{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "86b99dae",
   "metadata": {},
   "source": [
    "# Prepare protein structure dataset\n",
    "\n",
    "- Parse the PDB files into json documents\n",
    "- Parse the CATH labels from RCSB API, merge into the json documents\n",
    "- Create index on PDB ID\n",
    "- Insert json documents into DocumentDB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8ce3bebc",
   "metadata": {},
   "outputs": [],
   "source": [
    "stack_name = 'gnn-proteins' # name of CloudFormation stack"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "23e6be4c",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import json\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "plt.style.use('seaborn')\n",
    "import seaborn as sns\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "1be01d99",
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir -p data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d81e6a57",
   "metadata": {},
   "source": [
    "## Download data from [AlphaFold](https://alphafold.ebi.ac.uk/download)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "7cbd6740",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2021-09-08 20:20:01--  https://ftp.ebi.ac.uk/pub/databases/alphafold/UP000000805_243232_METJA.tar\n",
      "Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74\n",
      "Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 178278400 (170M) [application/octet-stream]\n",
      "Saving to: ‘data/UP000000805_243232_METJA.tar’\n",
      "\n",
      "data/UP000000805_24 100%[===================>] 170.02M  10.8MB/s    in 14s     \n",
      "\n",
      "2021-09-08 20:20:16 (12.2 MB/s) - ‘data/UP000000805_243232_METJA.tar’ saved [178278400/178278400]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget -O data/UP000000805_243232_METJA.tar \\\n",
    "    https://ftp.ebi.ac.uk/pub/databases/alphafold/UP000000805_243232_METJA.tar "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "1c10b129",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "AF-Q60392-F1-model_v1.pdb.gz\n"
     ]
    }
   ],
   "source": [
    "!cd data && tar -xvf UP000000805_243232_METJA.tar"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "72872663",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1773\n"
     ]
    }
   ],
   "source": [
    "# count number of pdb files\n",
    "!ls data/*pdb.gz | wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "ce96c681",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1773\n"
     ]
    }
   ],
   "source": [
    "## get uniprot ids from pdb filenames\n",
    "files = os.listdir('data/')\n",
    "\n",
    "uniprot_ids = []\n",
    "for file in files:\n",
    "    if file.startswith('AF-') and file.endswith('pdb.gz'):\n",
    "        uniprot_id = file.split('-')[1]\n",
    "        uniprot_ids.append(uniprot_id)\n",
    "print(len(uniprot_ids))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f373a974",
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://www.uniprot.org/help/api_idmapping\n",
    "# mapping uniprot id to pdb id\n",
    "import urllib.parse\n",
    "import urllib.request\n",
    "\n",
    "url = 'https://www.uniprot.org/uploadlists/'\n",
    "\n",
    "params = {\n",
    "    'from': 'ACC+ID',\n",
    "    'to': 'PDB_ID',\n",
    "    'format': 'tab',\n",
    "    'query': ' '.join(uniprot_ids)\n",
    "}\n",
    "\n",
    "data = urllib.parse.urlencode(params)\n",
    "data = data.encode('utf-8')\n",
    "req = urllib.request.Request(url, data)\n",
    "with urllib.request.urlopen(req) as f:\n",
    "    response = f.read()\n",
    "\n",
    "res = response.decode('utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "38a1c8b1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(510, 2)\n"
     ]
    },
    {
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       "        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>uniprot_id</th>\n",
       "      <th>pdb_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Q58256</td>\n",
       "      <td>6PEU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Q58346</td>\n",
       "      <td>1S3L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Q58346</td>\n",
       "      <td>1S3M</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Q58346</td>\n",
       "      <td>1S3N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Q58346</td>\n",
       "      <td>2AHD</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  uniprot_id pdb_id\n",
       "0     Q58256   6PEU\n",
       "1     Q58346   1S3L\n",
       "2     Q58346   1S3M\n",
       "3     Q58346   1S3N\n",
       "4     Q58346   2AHD"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import io\n",
    "id_mappings = pd.read_csv(io.StringIO(res), sep='\\t')\n",
    "id_mappings.columns = ['uniprot_id', 'pdb_id']\n",
    "print(id_mappings.shape)\n",
    "id_mappings.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c7d14ab2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "uniprot_id    211\n",
       "pdb_id        462\n",
       "dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_mappings.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "ed6d3828",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(510, 2)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_mappings.drop_duplicates().shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "bddb2b0f",
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb_ids = id_mappings['pdb_id'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "607aba53",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('pdb_ids.txt', 'w') as out:\n",
    "    out.write(','.join(list(pdb_ids)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "d5aeb6ea",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloading https://files.rcsb.org/download/6PEU.pdb.gz to ./6PEU.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1S3L.pdb.gz to ./1S3L.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1S3M.pdb.gz to ./1S3M.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1S3N.pdb.gz to ./1S3N.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2AHD.pdb.gz to ./2AHD.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M25.pdb.gz to ./6M25.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M26.pdb.gz to ./6M26.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M27.pdb.gz to ./6M27.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M28.pdb.gz to ./6M28.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M29.pdb.gz to ./6M29.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M2A.pdb.gz to ./6M2A.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M2E.pdb.gz to ./6M2E.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M2F.pdb.gz to ./6M2F.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6M2G.pdb.gz to ./6M2G.pdb.gz\n",
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      "Downloading https://files.rcsb.org/download/6K0A.pdb.gz to ./6K0A.pdb.gz\n",
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      "Downloading https://files.rcsb.org/download/3H65.pdb.gz to ./3H65.pdb.gz\n",
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      "Failed to download https://files.rcsb.org/download/4V4N.pdb.gz\n",
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      "Downloading https://files.rcsb.org/download/2EB0.pdb.gz to ./2EB0.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1B78.pdb.gz to ./1B78.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2MJP.pdb.gz to ./2MJP.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3WKR.pdb.gz to ./3WKR.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3WKS.pdb.gz to ./3WKS.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5X6B.pdb.gz to ./5X6B.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2QTX.pdb.gz to ./2QTX.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4X9C.pdb.gz to ./4X9C.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4X9D.pdb.gz to ./4X9D.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5DY9.pdb.gz to ./5DY9.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1G61.pdb.gz to ./1G61.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2GTV.pdb.gz to ./2GTV.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2MZB.pdb.gz to ./2MZB.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3RSB.pdb.gz to ./3RSB.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4MO0.pdb.gz to ./4MO0.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JB3.pdb.gz to ./5JB3.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JBH.pdb.gz to ./5JBH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4YT2.pdb.gz to ./4YT2.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4YT4.pdb.gz to ./4YT4.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4YT5.pdb.gz to ./4YT5.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4YT8.pdb.gz to ./4YT8.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/6HUX.pdb.gz to ./6HUX.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2K8Y.pdb.gz to ./2K8Y.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/7KJT.pdb.gz to ./7KJT.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5YA6.pdb.gz to ./5YA6.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2YXG.pdb.gz to ./2YXG.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2B98.pdb.gz to ./2B98.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2B99.pdb.gz to ./2B99.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4Y7J.pdb.gz to ./4Y7J.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4Y7K.pdb.gz to ./4Y7K.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5IM5.pdb.gz to ./5IM5.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1KKH.pdb.gz to ./1KKH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1VIS.pdb.gz to ./1VIS.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3V5S.pdb.gz to ./3V5S.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3V5U.pdb.gz to ./3V5U.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HWX.pdb.gz to ./5HWX.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HWY.pdb.gz to ./5HWY.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HXC.pdb.gz to ./5HXC.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HXE.pdb.gz to ./5HXE.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HXH.pdb.gz to ./5HXH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HXR.pdb.gz to ./5HXR.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HXS.pdb.gz to ./5HXS.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5HYA.pdb.gz to ./5HYA.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDF.pdb.gz to ./5JDF.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDG.pdb.gz to ./5JDG.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDH.pdb.gz to ./5JDH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDL.pdb.gz to ./5JDL.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDM.pdb.gz to ./5JDM.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDN.pdb.gz to ./5JDN.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5JDQ.pdb.gz to ./5JDQ.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/4Y4M.pdb.gz to ./4Y4M.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2P5D.pdb.gz to ./2P5D.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2YYY.pdb.gz to ./2YYY.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5C8J.pdb.gz to ./5C8J.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3EO4.pdb.gz to ./3EO4.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3AUX.pdb.gz to ./3AUX.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3AUY.pdb.gz to ./3AUY.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2EKY.pdb.gz to ./2EKY.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2EPI.pdb.gz to ./2EPI.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2B0A.pdb.gz to ./2B0A.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2DU7.pdb.gz to ./2DU7.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5X6C.pdb.gz to ./5X6C.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2WJG.pdb.gz to ./2WJG.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2WJH.pdb.gz to ./2WJH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2WJI.pdb.gz to ./2WJI.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2WJJ.pdb.gz to ./2WJJ.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1QWG.pdb.gz to ./1QWG.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3H92.pdb.gz to ./3H92.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3WVA.pdb.gz to ./3WVA.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3WVB.pdb.gz to ./3WVB.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3WVC.pdb.gz to ./3WVC.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1OGH.pdb.gz to ./1OGH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1PKH.pdb.gz to ./1PKH.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1PKJ.pdb.gz to ./1PKJ.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/1PKK.pdb.gz to ./1PKK.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2HXB.pdb.gz to ./2HXB.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2HXD.pdb.gz to ./2HXD.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/3GF0.pdb.gz to ./3GF0.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/5L8X.pdb.gz to ./5L8X.pdb.gz\n",
      "Downloading https://files.rcsb.org/download/2F4N.pdb.gz to ./2F4N.pdb.gz\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "# download from RCSB PDB\n",
    "\n",
    "cd data\n",
    "bash ../batch_download.sh -f ../pdb_ids.txt -p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "53049bd2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2233\n"
     ]
    }
   ],
   "source": [
    "!ls data/*.pdb.gz | wc -l"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1f8e17d7",
   "metadata": {},
   "source": [
    "## Connect to DocumentDB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "5208da58",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pymongo import MongoClient\n",
    "from utils import get_secret"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "28a67c3b",
   "metadata": {},
   "outputs": [],
   "source": [
    "secrets = get_secret(stack_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "7de1b9ec",
   "metadata": {},
   "outputs": [],
   "source": [
    "uri = 'mongodb://{}:{}@{}:{}/?tls=true&tlsCAFile=rds-combined-ca-bundle.pem&replicaSet=rs0&readPreference=secondaryPreferred&retryWrites=false'\\\n",
    "    .format(secrets['username'], secrets['password'], secrets['host'], secrets['port'])\n",
    "\n",
    "client = MongoClient(uri)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "64936b46",
   "metadata": {},
   "outputs": [],
   "source": [
    "db = client['proteins'] # create a database\n",
    "collection = db['proteins'] # create a collection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "35c2f044",
   "metadata": {},
   "outputs": [],
   "source": [
    "# collection.delete_many({}) # to delete all documents in this collection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "e652fefc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'id_1'"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "collection.create_index('id', unique=True) # unique index in the collection"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "29ef701f",
   "metadata": {},
   "source": [
    "## Parse PDB files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "f1f7b3cc",
   "metadata": {},
   "outputs": [],
   "source": [
    "from tqdm import tqdm\n",
    "from Bio.PDB import PDBParser\n",
    "\n",
    "import xpdb\n",
    "from pdb_parse import parse_pdb_file_to_json_record"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "dd91fd1c",
   "metadata": {},
   "outputs": [],
   "source": [
    "# PDB parser\n",
    "pdb_parser = PDBParser(\n",
    "    QUIET=True,\n",
    "    PERMISSIVE=True,\n",
    "    structure_builder=xpdb.SloppyStructureBuilder(),\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f28f8b34",
   "metadata": {},
   "source": [
    "## Parse and save data to DB\n",
    "\n",
    "- for rcsb, use PDB-chain as id, add identifiers {uniprot_ids: [], pdb_ids: []}\n",
    "- for AF, use `AF-Q58321` as id, add identifiers {uniprot_ids: [], pdb_ids: []}\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "cacaf2b4",
   "metadata": {},
   "outputs": [],
   "source": [
    "import glob"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "4252bf2d",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1773/1773 [01:49<00:00, 16.19it/s]\n"
     ]
    }
   ],
   "source": [
    "# Parse PDB files from AlphaFold DB\n",
    "for pdb_file in tqdm(glob.glob('data/AF-*.pdb.gz')):\n",
    "    # AlphaFold structure\n",
    "    id_ = '-'.join(os.path.basename(pdb_file).split('-')[:2])\n",
    "    rec = parse_pdb_file_to_json_record(\n",
    "        pdb_parser,\n",
    "        pdb_file,\n",
    "        id_\n",
    "    )[0]\n",
    "    \n",
    "    uniprot_id = os.path.basename(pdb_file).split('-')[1]\n",
    "    # look up pdb id\n",
    "    pdb_ids = list(id_mappings.loc[id_mappings['uniprot_id']==uniprot_id, 'pdb_id'])\n",
    "    identifiers = {\n",
    "        'uniprot_ids': [uniprot_id],\n",
    "        'pdb_ids': pdb_ids\n",
    "    }\n",
    "    rec['id'] = id_\n",
    "    rec['identifiers'] = identifiers\n",
    "    rec['is_AF'] = 1\n",
    "\n",
    "    collection.insert_one(rec)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "5f1d325d",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 2233/2233 [01:29<00:00, 24.85it/s]\n"
     ]
    }
   ],
   "source": [
    "# Parse PDB files from RCSB\n",
    "for pdb_file in tqdm(glob.glob('data/*.pdb.gz')):\n",
    "    if not os.path.basename(pdb_file).startswith('AF-'):\n",
    "        # RCSB structure\n",
    "        pdb_id = os.path.basename(pdb_file).split('.')[0]\n",
    "        recs = parse_pdb_file_to_json_record(\n",
    "            pdb_parser,\n",
    "            pdb_file,\n",
    "            pdb_id\n",
    "        )\n",
    "        \n",
    "        # look up uniprot_ids\n",
    "        uniprot_ids = list(id_mappings.loc[id_mappings['pdb_id']==pdb_id, 'uniprot_id'])\n",
    "        identifiers = {\n",
    "            'uniprot_ids': uniprot_ids,\n",
    "            'pdb_ids': [pdb_id]\n",
    "        }\n",
    "        for rec in recs:\n",
    "            rec['id'] = rec['name']\n",
    "            rec['identifiers'] = identifiers\n",
    "            rec['is_AF'] = 0\n",
    "        \n",
    "        collection.insert_many(recs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "6ecff6ff",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of protein chains in the DocumentDB: 3151\n"
     ]
    }
   ],
   "source": [
    "print('Number of protein chains in the DocumentDB:', \n",
    "      collection.count_documents({}))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "82fdd8df",
   "metadata": {},
   "source": [
    "## Load protein metadata from DocumentDB to split train/valid/test"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "c9dc6235",
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.model_selection import train_test_split"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "5d769857",
   "metadata": {},
   "outputs": [],
   "source": [
    "match = {\"is_AF\": {\"$exists\": True}}\n",
    "project = {\"y\": \"$is_AF\"}\n",
    "\n",
    "pipeline = [\n",
    "    {\"$match\": match},\n",
    "    {\"$project\": project},\n",
    "]\n",
    "# aggregation pipeline\n",
    "cur = collection.aggregate(pipeline)\n",
    "# retrieve documents from the DB cursor\n",
    "docs = [doc for doc in cur]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "b222e899",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(3151, 2)\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>_id</th>\n",
       "      <th>y</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>61391b70f03d70e1ee9122f3</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>61391b70f03d70e1ee9122f4</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>61391b70f03d70e1ee9122f5</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>61391b71f03d70e1ee9122f6</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>61391b71f03d70e1ee9122f7</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                        _id  y\n",
       "0  61391b70f03d70e1ee9122f3  1\n",
       "1  61391b70f03d70e1ee9122f4  1\n",
       "2  61391b70f03d70e1ee9122f5  1\n",
       "3  61391b71f03d70e1ee9122f6  1\n",
       "4  61391b71f03d70e1ee9122f7  1"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# split train/valid/test\n",
    "df = pd.DataFrame(docs)\n",
    "print(df.shape)\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "91ff1c0e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(2520, 2) (631, 2)\n"
     ]
    }
   ],
   "source": [
    "# stratified split: full -> train/test\n",
    "df_train, df_test = train_test_split(\n",
    "    df, \n",
    "    test_size=0.2,\n",
    "    stratify=df['y'], \n",
    "    random_state=42\n",
    ")\n",
    "print(df_train.shape, df_test.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "9e32ac8b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(0.5626984126984127, 0.5625990491283677)"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_train['y'].mean(), df_test['y'].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "b090b945",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(2016, 2) (504, 2) (631, 2)\n"
     ]
    }
   ],
   "source": [
    "# stratified split: train -> train/valid\n",
    "df_train, df_valid = train_test_split(\n",
    "    df_train, \n",
    "    test_size=0.2,\n",
    "    stratify=df_train['y'], \n",
    "    random_state=42\n",
    ")\n",
    "print(df_train.shape, df_valid.shape, df_test.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "64eaa16f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of documents modified: 2016\n",
      "Number of documents modified: 504\n",
      "Number of documents modified: 631\n"
     ]
    }
   ],
   "source": [
    "# Add split information into Documents\n",
    "for split, df_split in zip(\n",
    "    ['train', 'valid', 'test'],\n",
    "    [df_train, df_valid, df_test]\n",
    "):\n",
    "    result = collection.update_many(\n",
    "        {'_id': {'$in': df_split['_id'].tolist()}}, \n",
    "        {'$set': {'split': split}}\n",
    "    )\n",
    "    print('Number of documents modified:',result.modified_count)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3cd65d61",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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