{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "94dca4f5",
   "metadata": {},
   "source": [
    "## Prepare groundtruth binding sites data obtained from BioLiP \n",
    "\n",
    "Link to the original data source https://zhanggroup.org/BioLiP/download.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "0e6d908e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pickle\n",
    "import os\n",
    "\n",
    "data = {'ATP binding': {}, 'GTP binding': {}, 'heme binding': {}}\n",
    "\n",
    "with open('./binding_sites_data/BioLiP_2013-03-6.txt', 'r') as f:\n",
    "    for l in f:\n",
    "        if len(l.split('\\t')) > 8:\n",
    "            if l.split('\\t')[4] in ['HEM', 'ATP', 'GTP']:\n",
    "                name = '-'.join(l.split('\\t')[:2]).upper()\n",
    "                mf = {'ATP': 'ATP binding', 'GTP': 'GTP binding', 'HEM': 'heme binding' }[l.split('\\t')[4]]\n",
    "                sites = [int(w[1:])-1 for w in l.split('\\t')[8].split(' ')]\n",
    "                data[mf][name] = {\n",
    "                    'name': name,\n",
    "                    'mf_term': mf,\n",
    "                    'sites': sites\n",
    "                }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "75c26907",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pickle\n",
    "with open('./binding_sites_data/processed.pickle', 'wb') as f:\n",
    "    pickle.dump(data, f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6fec188a",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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