https://pdbj.org/rest/newweb/search/sql?format=csv&q='"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sql_query = 'SELECT pdbid, release_date AS releasedate, pdbx_descriptor AS description, struct_title AS title, exptl_method AS methods, resolution FROM brief_summary'\n",
    "encoded_query = urllib.parse.quote(sql_query)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "summary_url = URL + encoded_query\n",
    "df_summary = pd.read_csv(summary_url, dtype=str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbid</th>\n",
       "      <th>releasedate</th>\n",
       "      <th>description</th>\n",
       "      <th>title</th>\n",
       "      <th>methods</th>\n",
       "      <th>resolution</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>3q7d</td>\n",
       "      <td>2011-11-09</td>\n",
       "      <td>(2R)-2-(6-methoxynaphthalen-2-yl)propanoic aci...</td>\n",
       "      <td>Structure of (R)-naproxen bound to mCOX-2.</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1wgi</td>\n",
       "      <td>1997-11-19</td>\n",
       "      <td>INORGANIC PYROPHOSPHATASE, MANGANESE (II) ION,...</td>\n",
       "      <td>STRUCTURE OF INORGANIC PYROPHOSPHATASE</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>5z3f</td>\n",
       "      <td>2019-05-15</td>\n",
       "      <td>CITRIC ACID, GLYCEROL, Glycoside hydrolase 15-...</td>\n",
       "      <td>Glycosidase E335A in complex with glucose</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1wgm</td>\n",
       "      <td>2004-11-28</td>\n",
       "      <td>Ubiquitin conjugation factor E4A</td>\n",
       "      <td>Solution structure of the U-box in human ubiqu...</td>\n",
       "      <td>SOLUTION NMR</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1wiu</td>\n",
       "      <td>1996-12-23</td>\n",
       "      <td>TWITCHIN 18TH IGSF MODULE</td>\n",
       "      <td>TWITCHIN IMMUNOGLOBULIN SUPERFAMILY DOMAIN (IG...</td>\n",
       "      <td>SOLUTION NMR</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  pdbid releasedate                                        description  \\\n",
       "0  3q7d  2011-11-09  (2R)-2-(6-methoxynaphthalen-2-yl)propanoic aci...   \n",
       "1  1wgi  1997-11-19  INORGANIC PYROPHOSPHATASE, MANGANESE (II) ION,...   \n",
       "2  5z3f  2019-05-15  CITRIC ACID, GLYCEROL, Glycoside hydrolase 15-...   \n",
       "3  1wgm  2004-11-28                   Ubiquitin conjugation factor E4A   \n",
       "4  1wiu  1996-12-23                          TWITCHIN 18TH IGSF MODULE   \n",
       "\n",
       "                                               title            methods  \\\n",
       "0         Structure of (R)-naproxen bound to mCOX-2.  X-RAY DIFFRACTION   \n",
       "1             STRUCTURE OF INORGANIC PYROPHOSPHATASE  X-RAY DIFFRACTION   \n",
       "2          Glycosidase E335A in complex with glucose  X-RAY DIFFRACTION   \n",
       "3  Solution structure of the U-box in human ubiqu...       SOLUTION NMR   \n",
       "4  TWITCHIN IMMUNOGLOBULIN SUPERFAMILY DOMAIN (IG...       SOLUTION NMR   \n",
       "\n",
       "  resolution  \n",
       "0        2.4  \n",
       "1        2.2  \n",
       "2        1.1  \n",
       "3        NaN  \n",
       "4        NaN  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_summary.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_summary.rename(columns={'pdbid': 'pdbId'}, inplace=True)\n",
    "df_summary['pdbId'] = df_summary['pdbId'].str.upper()\n",
    "df_summary.rename(columns={'releasedate': 'releaseDate'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of records: 178451\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>releaseDate</th>\n",
       "      <th>description</th>\n",
       "      <th>title</th>\n",
       "      <th>methods</th>\n",
       "      <th>resolution</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>3Q7D</td>\n",
       "      <td>2011-11-09</td>\n",
       "      <td>(2R)-2-(6-methoxynaphthalen-2-yl)propanoic aci...</td>\n",
       "      <td>Structure of (R)-naproxen bound to mCOX-2.</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1WGI</td>\n",
       "      <td>1997-11-19</td>\n",
       "      <td>INORGANIC PYROPHOSPHATASE, MANGANESE (II) ION,...</td>\n",
       "      <td>STRUCTURE OF INORGANIC PYROPHOSPHATASE</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>5Z3F</td>\n",
       "      <td>2019-05-15</td>\n",
       "      <td>CITRIC ACID, GLYCEROL, Glycoside hydrolase 15-...</td>\n",
       "      <td>Glycosidase E335A in complex with glucose</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1WGM</td>\n",
       "      <td>2004-11-28</td>\n",
       "      <td>Ubiquitin conjugation factor E4A</td>\n",
       "      <td>Solution structure of the U-box in human ubiqu...</td>\n",
       "      <td>SOLUTION NMR</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1WIU</td>\n",
       "      <td>1996-12-23</td>\n",
       "      <td>TWITCHIN 18TH IGSF MODULE</td>\n",
       "      <td>TWITCHIN IMMUNOGLOBULIN SUPERFAMILY DOMAIN (IG...</td>\n",
       "      <td>SOLUTION NMR</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  pdbId releaseDate                                        description  \\\n",
       "0  3Q7D  2011-11-09  (2R)-2-(6-methoxynaphthalen-2-yl)propanoic aci...   \n",
       "1  1WGI  1997-11-19  INORGANIC PYROPHOSPHATASE, MANGANESE (II) ION,...   \n",
       "2  5Z3F  2019-05-15  CITRIC ACID, GLYCEROL, Glycoside hydrolase 15-...   \n",
       "3  1WGM  2004-11-28                   Ubiquitin conjugation factor E4A   \n",
       "4  1WIU  1996-12-23                          TWITCHIN 18TH IGSF MODULE   \n",
       "\n",
       "                                               title            methods  \\\n",
       "0         Structure of (R)-naproxen bound to mCOX-2.  X-RAY DIFFRACTION   \n",
       "1             STRUCTURE OF INORGANIC PYROPHOSPHATASE  X-RAY DIFFRACTION   \n",
       "2          Glycosidase E335A in complex with glucose  X-RAY DIFFRACTION   \n",
       "3  Solution structure of the U-box in human ubiqu...       SOLUTION NMR   \n",
       "4  TWITCHIN IMMUNOGLOBULIN SUPERFAMILY DOMAIN (IG...       SOLUTION NMR   \n",
       "\n",
       "  resolution  \n",
       "0        2.4  \n",
       "1        2.2  \n",
       "2        1.1  \n",
       "3        NaN  \n",
       "4        NaN  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print('Number of records:', df_summary.shape[0])\n",
    "df_summary.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get refinement data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "sqlQuery = 'SELECT \"ls_R_factor_R_free\", entry_id FROM refine'\n",
    "encoded_query = urllib.parse.quote(sqlQuery)\n",
    "refine_url = URL + encoded_query"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "#df_refine = pd.read_csv(refine_url, usecols=['ls_R_factor_R_free', 'entry_id'], dtype=str)\n",
    "df_refine = pd.read_csv(refine_url, dtype=str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ls_R_factor_R_free</th>\n",
       "      <th>entry_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NaN</td>\n",
       "      <td>100D</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.252</td>\n",
       "      <td>101D</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.202</td>\n",
       "      <td>101M</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NaN</td>\n",
       "      <td>102D</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NaN</td>\n",
       "      <td>102L</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  ls_R_factor_R_free entry_id\n",
       "0                NaN     100D\n",
       "1              0.252     101D\n",
       "2              0.202     101M\n",
       "3                NaN     102D\n",
       "4                NaN     102L"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_refine.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_refine.rename(columns={'ls_R_factor_R_free': 'rFree', 'entry_id': 'pdbId'}, inplace=True)\n",
    "df_refine.fillna('', inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of records: 160748\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>rFree</th>\n",
       "      <th>pdbId</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>90063</th>\n",
       "      <td>0.216</td>\n",
       "      <td>4O6Y</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28993</th>\n",
       "      <td>0.223</td>\n",
       "      <td>2DKG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20615</th>\n",
       "      <td>0.244</td>\n",
       "      <td>1UR0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59883</th>\n",
       "      <td>0.24293</td>\n",
       "      <td>3MFF</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45689</th>\n",
       "      <td>0.285</td>\n",
       "      <td>2ZYK</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         rFree pdbId\n",
       "90063    0.216  4O6Y\n",
       "28993    0.223  2DKG\n",
       "20615    0.244  1UR0\n",
       "59883  0.24293  3MFF\n",
       "45689    0.285  2ZYK"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print('Number of records:', df_refine.shape[0])\n",
    "df_refine.sample(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "structures = df_summary.merge(df_refine, on='pdbId', how='left')\n",
    "structures.fillna('', inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "structures.drop_duplicates(subset=['pdbId'], inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of structures: 178451\n"
     ]
    },
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>releaseDate</th>\n",
       "      <th>description</th>\n",
       "      <th>title</th>\n",
       "      <th>methods</th>\n",
       "      <th>resolution</th>\n",
       "      <th>rFree</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>44883</th>\n",
       "      <td>5R7W</td>\n",
       "      <td>2020-04-22</td>\n",
       "      <td>Interleukin-1 beta, SULFATE ION, water</td>\n",
       "      <td>PanDDA analysis group deposition of ground-sta...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.27</td>\n",
       "      <td>0.2026</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>157446</th>\n",
       "      <td>3BED</td>\n",
       "      <td>2007-11-27</td>\n",
       "      <td>PTS system, IIA component, water</td>\n",
       "      <td>Mannose/sorbose specific IIA subunit of phosph...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.45</td>\n",
       "      <td>0.1967</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>111002</th>\n",
       "      <td>7AEJ</td>\n",
       "      <td>2021-05-26</td>\n",
       "      <td>2H10, Envelope glycoprotein gp160,Envelope gly...</td>\n",
       "      <td>Crystal structure of asymmetric HIV-1 gp41 con...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>3.8</td>\n",
       "      <td>0.3077</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113828</th>\n",
       "      <td>5P8V</td>\n",
       "      <td>2016-08-03</td>\n",
       "      <td>Endothiapepsin, water</td>\n",
       "      <td>Automated refinement of diffraction data obtai...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.579</td>\n",
       "      <td>0.1735</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>125444</th>\n",
       "      <td>1HG8</td>\n",
       "      <td>2001-11-10</td>\n",
       "      <td>2-acetamido-2-deoxy-beta-D-glucopyranose, 2-ac...</td>\n",
       "      <td>Endopolygalacturonase from the phytopathogenic...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.73</td>\n",
       "      <td>0.203</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7148</th>\n",
       "      <td>3BHP</td>\n",
       "      <td>2007-12-11</td>\n",
       "      <td>UPF0291 protein ynzC, water</td>\n",
       "      <td>Crystal structure of UPF0291 protein ynzC from...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.01</td>\n",
       "      <td>0.2623</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72835</th>\n",
       "      <td>1U1L</td>\n",
       "      <td>2004-09-21</td>\n",
       "      <td>5'-D(*TP*AP*GP*GP*GP*TP*TP*(PRN)P*GP*GP*G)-3',...</td>\n",
       "      <td>Crystal Structure of UP1 Complexed With d(TTAG...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2</td>\n",
       "      <td>0.274</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104563</th>\n",
       "      <td>5KL8</td>\n",
       "      <td>2016-08-17</td>\n",
       "      <td>Maternal protein pumilio, Protein nanos, RNA (...</td>\n",
       "      <td>Crystal structure of the Pumilio-Nos-CyclinB R...</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>4</td>\n",
       "      <td>0.3119</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>111008</th>\n",
       "      <td>3GMO</td>\n",
       "      <td>2009-11-10</td>\n",
       "      <td>1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glu...</td>\n",
       "      <td>Structure of mouse CD1d in complex with C8PhF</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.6</td>\n",
       "      <td>0.2156</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>107698</th>\n",
       "      <td>7JSI</td>\n",
       "      <td>2020-12-16</td>\n",
       "      <td>DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3'), Prote...</td>\n",
       "      <td>Adeno-Associated Virus 2 Rep68 HD Hexamer-ssDN...</td>\n",
       "      <td>ELECTRON MICROSCOPY</td>\n",
       "      <td>5.01</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       pdbId releaseDate                                        description  \\\n",
       "44883   5R7W  2020-04-22             Interleukin-1 beta, SULFATE ION, water   \n",
       "157446  3BED  2007-11-27                   PTS system, IIA component, water   \n",
       "111002  7AEJ  2021-05-26  2H10, Envelope glycoprotein gp160,Envelope gly...   \n",
       "113828  5P8V  2016-08-03                              Endothiapepsin, water   \n",
       "125444  1HG8  2001-11-10  2-acetamido-2-deoxy-beta-D-glucopyranose, 2-ac...   \n",
       "7148    3BHP  2007-12-11                        UPF0291 protein ynzC, water   \n",
       "72835   1U1L  2004-09-21  5'-D(*TP*AP*GP*GP*GP*TP*TP*(PRN)P*GP*GP*G)-3',...   \n",
       "104563  5KL8  2016-08-17  Maternal protein pumilio, Protein nanos, RNA (...   \n",
       "111008  3GMO  2009-11-10  1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glu...   \n",
       "107698  7JSI  2020-12-16  DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3'), Prote...   \n",
       "\n",
       "                                                    title  \\\n",
       "44883   PanDDA analysis group deposition of ground-sta...   \n",
       "157446  Mannose/sorbose specific IIA subunit of phosph...   \n",
       "111002  Crystal structure of asymmetric HIV-1 gp41 con...   \n",
       "113828  Automated refinement of diffraction data obtai...   \n",
       "125444  Endopolygalacturonase from the phytopathogenic...   \n",
       "7148    Crystal structure of UPF0291 protein ynzC from...   \n",
       "72835   Crystal Structure of UP1 Complexed With d(TTAG...   \n",
       "104563  Crystal structure of the Pumilio-Nos-CyclinB R...   \n",
       "111008      Structure of mouse CD1d in complex with C8PhF   \n",
       "107698  Adeno-Associated Virus 2 Rep68 HD Hexamer-ssDN...   \n",
       "\n",
       "                    methods resolution   rFree  \n",
       "44883     X-RAY DIFFRACTION       1.27  0.2026  \n",
       "157446    X-RAY DIFFRACTION       1.45  0.1967  \n",
       "111002    X-RAY DIFFRACTION        3.8  0.3077  \n",
       "113828    X-RAY DIFFRACTION      1.579  0.1735  \n",
       "125444    X-RAY DIFFRACTION       1.73   0.203  \n",
       "7148      X-RAY DIFFRACTION       2.01  0.2623  \n",
       "72835     X-RAY DIFFRACTION          2   0.274  \n",
       "104563    X-RAY DIFFRACTION          4  0.3119  \n",
       "111008    X-RAY DIFFRACTION        1.6  0.2156  \n",
       "107698  ELECTRON MICROSCOPY       5.01          "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print('Number of structures:', structures.shape[0])\n",
    "structures.sample(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "structures['pdbId'] = 'pdb:' + structures['pdbId']\n",
    "\n",
    "# convert methods string to a semicolon separated list (our default one-to-many representation in CSV files)\n",
    "structures['methods'] = structures['methods'].str.replace('[', '', regex=False)\n",
    "structures['methods'] = structures['methods'].str.replace(']', '', regex=False)\n",
    "structures['methods'] = structures['methods'].str.replace(\"'\", '', regex=False)\n",
    "structures['methods'] = structures['methods'].str.replace(',', ';', regex=False)\n",
    "structures['methods'] = structures['methods'].str.replace('; ', ';', regex=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['X-RAY DIFFRACTION', 'SOLUTION NMR', 'SOLID-STATE NMR',\n",
       "       'ELECTRON MICROSCOPY', 'NEUTRON DIFFRACTION',\n",
       "       'ELECTRON CRYSTALLOGRAPHY',\n",
       "       'ELECTRON MICROSCOPY;SOLID-STATE NMR;SOLUTION SCATTERING;HYBRID',\n",
       "       'SOLID-STATE NMR;SOLUTION NMR;HYBRID',\n",
       "       'SOLUTION NMR;SOLUTION SCATTERING;HYBRID', 'SOLUTION SCATTERING',\n",
       "       'FIBER DIFFRACTION',\n",
       "       'NEUTRON DIFFRACTION;X-RAY DIFFRACTION;HYBRID',\n",
       "       'EPR;X-RAY DIFFRACTION;HYBRID',\n",
       "       'SOLUTION NMR;THEORETICAL MODEL;HYBRID',\n",
       "       'SOLUTION SCATTERING;X-RAY DIFFRACTION;HYBRID',\n",
       "       'NEUTRON DIFFRACTION;SOLUTION NMR;HYBRID', 'INFRARED SPECTROSCOPY',\n",
       "       'POWDER DIFFRACTION', 'EPR;SOLUTION NMR;HYBRID',\n",
       "       'ELECTRON MICROSCOPY;SOLID-STATE NMR;HYBRID',\n",
       "       'FLUORESCENCE TRANSFER',\n",
       "       'ELECTRON MICROSCOPY;SOLUTION SCATTERING;HYBRID',\n",
       "       'ELECTRON MICROSCOPY;SOLUTION NMR;HYBRID',\n",
       "       'FIBER DIFFRACTION;SOLID-STATE NMR;HYBRID',\n",
       "       'SOLUTION NMR;X-RAY DIFFRACTION;HYBRID',\n",
       "       'ELECTRON MICROSCOPY;SOLID-STATE NMR;SOLUTION NMR;HYBRID'],\n",
       "      dtype=object)"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structures['methods'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>releaseDate</th>\n",
       "      <th>description</th>\n",
       "      <th>title</th>\n",
       "      <th>methods</th>\n",
       "      <th>resolution</th>\n",
       "      <th>rFree</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>pdb:3Q7D</td>\n",
       "      <td>2011-11-09</td>\n",
       "      <td>(2R)-2-(6-methoxynaphthalen-2-yl)propanoic aci...</td>\n",
       "      <td>Structure of (R)-naproxen bound to mCOX-2.</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.4</td>\n",
       "      <td>0.2329</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>pdb:1WGI</td>\n",
       "      <td>1997-11-19</td>\n",
       "      <td>INORGANIC PYROPHOSPHATASE, MANGANESE (II) ION,...</td>\n",
       "      <td>STRUCTURE OF INORGANIC PYROPHOSPHATASE</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>2.2</td>\n",
       "      <td>0.211</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>pdb:5Z3F</td>\n",
       "      <td>2019-05-15</td>\n",
       "      <td>CITRIC ACID, GLYCEROL, Glycoside hydrolase 15-...</td>\n",
       "      <td>Glycosidase E335A in complex with glucose</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>1.1</td>\n",
       "      <td>0.12089</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>pdb:1WGM</td>\n",
       "      <td>2004-11-28</td>\n",
       "      <td>Ubiquitin conjugation factor E4A</td>\n",
       "      <td>Solution structure of the U-box in human ubiqu...</td>\n",
       "      <td>SOLUTION NMR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>pdb:1WIU</td>\n",
       "      <td>1996-12-23</td>\n",
       "      <td>TWITCHIN 18TH IGSF MODULE</td>\n",
       "      <td>TWITCHIN IMMUNOGLOBULIN SUPERFAMILY DOMAIN (IG...</td>\n",
       "      <td>SOLUTION NMR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      pdbId releaseDate                                        description  \\\n",
       "0  pdb:3Q7D  2011-11-09  (2R)-2-(6-methoxynaphthalen-2-yl)propanoic aci...   \n",
       "1  pdb:1WGI  1997-11-19  INORGANIC PYROPHOSPHATASE, MANGANESE (II) ION,...   \n",
       "2  pdb:5Z3F  2019-05-15  CITRIC ACID, GLYCEROL, Glycoside hydrolase 15-...   \n",
       "3  pdb:1WGM  2004-11-28                   Ubiquitin conjugation factor E4A   \n",
       "4  pdb:1WIU  1996-12-23                          TWITCHIN 18TH IGSF MODULE   \n",
       "\n",
       "                                               title            methods  \\\n",
       "0         Structure of (R)-naproxen bound to mCOX-2.  X-RAY DIFFRACTION   \n",
       "1             STRUCTURE OF INORGANIC PYROPHOSPHATASE  X-RAY DIFFRACTION   \n",
       "2          Glycosidase E335A in complex with glucose  X-RAY DIFFRACTION   \n",
       "3  Solution structure of the U-box in human ubiqu...       SOLUTION NMR   \n",
       "4  TWITCHIN IMMUNOGLOBULIN SUPERFAMILY DOMAIN (IG...       SOLUTION NMR   \n",
       "\n",
       "  resolution    rFree  \n",
       "0        2.4   0.2329  \n",
       "1        2.2    0.211  \n",
       "2        1.1  0.12089  \n",
       "3                      \n",
       "4                      "
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structures.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "structures.to_csv(NEO4J_IMPORT / \"01f-PDBStructure.csv\", index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get PDB Entity info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "sqlQuery = \"select pdbid, id, pdbx_description from entity\"\n",
    "encodedSQL = urllib.parse.quote(sqlQuery)\n",
    "entity_url = URL + encodedSQL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_entity = pd.read_csv(entity_url, dtype=str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_entity.rename(columns={'pdbid': 'pdbId', 'id': 'entityId', 'pdbx_description': 'description'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_entity['pdbId'] = df_entity['pdbId'].str.upper()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of entities: 810321\n"
     ]
    }
   ],
   "source": [
    "print('Number of entities:', df_entity.shape[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>entityId</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>1</td>\n",
       "      <td>RETINOIC ACID RECEPTOR RXR-ALPHA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>2</td>\n",
       "      <td>RETINOIC ACID RECEPTOR RXR-ALPHA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>3</td>\n",
       "      <td>5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>4</td>\n",
       "      <td>5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>5</td>\n",
       "      <td>ZINC ION</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  pdbId entityId                                        description\n",
       "0  4CN3        1                   RETINOIC ACID RECEPTOR RXR-ALPHA\n",
       "1  4CN3        2                   RETINOIC ACID RECEPTOR RXR-ALPHA\n",
       "2  4CN3        3  5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*C...\n",
       "3  4CN3        4  5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*C...\n",
       "4  4CN3        5                                           ZINC ION"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_entity.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "def categorize(description):\n",
    "    words = re.split('[ ,\\-()]', str(description).lower())\n",
    "    \n",
    "    keywords_ab = ['antibody', 'fab', 'nanobody']\n",
    "    keywords_hc = ['heavy', 'h', 'hc']\n",
    "    keywords_lc = ['light', 'l', 'lc']\n",
    "    \n",
    "    category = ''\n",
    "    \n",
    "    if any(w in words for w in keywords_ab):\n",
    "        category = 'antibody'\n",
    "        if any(w in words for w in keywords_hc):\n",
    "            category = 'antibody heavy chain'\n",
    "            \n",
    "        if any(w in words for w in keywords_lc):\n",
    "            category = 'antibody light chain'\n",
    "    \n",
    "    return category"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_entity['category'] = df_entity['description'].apply(categorize)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>entityId</th>\n",
       "      <th>description</th>\n",
       "      <th>category</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2425</th>\n",
       "      <td>4D3C</td>\n",
       "      <td>2</td>\n",
       "      <td>SFN68 FAB</td>\n",
       "      <td>antibody</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2426</th>\n",
       "      <td>4D3C</td>\n",
       "      <td>3</td>\n",
       "      <td>SFN68 FAB</td>\n",
       "      <td>antibody</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2769</th>\n",
       "      <td>4D9L</td>\n",
       "      <td>1</td>\n",
       "      <td>Light chain of Fab fragment of anti-HIV1 gp120...</td>\n",
       "      <td>antibody light chain</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2770</th>\n",
       "      <td>4D9L</td>\n",
       "      <td>2</td>\n",
       "      <td>Heavy chain of Fab fragment of anti-HIV1 gp120...</td>\n",
       "      <td>antibody heavy chain</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3559</th>\n",
       "      <td>4D9R</td>\n",
       "      <td>2</td>\n",
       "      <td>Fab light chain</td>\n",
       "      <td>antibody light chain</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     pdbId entityId                                        description  \\\n",
       "2425  4D3C        2                                          SFN68 FAB   \n",
       "2426  4D3C        3                                          SFN68 FAB   \n",
       "2769  4D9L        1  Light chain of Fab fragment of anti-HIV1 gp120...   \n",
       "2770  4D9L        2  Heavy chain of Fab fragment of anti-HIV1 gp120...   \n",
       "3559  4D9R        2                                    Fab light chain   \n",
       "\n",
       "                  category  \n",
       "2425              antibody  \n",
       "2426              antibody  \n",
       "2769  antibody light chain  \n",
       "2770  antibody heavy chain  \n",
       "3559  antibody light chain  "
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_entity.query(\"category != ''\").head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get PDB Polymer Entities"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "sqlQuery = \"select pdbid, entity_id, pdbx_strand_id, type, pdbx_seq_one_letter_code_can from entity_poly\"\n",
    "encodedSQL = urllib.parse.quote(sqlQuery)\n",
    "poly_url = URL + encodedSQL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_poly = pd.read_csv(poly_url, dtype=str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_poly.rename(columns={'pdbid': 'pdbId', 'entity_id': 'entityId', 'pdbx_seq_one_letter_code_can': 'sequence'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_poly['pdbId'] = df_poly['pdbId'].str.upper()\n",
    "df_poly['chainId'] = df_poly['pdbx_strand_id'].str.split(',')\n",
    "df_poly = df_poly.explode('chainId')\n",
    "df_poly = df_poly[['pdbId', 'entityId', 'chainId', 'type', 'sequence']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of polymer entities: 636117\n"
     ]
    }
   ],
   "source": [
    "print(\"Number of polymer entities:\", df_poly.shape[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>entityId</th>\n",
       "      <th>chainId</th>\n",
       "      <th>type</th>\n",
       "      <th>sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>100D</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>polydeoxyribonucleotide/polyribonucleotide hybrid</td>\n",
       "      <td>CCGGCGCCGG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>100D</td>\n",
       "      <td>1</td>\n",
       "      <td>B</td>\n",
       "      <td>polydeoxyribonucleotide/polyribonucleotide hybrid</td>\n",
       "      <td>CCGGCGCCGG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>101D</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>polydeoxyribonucleotide</td>\n",
       "      <td>CGCGAATTCGCG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>101D</td>\n",
       "      <td>1</td>\n",
       "      <td>B</td>\n",
       "      <td>polydeoxyribonucleotide</td>\n",
       "      <td>CGCGAATTCGCG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>101M</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  pdbId entityId chainId                                               type  \\\n",
       "0  100D        1       A  polydeoxyribonucleotide/polyribonucleotide hybrid   \n",
       "0  100D        1       B  polydeoxyribonucleotide/polyribonucleotide hybrid   \n",
       "1  101D        1       A                            polydeoxyribonucleotide   \n",
       "1  101D        1       B                            polydeoxyribonucleotide   \n",
       "2  101M        1       A                                     polypeptide(L)   \n",
       "\n",
       "                                            sequence  \n",
       "0                                         CCGGCGCCGG  \n",
       "0                                         CCGGCGCCGG  \n",
       "1                                       CGCGAATTCGCG  \n",
       "1                                       CGCGAATTCGCG  \n",
       "2  MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDR...  "
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_poly.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_chain = pd.merge(df_entity, df_poly, on=['pdbId', 'entityId'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of polymer chains: 636117\n"
     ]
    }
   ],
   "source": [
    "print('Number of polymer chains:', df_chain.shape[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>entityId</th>\n",
       "      <th>description</th>\n",
       "      <th>category</th>\n",
       "      <th>chainId</th>\n",
       "      <th>type</th>\n",
       "      <th>sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>1</td>\n",
       "      <td>RETINOIC ACID RECEPTOR RXR-ALPHA</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>1</td>\n",
       "      <td>RETINOIC ACID RECEPTOR RXR-ALPHA</td>\n",
       "      <td></td>\n",
       "      <td>B</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>1</td>\n",
       "      <td>RETINOIC ACID RECEPTOR RXR-ALPHA</td>\n",
       "      <td></td>\n",
       "      <td>C</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>2</td>\n",
       "      <td>RETINOIC ACID RECEPTOR RXR-ALPHA</td>\n",
       "      <td></td>\n",
       "      <td>D</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4CN3</td>\n",
       "      <td>3</td>\n",
       "      <td>5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*C...</td>\n",
       "      <td></td>\n",
       "      <td>E</td>\n",
       "      <td>polydeoxyribonucleotide</td>\n",
       "      <td>CTAGTTCAAAGTTCACA</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  pdbId entityId                                        description category  \\\n",
       "0  4CN3        1                   RETINOIC ACID RECEPTOR RXR-ALPHA            \n",
       "1  4CN3        1                   RETINOIC ACID RECEPTOR RXR-ALPHA            \n",
       "2  4CN3        1                   RETINOIC ACID RECEPTOR RXR-ALPHA            \n",
       "3  4CN3        2                   RETINOIC ACID RECEPTOR RXR-ALPHA            \n",
       "4  4CN3        3  5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*C...            \n",
       "\n",
       "  chainId                     type  \\\n",
       "0       A           polypeptide(L)   \n",
       "1       B           polypeptide(L)   \n",
       "2       C           polypeptide(L)   \n",
       "3       D           polypeptide(L)   \n",
       "4       E  polydeoxyribonucleotide   \n",
       "\n",
       "                                            sequence  \n",
       "0  GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...  \n",
       "1  GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...  \n",
       "2  GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...  \n",
       "3  GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTC...  \n",
       "4                                  CTAGTTCAAAGTTCACA  "
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_chain.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get PDB Chain - UniProt sequence mappings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "sifts_url = 'http://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/uniprot_segments_observed.tsv.gz'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of chains: 839171\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>PDB</th>\n",
       "      <th>CHAIN</th>\n",
       "      <th>SP_PRIMARY</th>\n",
       "      <th>RES_BEG</th>\n",
       "      <th>RES_END</th>\n",
       "      <th>PDB_BEG</th>\n",
       "      <th>PDB_END</th>\n",
       "      <th>SP_BEG</th>\n",
       "      <th>SP_END</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>123l</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>113l</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>105m</td>\n",
       "      <td>A</td>\n",
       "      <td>P02185</td>\n",
       "      <td>1</td>\n",
       "      <td>153</td>\n",
       "      <td>1</td>\n",
       "      <td>153</td>\n",
       "      <td>2</td>\n",
       "      <td>154</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>128l</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>156l</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    PDB CHAIN SP_PRIMARY RES_BEG RES_END PDB_BEG PDB_END SP_BEG SP_END\n",
       "0  123l     A     P00720       1     162       1     162      1    162\n",
       "1  113l     A     P00720       1     162       1     162      1    162\n",
       "2  105m     A     P02185       1     153       1     153      2    154\n",
       "3  128l     A     P00720       1     162       1     162      1    162\n",
       "4  156l     A     P00720       1     162       1     162      1    162"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chains = pd.read_csv(sifts_url, sep='\\t', skiprows=1, dtype=str)\n",
    "print(\"Number of chains:\", chains.shape[0])\n",
    "chains.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains.rename(columns={'PDB': 'pdbId', 'CHAIN': 'chainId', 'SP_PRIMARY': 'accession'}, inplace=True)\n",
    "chains.rename(columns={'RES_BEG': 'seqresStart', 'RES_END': 'seqresEnd'}, inplace=True)\n",
    "chains.rename(columns={'PDB_BEG': 'pdbStart', 'PDB_END': 'pdbEnd'}, inplace=True)\n",
    "chains.rename(columns={'SP_BEG': 'uniprotStart', 'SP_END': 'uniprotEnd'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains['pdbId'] = chains['pdbId'].str.upper()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>chainId</th>\n",
       "      <th>accession</th>\n",
       "      <th>seqresStart</th>\n",
       "      <th>seqresEnd</th>\n",
       "      <th>pdbStart</th>\n",
       "      <th>pdbEnd</th>\n",
       "      <th>uniprotStart</th>\n",
       "      <th>uniprotEnd</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>123L</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>113L</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>105M</td>\n",
       "      <td>A</td>\n",
       "      <td>P02185</td>\n",
       "      <td>1</td>\n",
       "      <td>153</td>\n",
       "      <td>1</td>\n",
       "      <td>153</td>\n",
       "      <td>2</td>\n",
       "      <td>154</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>128L</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>156L</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  pdbId chainId accession seqresStart seqresEnd pdbStart pdbEnd uniprotStart  \\\n",
       "0  123L       A    P00720           1       162        1    162            1   \n",
       "1  113L       A    P00720           1       162        1    162            1   \n",
       "2  105M       A    P02185           1       153        1    153            2   \n",
       "3  128L       A    P00720           1       162        1    162            1   \n",
       "4  156L       A    P00720           1       162        1    162            1   \n",
       "\n",
       "  uniprotEnd  \n",
       "0        162  \n",
       "1        162  \n",
       "2        154  \n",
       "3        162  \n",
       "4        162  "
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chains.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Sort chains by uniprot residue number"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains['uniprotStart'] = chains['uniprotStart'].astype(int)\n",
    "chains['uniprotEnd'] = chains['uniprotEnd'].astype(int)\n",
    "chains['length'] = chains['uniprotEnd'] - chains['uniprotStart'] + 1\n",
    "# TODO length seems to be string??\n",
    "chains['length'] = chains['length'].astype(int)\n",
    "#\n",
    "chains.sort_values(by='uniprotStart', inplace=True)\n",
    "chains['uniprotStart'] = chains['uniprotStart'].astype(str)\n",
    "chains['uniprotEnd'] = chains['uniprotEnd'].astype(str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>chainId</th>\n",
       "      <th>accession</th>\n",
       "      <th>seqresStart</th>\n",
       "      <th>seqresEnd</th>\n",
       "      <th>pdbStart</th>\n",
       "      <th>pdbEnd</th>\n",
       "      <th>uniprotStart</th>\n",
       "      <th>uniprotEnd</th>\n",
       "      <th>length</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>123L</td>\n",
       "      <td>A</td>\n",
       "      <td>P00720</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>324839</th>\n",
       "      <td>1Y5N</td>\n",
       "      <td>B</td>\n",
       "      <td>P11349</td>\n",
       "      <td>1</td>\n",
       "      <td>509</td>\n",
       "      <td>1</td>\n",
       "      <td>509</td>\n",
       "      <td>1</td>\n",
       "      <td>509</td>\n",
       "      <td>509</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>324840</th>\n",
       "      <td>1Y5N</td>\n",
       "      <td>C</td>\n",
       "      <td>P11350</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>324847</th>\n",
       "      <td>1Y5I</td>\n",
       "      <td>B</td>\n",
       "      <td>P11349</td>\n",
       "      <td>1</td>\n",
       "      <td>509</td>\n",
       "      <td>1</td>\n",
       "      <td>509</td>\n",
       "      <td>1</td>\n",
       "      <td>509</td>\n",
       "      <td>509</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>324848</th>\n",
       "      <td>1Y5I</td>\n",
       "      <td>C</td>\n",
       "      <td>P11350</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       pdbId chainId accession seqresStart seqresEnd pdbStart pdbEnd  \\\n",
       "0       123L       A    P00720           1       162        1    162   \n",
       "324839  1Y5N       B    P11349           1       509        1    509   \n",
       "324840  1Y5N       C    P11350           1        72        1     72   \n",
       "324847  1Y5I       B    P11349           1       509        1    509   \n",
       "324848  1Y5I       C    P11350           1        72        1     72   \n",
       "\n",
       "       uniprotStart uniprotEnd  length  \n",
       "0                 1        162     162  \n",
       "324839            1        509     509  \n",
       "324840            1         72      72  \n",
       "324847            1        509     509  \n",
       "324848            1         72      72  "
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chains.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Int64Index: 839171 entries, 0 to 345771\n",
      "Data columns (total 10 columns):\n",
      " #   Column        Non-Null Count   Dtype \n",
      "---  ------        --------------   ----- \n",
      " 0   pdbId         839171 non-null  object\n",
      " 1   chainId       839129 non-null  object\n",
      " 2   accession     839171 non-null  object\n",
      " 3   seqresStart   839171 non-null  object\n",
      " 4   seqresEnd     839171 non-null  object\n",
      " 5   pdbStart      839171 non-null  object\n",
      " 6   pdbEnd        839171 non-null  object\n",
      " 7   uniprotStart  839171 non-null  object\n",
      " 8   uniprotEnd    839171 non-null  object\n",
      " 9   length        839171 non-null  int64 \n",
      "dtypes: int64(1), object(9)\n",
      "memory usage: 70.4+ MB\n"
     ]
    }
   ],
   "source": [
    "chains.info()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Group data by PDB chains"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains = chains.groupby(['pdbId','chainId','accession']).agg(list).reset_index()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create semicolon separated string of residue numbers so they can be represented in a csv file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains['uniprotStart'] = chains['uniprotStart'].apply(lambda x: ';'.join(x))\n",
    "chains['uniprotEnd'] = chains['uniprotEnd'].apply(lambda x: ';'.join(x))\n",
    "chains['seqresStart'] = chains['seqresStart'].apply(lambda x: ';'.join(x))\n",
    "chains['seqresEnd'] = chains['seqresEnd'].apply(lambda x: ';'.join(x))\n",
    "chains['pdbStart'] = chains['pdbStart'].apply(lambda x: ';'.join(x))\n",
    "chains['pdbEnd'] = chains['pdbEnd'].apply(lambda x: ';'.join(x))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains['residues'] = chains['length'].apply(lambda x: sum(x))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of chains with UniProt mapping: 555057\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>chainId</th>\n",
       "      <th>accession</th>\n",
       "      <th>seqresStart</th>\n",
       "      <th>seqresEnd</th>\n",
       "      <th>pdbStart</th>\n",
       "      <th>pdbEnd</th>\n",
       "      <th>uniprotStart</th>\n",
       "      <th>uniprotEnd</th>\n",
       "      <th>length</th>\n",
       "      <th>residues</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>555052</th>\n",
       "      <td>9XIA</td>\n",
       "      <td>A</td>\n",
       "      <td>P24300</td>\n",
       "      <td>1</td>\n",
       "      <td>387</td>\n",
       "      <td>1</td>\n",
       "      <td>387</td>\n",
       "      <td>1</td>\n",
       "      <td>387</td>\n",
       "      <td>[387]</td>\n",
       "      <td>387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>555053</th>\n",
       "      <td>9XIM</td>\n",
       "      <td>A</td>\n",
       "      <td>P12851</td>\n",
       "      <td>2</td>\n",
       "      <td>393</td>\n",
       "      <td>3</td>\n",
       "      <td>394</td>\n",
       "      <td>3</td>\n",
       "      <td>394</td>\n",
       "      <td>[392]</td>\n",
       "      <td>392</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>555054</th>\n",
       "      <td>9XIM</td>\n",
       "      <td>B</td>\n",
       "      <td>P12851</td>\n",
       "      <td>2</td>\n",
       "      <td>393</td>\n",
       "      <td>3</td>\n",
       "      <td>394</td>\n",
       "      <td>3</td>\n",
       "      <td>394</td>\n",
       "      <td>[392]</td>\n",
       "      <td>392</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>555055</th>\n",
       "      <td>9XIM</td>\n",
       "      <td>C</td>\n",
       "      <td>P12851</td>\n",
       "      <td>3</td>\n",
       "      <td>393</td>\n",
       "      <td>4</td>\n",
       "      <td>394</td>\n",
       "      <td>4</td>\n",
       "      <td>394</td>\n",
       "      <td>[391]</td>\n",
       "      <td>391</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>555056</th>\n",
       "      <td>9XIM</td>\n",
       "      <td>D</td>\n",
       "      <td>P12851</td>\n",
       "      <td>2</td>\n",
       "      <td>393</td>\n",
       "      <td>3</td>\n",
       "      <td>394</td>\n",
       "      <td>3</td>\n",
       "      <td>394</td>\n",
       "      <td>[392]</td>\n",
       "      <td>392</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       pdbId chainId accession seqresStart seqresEnd pdbStart pdbEnd  \\\n",
       "555052  9XIA       A    P24300           1       387        1    387   \n",
       "555053  9XIM       A    P12851           2       393        3    394   \n",
       "555054  9XIM       B    P12851           2       393        3    394   \n",
       "555055  9XIM       C    P12851           3       393        4    394   \n",
       "555056  9XIM       D    P12851           2       393        3    394   \n",
       "\n",
       "       uniprotStart uniprotEnd length  residues  \n",
       "555052            1        387  [387]       387  \n",
       "555053            3        394  [392]       392  \n",
       "555054            3        394  [392]       392  \n",
       "555055            4        394  [391]       391  \n",
       "555056            3        394  [392]       392  "
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(\"Number of chains with UniProt mapping:\", chains.shape[0])\n",
    "chains.tail()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>chainId</th>\n",
       "      <th>accession</th>\n",
       "      <th>seqresStart</th>\n",
       "      <th>seqresEnd</th>\n",
       "      <th>pdbStart</th>\n",
       "      <th>pdbEnd</th>\n",
       "      <th>uniprotStart</th>\n",
       "      <th>uniprotEnd</th>\n",
       "      <th>length</th>\n",
       "      <th>residues</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>512864</th>\n",
       "      <td>6XDG</td>\n",
       "      <td>E</td>\n",
       "      <td>P0DTC2</td>\n",
       "      <td>15</td>\n",
       "      <td>208</td>\n",
       "      <td>333</td>\n",
       "      <td>526</td>\n",
       "      <td>333</td>\n",
       "      <td>526</td>\n",
       "      <td>[194]</td>\n",
       "      <td>194</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       pdbId chainId accession seqresStart seqresEnd pdbStart pdbEnd  \\\n",
       "512864  6XDG       E    P0DTC2          15       208      333    526   \n",
       "\n",
       "       uniprotStart uniprotEnd length  residues  \n",
       "512864          333        526  [194]       194  "
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chains.query('pdbId == \"6XDG\"')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains = df_chain.merge(chains, on=['pdbId', 'chainId'], how='left')\n",
    "chains.fillna('', inplace=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Assign CURIES"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains['accession'] = chains['accession'].apply(lambda x: x if x == '' else 'uniprot:' + x)\n",
    "chains['pdbId'] = 'pdb:' + chains['pdbId']\n",
    "chains['pdbChainId'] = chains['pdbId'] + '.' + chains['chainId']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total number of polymer chains: 641041\n"
     ]
    }
   ],
   "source": [
    "print(\"Total number of polymer chains:\", chains.shape[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbId</th>\n",
       "      <th>entityId</th>\n",
       "      <th>description</th>\n",
       "      <th>category</th>\n",
       "      <th>chainId</th>\n",
       "      <th>type</th>\n",
       "      <th>sequence</th>\n",
       "      <th>accession</th>\n",
       "      <th>seqresStart</th>\n",
       "      <th>seqresEnd</th>\n",
       "      <th>pdbStart</th>\n",
       "      <th>pdbEnd</th>\n",
       "      <th>uniprotStart</th>\n",
       "      <th>uniprotEnd</th>\n",
       "      <th>length</th>\n",
       "      <th>residues</th>\n",
       "      <th>pdbChainId</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>150218</th>\n",
       "      <td>pdb:5KR2</td>\n",
       "      <td>1</td>\n",
       "      <td>Protease PR5-SQV</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>PQITLWKRPLVTIKVGGQLKEALLNTGADDTVIEDMNLPGKWKPKM...</td>\n",
       "      <td>uniprot:V5YAB1</td>\n",
       "      <td>1</td>\n",
       "      <td>99</td>\n",
       "      <td>1</td>\n",
       "      <td>99</td>\n",
       "      <td>1</td>\n",
       "      <td>99</td>\n",
       "      <td>[99]</td>\n",
       "      <td>99.0</td>\n",
       "      <td>pdb:5KR2.A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>190697</th>\n",
       "      <td>pdb:5V3Z</td>\n",
       "      <td>1</td>\n",
       "      <td>Polyketide synthase Pks13 (Termination polyket...</td>\n",
       "      <td></td>\n",
       "      <td>B</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>SNAQIDGFVRTLRARPEAGGKVPVFVFHPAGGSTVVYEPLLGRLPA...</td>\n",
       "      <td>uniprot:I6X8D2</td>\n",
       "      <td>4;145</td>\n",
       "      <td>142;279</td>\n",
       "      <td>1451;1592</td>\n",
       "      <td>1589;1726</td>\n",
       "      <td>1451;1592</td>\n",
       "      <td>1589;1726</td>\n",
       "      <td>[139, 135]</td>\n",
       "      <td>274.0</td>\n",
       "      <td>pdb:5V3Z.B</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>317530</th>\n",
       "      <td>pdb:6S5J</td>\n",
       "      <td>1</td>\n",
       "      <td>Strictosidine synthase</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>MASSPEFFEFIEAPSYGPNAYAFDSDGELYASVEDGRIIKYDKPSN...</td>\n",
       "      <td>uniprot:Q94LW9</td>\n",
       "      <td>4</td>\n",
       "      <td>306</td>\n",
       "      <td>4</td>\n",
       "      <td>306</td>\n",
       "      <td>26</td>\n",
       "      <td>328</td>\n",
       "      <td>[303]</td>\n",
       "      <td>303.0</td>\n",
       "      <td>pdb:6S5J.A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309274</th>\n",
       "      <td>pdb:6QZ0</td>\n",
       "      <td>1</td>\n",
       "      <td>Major capsid protein</td>\n",
       "      <td></td>\n",
       "      <td>5J</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>MRITFNDVKTSLGITESYDIVNAIRNSQGDNFKSYVPLATANNVAE...</td>\n",
       "      <td>uniprot:P13849</td>\n",
       "      <td>4</td>\n",
       "      <td>438</td>\n",
       "      <td>4</td>\n",
       "      <td>438</td>\n",
       "      <td>4</td>\n",
       "      <td>438</td>\n",
       "      <td>[435]</td>\n",
       "      <td>435.0</td>\n",
       "      <td>pdb:6QZ0.5J</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>242328</th>\n",
       "      <td>pdb:6FML</td>\n",
       "      <td>11</td>\n",
       "      <td>Histone H2A type 1</td>\n",
       "      <td></td>\n",
       "      <td>O</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAG...</td>\n",
       "      <td>uniprot:P0C0S8</td>\n",
       "      <td>16</td>\n",
       "      <td>119</td>\n",
       "      <td>16</td>\n",
       "      <td>119</td>\n",
       "      <td>17</td>\n",
       "      <td>120</td>\n",
       "      <td>[104]</td>\n",
       "      <td>104.0</td>\n",
       "      <td>pdb:6FML.O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306314</th>\n",
       "      <td>pdb:6QN1</td>\n",
       "      <td>2</td>\n",
       "      <td>BMC domain-containing protein</td>\n",
       "      <td></td>\n",
       "      <td>AP</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>MKEALGLIETKGLVACIEAADAMCKAANVELIGYENVGSGLVTAMV...</td>\n",
       "      <td>uniprot:A0A0J4R4X1</td>\n",
       "      <td>3</td>\n",
       "      <td>87</td>\n",
       "      <td>3</td>\n",
       "      <td>87</td>\n",
       "      <td>3</td>\n",
       "      <td>87</td>\n",
       "      <td>[85]</td>\n",
       "      <td>85.0</td>\n",
       "      <td>pdb:6QN1.AP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116839</th>\n",
       "      <td>pdb:5DDP</td>\n",
       "      <td>1</td>\n",
       "      <td>RNA (61-MER)</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "      <td>polyribonucleotide</td>\n",
       "      <td>CGUUGACCCAGGAAACUGGGCGGAAGUAAGGUCCAUUGCACUCCGG...</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>pdb:5DDP.A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76153</th>\n",
       "      <td>pdb:4V74</td>\n",
       "      <td>31</td>\n",
       "      <td>50S ribosomal protein L11</td>\n",
       "      <td></td>\n",
       "      <td>BI</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKT...</td>\n",
       "      <td>uniprot:P0A7J7</td>\n",
       "      <td>2</td>\n",
       "      <td>142</td>\n",
       "      <td>1</td>\n",
       "      <td>141</td>\n",
       "      <td>2</td>\n",
       "      <td>142</td>\n",
       "      <td>[141]</td>\n",
       "      <td>141.0</td>\n",
       "      <td>pdb:4V74.BI</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>488050</th>\n",
       "      <td>pdb:2CXI</td>\n",
       "      <td>1</td>\n",
       "      <td>Phenylalanyl-tRNA synthetase beta chain</td>\n",
       "      <td></td>\n",
       "      <td>C</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>MPKFDVSKSDLERLIGRSFSIEEWEDLVLYAKCELDDVWEENGKVY...</td>\n",
       "      <td>uniprot:O73984</td>\n",
       "      <td>2</td>\n",
       "      <td>348</td>\n",
       "      <td>2</td>\n",
       "      <td>348</td>\n",
       "      <td>2</td>\n",
       "      <td>348</td>\n",
       "      <td>[347]</td>\n",
       "      <td>347.0</td>\n",
       "      <td>pdb:2CXI.C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>322583</th>\n",
       "      <td>pdb:6T68</td>\n",
       "      <td>1</td>\n",
       "      <td>MORN repeat-containing protein 1</td>\n",
       "      <td></td>\n",
       "      <td>B</td>\n",
       "      <td>polypeptide(L)</td>\n",
       "      <td>SEKYDGEWNEGRMQGWGKYFYADGGVYEGEWVDGRMHGRGTYVFPN...</td>\n",
       "      <td>uniprot:Q587D3</td>\n",
       "      <td>13</td>\n",
       "      <td>209</td>\n",
       "      <td>155</td>\n",
       "      <td>351</td>\n",
       "      <td>155</td>\n",
       "      <td>351</td>\n",
       "      <td>[197]</td>\n",
       "      <td>197.0</td>\n",
       "      <td>pdb:6T68.B</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           pdbId entityId                                        description  \\\n",
       "150218  pdb:5KR2        1                                   Protease PR5-SQV   \n",
       "190697  pdb:5V3Z        1  Polyketide synthase Pks13 (Termination polyket...   \n",
       "317530  pdb:6S5J        1                             Strictosidine synthase   \n",
       "309274  pdb:6QZ0        1                               Major capsid protein   \n",
       "242328  pdb:6FML       11                                 Histone H2A type 1   \n",
       "306314  pdb:6QN1        2                      BMC domain-containing protein   \n",
       "116839  pdb:5DDP        1                                       RNA (61-MER)   \n",
       "76153   pdb:4V74       31                          50S ribosomal protein L11   \n",
       "488050  pdb:2CXI        1            Phenylalanyl-tRNA synthetase beta chain   \n",
       "322583  pdb:6T68        1                   MORN repeat-containing protein 1   \n",
       "\n",
       "       category chainId                type  \\\n",
       "150218                A      polypeptide(L)   \n",
       "190697                B      polypeptide(L)   \n",
       "317530                A      polypeptide(L)   \n",
       "309274               5J      polypeptide(L)   \n",
       "242328                O      polypeptide(L)   \n",
       "306314               AP      polypeptide(L)   \n",
       "116839                A  polyribonucleotide   \n",
       "76153                BI      polypeptide(L)   \n",
       "488050                C      polypeptide(L)   \n",
       "322583                B      polypeptide(L)   \n",
       "\n",
       "                                                 sequence           accession  \\\n",
       "150218  PQITLWKRPLVTIKVGGQLKEALLNTGADDTVIEDMNLPGKWKPKM...      uniprot:V5YAB1   \n",
       "190697  SNAQIDGFVRTLRARPEAGGKVPVFVFHPAGGSTVVYEPLLGRLPA...      uniprot:I6X8D2   \n",
       "317530  MASSPEFFEFIEAPSYGPNAYAFDSDGELYASVEDGRIIKYDKPSN...      uniprot:Q94LW9   \n",
       "309274  MRITFNDVKTSLGITESYDIVNAIRNSQGDNFKSYVPLATANNVAE...      uniprot:P13849   \n",
       "242328  SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAG...      uniprot:P0C0S8   \n",
       "306314  MKEALGLIETKGLVACIEAADAMCKAANVELIGYENVGSGLVTAMV...  uniprot:A0A0J4R4X1   \n",
       "116839  CGUUGACCCAGGAAACUGGGCGGAAGUAAGGUCCAUUGCACUCCGG...                       \n",
       "76153   MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKT...      uniprot:P0A7J7   \n",
       "488050  MPKFDVSKSDLERLIGRSFSIEEWEDLVLYAKCELDDVWEENGKVY...      uniprot:O73984   \n",
       "322583  SEKYDGEWNEGRMQGWGKYFYADGGVYEGEWVDGRMHGRGTYVFPN...      uniprot:Q587D3   \n",
       "\n",
       "       seqresStart seqresEnd   pdbStart     pdbEnd uniprotStart uniprotEnd  \\\n",
       "150218           1        99          1         99            1         99   \n",
       "190697       4;145   142;279  1451;1592  1589;1726    1451;1592  1589;1726   \n",
       "317530           4       306          4        306           26        328   \n",
       "309274           4       438          4        438            4        438   \n",
       "242328          16       119         16        119           17        120   \n",
       "306314           3        87          3         87            3         87   \n",
       "116839                                                                       \n",
       "76153            2       142          1        141            2        142   \n",
       "488050           2       348          2        348            2        348   \n",
       "322583          13       209        155        351          155        351   \n",
       "\n",
       "            length residues   pdbChainId  \n",
       "150218        [99]     99.0   pdb:5KR2.A  \n",
       "190697  [139, 135]    274.0   pdb:5V3Z.B  \n",
       "317530       [303]    303.0   pdb:6S5J.A  \n",
       "309274       [435]    435.0  pdb:6QZ0.5J  \n",
       "242328       [104]    104.0   pdb:6FML.O  \n",
       "306314        [85]     85.0  pdb:6QN1.AP  \n",
       "116839                        pdb:5DDP.A  \n",
       "76153        [141]    141.0  pdb:4V74.BI  \n",
       "488050       [347]    347.0   pdb:2CXI.C  \n",
       "322583       [197]    197.0   pdb:6T68.B  "
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chains.sample(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "chains.to_csv(NEO4J_IMPORT / \"01f-PDBChain.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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