data_summary.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_sabdab_90 = pd.read_csv('structures/sabdab_summary_90_May2022.tsv', sep=\"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Original SabDab\n",
      "AbAg Complexes: 3890\n",
      "PDB Files: 1800\n"
     ]
    }
   ],
   "source": [
    "print(f\"Original SabDab\\nAbAg Complexes: {len(df_sabdab_90)}\\nPDB Files: {len(set(df_sabdab_90.pdb.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "With both chains\n",
      "AbAg Complexes: 3735\n",
      "PDB Files: 1743\n"
     ]
    }
   ],
   "source": [
    "df_sabdab_90_ = df_sabdab_90.query(\"Hchain == Hchain and Lchain == Lchain\")\n",
    "df_sabdab_90_ = df_sabdab_90_.query(\"Hchain != Lchain\")\n",
    "print(f\"With both chains\\nAbAg Complexes: {len(df_sabdab_90_)}\\nPDB Files: {len(set(df_sabdab_90_.pdb.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dropped duplicates\n",
      "AbAg Complexes: 3581\n",
      "PDB Files: 1743\n"
     ]
    }
   ],
   "source": [
    "df_sabdab_90_ = df_sabdab_90_.drop_duplicates()\n",
    "print(f\"Dropped duplicates\\nAbAg Complexes: {len(df_sabdab_90_)}\\nPDB Files: {len(set(df_sabdab_90_.pdb.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "With a protein antigen\n",
      "AbAg Complexes: 2786\n",
      "PDB Files: 1309\n"
     ]
    }
   ],
   "source": [
    "df_sabdab_90_ = df_sabdab_90_.query(\n",
    "        \"antigen_type == antigen_type and antigen_type.str.contains('protein')\"\n",
    ")\n",
    "print(f\"With a protein antigen\\nAbAg Complexes: {len(df_sabdab_90_)}\\nPDB Files: {len(set(df_sabdab_90_.pdb.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_sabdab_90_.to_pickle('data/sabdad_90_cleaned.pickle')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_cdrs = pd.read_pickle('data/cdr_epitope.pickle')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processed, CDR-specific epitopes calculated and removed redundant Abs in the same structure \n",
      "AbAg Complexes: 1483.0\n",
      "PDB Files: 1309\n"
     ]
    }
   ],
   "source": [
    "print(f\"Processed, CDR-specific epitopes calculated and removed redundant Abs in the same structure \\nAbAg Complexes: {len(df_cdrs)/6}\\nPDB Files: {len(set(df_cdrs.idcode.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Calculated buried surfaces, paratopes and epitopes \n",
      "AbAg Complexes: 1426.0\n",
      "PDB Files: 1261\n"
     ]
    }
   ],
   "source": [
    "df_buried = pd.read_pickle('data/epitope_buried_.pickle')\n",
    "\n",
    "print(f\"Calculated buried surfaces, paratopes and epitopes \\nAbAg Complexes: {len(df_buried)/6}\\nPDB Files: {len(set(df_buried.idcode.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Failed PDB2PQR: 49\n",
      "Only partially: 2\n"
     ]
    }
   ],
   "source": [
    "failed_idcodes = set()\n",
    "with open(\"scripts/PDB2PQR_FAILS\") as f:\n",
    "    for line in f:\n",
    "        line = line.strip()\n",
    "        failed_idcodes.add(line)\n",
    "\n",
    "print(f\"Failed PDB2PQR: {len(failed_idcodes)}\\nOnly partially: {len(failed_idcodes - (failed_idcodes - set(df_buried.idcode.values)))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Bound (non-empty paratopes and epitopes) \n",
      "AbAg Complexes: 1425.0\n",
      "PDB Files: 1260\n"
     ]
    }
   ],
   "source": [
    "df_buried = df_buried[df_buried[\"ag_ab_interface\"] != set()]\n",
    "df_buried = df_buried[df_buried[\"ab_ag_interface\"] != set()]\n",
    "print(f\"Bound (non-empty paratopes and epitopes) \\nAbAg Complexes: {len(df_buried)/6}\\nPDB Files: {len(set(df_buried.idcode.values))}\")\n",
    "\n",
    "df_buried.to_pickle(\"data/epitope_buried_cleaned.pickle\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Final \n",
      "AbAg Complexes: 1425\n"
     ]
    }
   ],
   "source": [
    "buried_ab_ag_interface_res = df_buried[~df_buried[['idcode', 'ab_ag_interface']].astype(str).duplicated(keep='first')][['idcode', 'chainID', 'chain_type', 'ab_ag_interface_res', 'ag_ab_interface_res', 'cdr_seq']]\n",
    "buried_ab_ag_interface_res = buried_ab_ag_interface_res[['idcode', 'chainID', 'chain_type', 'ab_ag_interface_res', 'ag_ab_interface_res']]\n",
    "\n",
    "print(f\"Final \\nAbAg Complexes: {len(buried_ab_ag_interface_res)}\")\n",
    "\n",
    "buried_ab_ag_interface_res.to_pickle(\"data/buried_interface_res.pickle\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 171,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_cdrs = pd.read_pickle('data/cdr_epitope.pickle')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 172,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>idcode</th>\n",
       "      <th>chainID</th>\n",
       "      <th>chain_type</th>\n",
       "      <th>cdr</th>\n",
       "      <th>cdr_seq</th>\n",
       "      <th>cdr_begin</th>\n",
       "      <th>cdr_end</th>\n",
       "      <th>cdr_atoms</th>\n",
       "      <th>epitope_atoms</th>\n",
       "      <th>epitope_residues</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2496</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GFTFDDY</td>\n",
       "      <td>26</td>\n",
       "      <td>32</td>\n",
       "      <td>[3422, 3423, 3424, 3425, 3426, 3427, 3428, 342...</td>\n",
       "      <td>[120, 130, 131, 132, 133, 134, 135, 140, 141, ...</td>\n",
       "      <td>[ 252 ,  254 ,  254 ,  254 ,  254 ,  254 ,  25...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2497</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>2</td>\n",
       "      <td>SWNTGT</td>\n",
       "      <td>52</td>\n",
       "      <td>56</td>\n",
       "      <td>[3633, 3634, 3635, 3636, 3637, 3638, 3639, 364...</td>\n",
       "      <td>[123, 124, 126, 127, 129, 130, 131, 132, 133]</td>\n",
       "      <td>[ 253 ,  253 ,  253 ,  253 ,  254 ,  254 ,  25...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2498</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>3</td>\n",
       "      <td>TRSYVVAAEYYFHY</td>\n",
       "      <td>95</td>\n",
       "      <td>102</td>\n",
       "      <td>[4011, 4012, 4013, 4014, 4015, 4016, 4017, 401...</td>\n",
       "      <td>[107, 108, 113, 114, 115, 117, 118, 119, 120, ...</td>\n",
       "      <td>[ 251 ,  251 ,  252 ,  252 ,  252 ,  252 ,  25...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2499</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>GGNNIGSKSVH</td>\n",
       "      <td>24</td>\n",
       "      <td>34</td>\n",
       "      <td>[1807, 1808, 1809, 1810, 1811, 1812, 1813, 181...</td>\n",
       "      <td>[1569]</td>\n",
       "      <td>[ 433 ]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2500</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>DDSDRPP</td>\n",
       "      <td>50</td>\n",
       "      <td>56</td>\n",
       "      <td>[2007, 2008, 2009, 2010, 2011, 2012, 2013, 201...</td>\n",
       "      <td>[1482, 1483, 1499, 1500, 1565, 1567, 1568, 156...</td>\n",
       "      <td>[ 422 ,  422 ,  424 ,  424 ,  433 ,  433 ,  43...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2501</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>QVWDSSSDHAV</td>\n",
       "      <td>89</td>\n",
       "      <td>97</td>\n",
       "      <td>[2298, 2299, 2300, 2301, 2302, 2303, 2304, 230...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     idcode chainID chain_type cdr         cdr_seq cdr_begin cdr_end  \\\n",
       "2496   1adq       H          H   1         GFTFDDY       26      32    \n",
       "2497   1adq       H          H   2          SWNTGT       52      56    \n",
       "2498   1adq       H          H   3  TRSYVVAAEYYFHY       95     102    \n",
       "2499   1adq       L          L   1     GGNNIGSKSVH       24      34    \n",
       "2500   1adq       L          L   2         DDSDRPP       50      56    \n",
       "2501   1adq       L          L   3     QVWDSSSDHAV       89      97    \n",
       "\n",
       "                                              cdr_atoms  \\\n",
       "2496  [3422, 3423, 3424, 3425, 3426, 3427, 3428, 342...   \n",
       "2497  [3633, 3634, 3635, 3636, 3637, 3638, 3639, 364...   \n",
       "2498  [4011, 4012, 4013, 4014, 4015, 4016, 4017, 401...   \n",
       "2499  [1807, 1808, 1809, 1810, 1811, 1812, 1813, 181...   \n",
       "2500  [2007, 2008, 2009, 2010, 2011, 2012, 2013, 201...   \n",
       "2501  [2298, 2299, 2300, 2301, 2302, 2303, 2304, 230...   \n",
       "\n",
       "                                          epitope_atoms  \\\n",
       "2496  [120, 130, 131, 132, 133, 134, 135, 140, 141, ...   \n",
       "2497      [123, 124, 126, 127, 129, 130, 131, 132, 133]   \n",
       "2498  [107, 108, 113, 114, 115, 117, 118, 119, 120, ...   \n",
       "2499                                             [1569]   \n",
       "2500  [1482, 1483, 1499, 1500, 1565, 1567, 1568, 156...   \n",
       "2501                                                 []   \n",
       "\n",
       "                                       epitope_residues  \n",
       "2496  [ 252 ,  254 ,  254 ,  254 ,  254 ,  254 ,  25...  \n",
       "2497  [ 253 ,  253 ,  253 ,  253 ,  254 ,  254 ,  25...  \n",
       "2498  [ 251 ,  251 ,  252 ,  252 ,  252 ,  252 ,  25...  \n",
       "2499                                            [ 433 ]  \n",
       "2500  [ 422 ,  422 ,  424 ,  424 ,  433 ,  433 ,  43...  \n",
       "2501                                                 []  "
      ]
     },
     "execution_count": 172,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_cdrs.query(f\"idcode == '1adq'\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 170,
   "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>idcode</th>\n",
       "      <th>chainID</th>\n",
       "      <th>chain_type</th>\n",
       "      <th>cdr</th>\n",
       "      <th>cdr_seq</th>\n",
       "      <th>cdr_begin</th>\n",
       "      <th>cdr_end</th>\n",
       "      <th>cdr_atoms</th>\n",
       "      <th>epitope_atoms</th>\n",
       "      <th>epitope_residues</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2496</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GFTFDDY</td>\n",
       "      <td>26</td>\n",
       "      <td>32</td>\n",
       "      <td>[3422, 3423, 3424, 3425, 3426, 3427, 3428, 342...</td>\n",
       "      <td>[120, 130, 131, 132, 133, 134, 135, 140, 141, ...</td>\n",
       "      <td>[252, 254, 254, 254, 254, 254, 255, 255, 255, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2497</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>2</td>\n",
       "      <td>SWNTGT</td>\n",
       "      <td>52</td>\n",
       "      <td>56</td>\n",
       "      <td>[3633, 3634, 3635, 3636, 3637, 3638, 3639, 364...</td>\n",
       "      <td>[123, 124, 126, 127, 129, 130, 131, 132, 133]</td>\n",
       "      <td>[253, 253, 253, 253, 254, 254, 254, 254, 254]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2498</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>3</td>\n",
       "      <td>TRSYVVAAEYYFHY</td>\n",
       "      <td>95</td>\n",
       "      <td>102</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2499</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>GGNNIGSKSVH</td>\n",
       "      <td>24</td>\n",
       "      <td>34</td>\n",
       "      <td>[1807, 1808, 1809, 1810, 1811, 1812, 1813, 181...</td>\n",
       "      <td>[1569]</td>\n",
       "      <td>[433]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2500</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>DDSDRPP</td>\n",
       "      <td>50</td>\n",
       "      <td>56</td>\n",
       "      <td>[2007, 2008, 2009, 2010, 2011, 2012, 2013, 201...</td>\n",
       "      <td>[1482, 1483, 1499, 1500, 1565, 1567, 1568, 156...</td>\n",
       "      <td>[422, 422, 424, 424, 433, 433, 433, 433, 434, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2501</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>QVWDSSSDHAV</td>\n",
       "      <td>89</td>\n",
       "      <td>97</td>\n",
       "      <td>[2298, 2299, 2300, 2301, 2302, 2303, 2304, 230...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     idcode chainID chain_type cdr         cdr_seq cdr_begin cdr_end  \\\n",
       "2496   1adq       H          H   1         GFTFDDY        26      32   \n",
       "2497   1adq       H          H   2          SWNTGT        52      56   \n",
       "2498   1adq       H          H   3  TRSYVVAAEYYFHY        95     102   \n",
       "2499   1adq       L          L   1     GGNNIGSKSVH        24      34   \n",
       "2500   1adq       L          L   2         DDSDRPP        50      56   \n",
       "2501   1adq       L          L   3     QVWDSSSDHAV        89      97   \n",
       "\n",
       "                                              cdr_atoms  \\\n",
       "2496  [3422, 3423, 3424, 3425, 3426, 3427, 3428, 342...   \n",
       "2497  [3633, 3634, 3635, 3636, 3637, 3638, 3639, 364...   \n",
       "2498                                                 []   \n",
       "2499  [1807, 1808, 1809, 1810, 1811, 1812, 1813, 181...   \n",
       "2500  [2007, 2008, 2009, 2010, 2011, 2012, 2013, 201...   \n",
       "2501  [2298, 2299, 2300, 2301, 2302, 2303, 2304, 230...   \n",
       "\n",
       "                                          epitope_atoms  \\\n",
       "2496  [120, 130, 131, 132, 133, 134, 135, 140, 141, ...   \n",
       "2497      [123, 124, 126, 127, 129, 130, 131, 132, 133]   \n",
       "2498                                                 []   \n",
       "2499                                             [1569]   \n",
       "2500  [1482, 1483, 1499, 1500, 1565, 1567, 1568, 156...   \n",
       "2501                                                 []   \n",
       "\n",
       "                                       epitope_residues  \n",
       "2496  [252, 254, 254, 254, 254, 254, 255, 255, 255, ...  \n",
       "2497      [253, 253, 253, 253, 254, 254, 254, 254, 254]  \n",
       "2498                                                 []  \n",
       "2499                                              [433]  \n",
       "2500  [422, 422, 424, 424, 433, 433, 433, 433, 434, ...  \n",
       "2501                                                 []  "
      ]
     },
     "execution_count": 170,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_cdrs.query(f\"idcode == '1adq'\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 169,
   "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>idcode</th>\n",
       "      <th>chainID</th>\n",
       "      <th>chain_type</th>\n",
       "      <th>cdr</th>\n",
       "      <th>cdr_seq</th>\n",
       "      <th>cdr_begin</th>\n",
       "      <th>cdr_end</th>\n",
       "      <th>cdr_atoms</th>\n",
       "      <th>epitope_atoms</th>\n",
       "      <th>epitope_residues</th>\n",
       "      <th>ag_ab_interface</th>\n",
       "      <th>ag_cdrchain_interface</th>\n",
       "      <th>ag_cdr_interface</th>\n",
       "      <th>ab_ag_interface</th>\n",
       "      <th>ag_ab_interface_res</th>\n",
       "      <th>ag_cdrchain_interface_res</th>\n",
       "      <th>ag_cdr_interface_res</th>\n",
       "      <th>ab_ag_interface_res</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>24678</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GFTFDDY</td>\n",
       "      <td>26</td>\n",
       "      <td>32</td>\n",
       "      <td>[3422, 3423, 3424, 3425, 3426, 3427, 3428, 342...</td>\n",
       "      <td>[120, 130, 131, 132, 133, 134, 135, 140, 141, ...</td>\n",
       "      <td>[252, 254, 254, 254, 254, 254, 255, 255, 255, ...</td>\n",
       "      <td>{266, 274, 275, 2322, 277, 278, 2967, 3107, 31...</td>\n",
       "      <td>{266, 274, 275, 277, 278, 3107, 3108, 3110, 31...</td>\n",
       "      <td>{274, 278}</td>\n",
       "      <td>{3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...</td>\n",
       "      <td>[(A, 254, SER, CB, 1), (A, 254, SER, HB2, 1)]</td>\n",
       "      <td>[(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24679</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>2</td>\n",
       "      <td>SWNTGT</td>\n",
       "      <td>52</td>\n",
       "      <td>56</td>\n",
       "      <td>[3633, 3634, 3635, 3636, 3637, 3638, 3639, 364...</td>\n",
       "      <td>[123, 124, 126, 127, 129, 130, 131, 132, 133]</td>\n",
       "      <td>[253, 253, 253, 253, 254, 254, 254, 254, 254]</td>\n",
       "      <td>{266, 274, 275, 2322, 277, 278, 2967, 3107, 31...</td>\n",
       "      <td>{266, 274, 275, 277, 278, 3107, 3108, 3110, 31...</td>\n",
       "      <td>{266, 277}</td>\n",
       "      <td>{3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 2), (A, 254, SER, CB, 2),...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 2), (A, 254, SER, CB, 2),...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 2), (A, 254, SER, HA, 2)]</td>\n",
       "      <td>[(H, 31, ASP, CG, 2), (H, 99, VAL, CG2, 2), (H...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24680</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>3</td>\n",
       "      <td>TRSYVVAAEYYFHY</td>\n",
       "      <td>95</td>\n",
       "      <td>102</td>\n",
       "      <td>[4011, 4012, 4013, 4014, 4015, 4016, 4017, 401...</td>\n",
       "      <td>[107, 108, 113, 114, 115, 117, 118, 119, 120, ...</td>\n",
       "      <td>[251, 251, 252, 252, 252, 252, 252, 252, 252, ...</td>\n",
       "      <td>{266, 274, 275, 2322, 277, 278, 2967, 3107, 31...</td>\n",
       "      <td>{266, 274, 275, 277, 278, 3107, 3108, 3110, 31...</td>\n",
       "      <td>{3107, 3108, 3110, 3111, 3112, 3114, 3124, 312...</td>\n",
       "      <td>{3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 3), (A, 254, SER, CB, 3),...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 3), (A, 254, SER, CB, 3),...</td>\n",
       "      <td>[(A, 434, ASN, C, 3), (A, 434, ASN, O, 3), (A,...</td>\n",
       "      <td>[(H, 31, ASP, CG, 3), (H, 99, VAL, CG2, 3), (H...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24681</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>GGNNIGSKSVH</td>\n",
       "      <td>24</td>\n",
       "      <td>34</td>\n",
       "      <td>[1807, 1808, 1809, 1810, 1811, 1812, 1813, 181...</td>\n",
       "      <td>[1569]</td>\n",
       "      <td>[433]</td>\n",
       "      <td>{266, 274, 275, 2322, 277, 278, 2967, 3107, 31...</td>\n",
       "      <td>{3171, 3109, 3176, 3184, 2322, 2967, 3161, 2941}</td>\n",
       "      <td>{}</td>\n",
       "      <td>{3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...</td>\n",
       "      <td>[(A, 438, GLN, N, 1), (A, 434, ASN, CB, 1), (A...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24682</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>DDSDRPP</td>\n",
       "      <td>50</td>\n",
       "      <td>56</td>\n",
       "      <td>[2007, 2008, 2009, 2010, 2011, 2012, 2013, 201...</td>\n",
       "      <td>[1482, 1483, 1499, 1500, 1565, 1567, 1568, 156...</td>\n",
       "      <td>[422, 422, 424, 424, 433, 433, 433, 433, 434, ...</td>\n",
       "      <td>{266, 274, 275, 2322, 277, 278, 2967, 3107, 31...</td>\n",
       "      <td>{3171, 3109, 3176, 3184, 2322, 2967, 3161, 2941}</td>\n",
       "      <td>{3109, 2322, 2967, 3161, 2941}</td>\n",
       "      <td>{3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 2), (A, 254, SER, CB, 2),...</td>\n",
       "      <td>[(A, 438, GLN, N, 2), (A, 434, ASN, CB, 2), (A...</td>\n",
       "      <td>[(A, 434, ASN, CB, 2), (A, 382, GLU, HG3, 2), ...</td>\n",
       "      <td>[(H, 31, ASP, CG, 2), (H, 99, VAL, CG2, 2), (H...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24683</th>\n",
       "      <td>1adq</td>\n",
       "      <td>L</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>QVWDSSSDHAV</td>\n",
       "      <td>89</td>\n",
       "      <td>97</td>\n",
       "      <td>[2298, 2299, 2300, 2301, 2302, 2303, 2304, 230...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>{266, 274, 275, 2322, 277, 278, 2967, 3107, 31...</td>\n",
       "      <td>{3171, 3109, 3176, 3184, 2322, 2967, 3161, 2941}</td>\n",
       "      <td>{}</td>\n",
       "      <td>{3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 3), (A, 254, SER, CB, 3),...</td>\n",
       "      <td>[(A, 438, GLN, N, 3), (A, 434, ASN, CB, 3), (A...</td>\n",
       "      <td>[]</td>\n",
       "      <td>[(H, 31, ASP, CG, 3), (H, 99, VAL, CG2, 3), (H...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      idcode chainID chain_type  cdr         cdr_seq  cdr_begin  cdr_end  \\\n",
       "24678   1adq       H          H    1         GFTFDDY         26       32   \n",
       "24679   1adq       H          H    2          SWNTGT         52       56   \n",
       "24680   1adq       H          H    3  TRSYVVAAEYYFHY         95      102   \n",
       "24681   1adq       L          L    1     GGNNIGSKSVH         24       34   \n",
       "24682   1adq       L          L    2         DDSDRPP         50       56   \n",
       "24683   1adq       L          L    3     QVWDSSSDHAV         89       97   \n",
       "\n",
       "                                               cdr_atoms  \\\n",
       "24678  [3422, 3423, 3424, 3425, 3426, 3427, 3428, 342...   \n",
       "24679  [3633, 3634, 3635, 3636, 3637, 3638, 3639, 364...   \n",
       "24680  [4011, 4012, 4013, 4014, 4015, 4016, 4017, 401...   \n",
       "24681  [1807, 1808, 1809, 1810, 1811, 1812, 1813, 181...   \n",
       "24682  [2007, 2008, 2009, 2010, 2011, 2012, 2013, 201...   \n",
       "24683  [2298, 2299, 2300, 2301, 2302, 2303, 2304, 230...   \n",
       "\n",
       "                                           epitope_atoms  \\\n",
       "24678  [120, 130, 131, 132, 133, 134, 135, 140, 141, ...   \n",
       "24679      [123, 124, 126, 127, 129, 130, 131, 132, 133]   \n",
       "24680  [107, 108, 113, 114, 115, 117, 118, 119, 120, ...   \n",
       "24681                                             [1569]   \n",
       "24682  [1482, 1483, 1499, 1500, 1565, 1567, 1568, 156...   \n",
       "24683                                                 []   \n",
       "\n",
       "                                        epitope_residues  \\\n",
       "24678  [252, 254, 254, 254, 254, 254, 255, 255, 255, ...   \n",
       "24679      [253, 253, 253, 253, 254, 254, 254, 254, 254]   \n",
       "24680  [251, 251, 252, 252, 252, 252, 252, 252, 252, ...   \n",
       "24681                                              [433]   \n",
       "24682  [422, 422, 424, 424, 433, 433, 433, 433, 434, ...   \n",
       "24683                                                 []   \n",
       "\n",
       "                                         ag_ab_interface  \\\n",
       "24678  {266, 274, 275, 2322, 277, 278, 2967, 3107, 31...   \n",
       "24679  {266, 274, 275, 2322, 277, 278, 2967, 3107, 31...   \n",
       "24680  {266, 274, 275, 2322, 277, 278, 2967, 3107, 31...   \n",
       "24681  {266, 274, 275, 2322, 277, 278, 2967, 3107, 31...   \n",
       "24682  {266, 274, 275, 2322, 277, 278, 2967, 3107, 31...   \n",
       "24683  {266, 274, 275, 2322, 277, 278, 2967, 3107, 31...   \n",
       "\n",
       "                                   ag_cdrchain_interface  \\\n",
       "24678  {266, 274, 275, 277, 278, 3107, 3108, 3110, 31...   \n",
       "24679  {266, 274, 275, 277, 278, 3107, 3108, 3110, 31...   \n",
       "24680  {266, 274, 275, 277, 278, 3107, 3108, 3110, 31...   \n",
       "24681   {3171, 3109, 3176, 3184, 2322, 2967, 3161, 2941}   \n",
       "24682   {3171, 3109, 3176, 3184, 2322, 2967, 3161, 2941}   \n",
       "24683   {3171, 3109, 3176, 3184, 2322, 2967, 3161, 2941}   \n",
       "\n",
       "                                        ag_cdr_interface  \\\n",
       "24678                                         {274, 278}   \n",
       "24679                                         {266, 277}   \n",
       "24680  {3107, 3108, 3110, 3111, 3112, 3114, 3124, 312...   \n",
       "24681                                                 {}   \n",
       "24682                     {3109, 2322, 2967, 3161, 2941}   \n",
       "24683                                                 {}   \n",
       "\n",
       "                                         ab_ag_interface  \\\n",
       "24678  {3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...   \n",
       "24679  {3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...   \n",
       "24680  {3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...   \n",
       "24681  {3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...   \n",
       "24682  {3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...   \n",
       "24683  {3713, 4866, 3717, 4870, 3719, 4873, 7492, 749...   \n",
       "\n",
       "                                     ag_ab_interface_res  \\\n",
       "24678  [(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...   \n",
       "24679  [(A, 253, ILE, HG23, 2), (A, 254, SER, CB, 2),...   \n",
       "24680  [(A, 253, ILE, HG23, 3), (A, 254, SER, CB, 3),...   \n",
       "24681  [(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...   \n",
       "24682  [(A, 253, ILE, HG23, 2), (A, 254, SER, CB, 2),...   \n",
       "24683  [(A, 253, ILE, HG23, 3), (A, 254, SER, CB, 3),...   \n",
       "\n",
       "                               ag_cdrchain_interface_res  \\\n",
       "24678  [(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...   \n",
       "24679  [(A, 253, ILE, HG23, 2), (A, 254, SER, CB, 2),...   \n",
       "24680  [(A, 253, ILE, HG23, 3), (A, 254, SER, CB, 3),...   \n",
       "24681  [(A, 438, GLN, N, 1), (A, 434, ASN, CB, 1), (A...   \n",
       "24682  [(A, 438, GLN, N, 2), (A, 434, ASN, CB, 2), (A...   \n",
       "24683  [(A, 438, GLN, N, 3), (A, 434, ASN, CB, 3), (A...   \n",
       "\n",
       "                                    ag_cdr_interface_res  \\\n",
       "24678      [(A, 254, SER, CB, 1), (A, 254, SER, HB2, 1)]   \n",
       "24679     [(A, 253, ILE, HG23, 2), (A, 254, SER, HA, 2)]   \n",
       "24680  [(A, 434, ASN, C, 3), (A, 434, ASN, O, 3), (A,...   \n",
       "24681                                                 []   \n",
       "24682  [(A, 434, ASN, CB, 2), (A, 382, GLU, HG3, 2), ...   \n",
       "24683                                                 []   \n",
       "\n",
       "                                     ab_ag_interface_res  \n",
       "24678  [(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...  \n",
       "24679  [(H, 31, ASP, CG, 2), (H, 99, VAL, CG2, 2), (H...  \n",
       "24680  [(H, 31, ASP, CG, 3), (H, 99, VAL, CG2, 3), (H...  \n",
       "24681  [(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...  \n",
       "24682  [(H, 31, ASP, CG, 2), (H, 99, VAL, CG2, 2), (H...  \n",
       "24683  [(H, 31, ASP, CG, 3), (H, 99, VAL, CG2, 3), (H...  "
      ]
     },
     "execution_count": 169,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_buried_old.query(f\"idcode == '1adq'\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 163,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "data": {
      "text/plain": [
       "0    (9, 3, 3, 0, 5, 0, 2, 0, [THR, SER, TRP, ASN, ...\n",
       "dtype: object"
      ]
     },
     "execution_count": 163,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "buried_ab_ag_interface_res_old.iloc[:1].apply(lambda x: count_chains(x), axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 154,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<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>idcode</th>\n",
       "      <th>chainID</th>\n",
       "      <th>chain_type</th>\n",
       "      <th>ab_ag_interface_res</th>\n",
       "      <th>ag_ab_interface_res</th>\n",
       "      <th>chains</th>\n",
       "      <th>hchains</th>\n",
       "      <th>lchains</th>\n",
       "      <th>hcdr1</th>\n",
       "      <th>hcdr2</th>\n",
       "      <th>hcdr3</th>\n",
       "      <th>lcdr1</th>\n",
       "      <th>lcdr2</th>\n",
       "      <th>lcdr3</th>\n",
       "      <th>ab_res</th>\n",
       "      <th>ag_res</th>\n",
       "      <th>incomplete</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>24678</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>[(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...</td>\n",
       "      <td>(6, 3, 1, 1, 0, 1, 2, 0, [ASP, VAL, PRO, PRO, ...</td>\n",
       "      <td>6.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[ASP, VAL, PRO, PRO, ARG, PRO, PRO, ARG, ARG, ...</td>\n",
       "      <td>[SER, SER, SER, ASN, ASN, ASN, ASN, ASN, ASN, ...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      idcode chainID chain_type  \\\n",
       "24678   1adq       H          H   \n",
       "\n",
       "                                     ab_ag_interface_res  \\\n",
       "24678  [(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...   \n",
       "\n",
       "                                     ag_ab_interface_res  \\\n",
       "24678  [(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...   \n",
       "\n",
       "                                                  chains  hchains  lchains  \\\n",
       "24678  (6, 3, 1, 1, 0, 1, 2, 0, [ASP, VAL, PRO, PRO, ...      6.0      3.0   \n",
       "\n",
       "       hcdr1  hcdr2  hcdr3  lcdr1  lcdr2  lcdr3  \\\n",
       "24678    1.0    1.0    0.0    1.0    2.0    0.0   \n",
       "\n",
       "                                                  ab_res  \\\n",
       "24678  [ASP, VAL, PRO, PRO, ARG, PRO, PRO, ARG, ARG, ...   \n",
       "\n",
       "                                                  ag_res incomplete  \n",
       "24678  [SER, SER, SER, ASN, ASN, ASN, ASN, ASN, ASN, ...      False  "
      ]
     },
     "execution_count": 154,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "buried_ab_ag_interface_res_old.query(\"idcode == '1adq'\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 141,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('H', '31', 'ASP', 'CG', 1),\n",
       " ('H', '99', 'VAL', 'CG2', 1),\n",
       " ('H', '31', 'ASP', 'HA', 1),\n",
       " ('H', '99', 'VAL', 'HG11', 1),\n",
       " ('H', '31', 'ASP', 'HB3', 1),\n",
       " ('H', '99', 'VAL', 'HG21', 1),\n",
       " ('L', '56', 'PRO', 'C', 1),\n",
       " ('L', '56', 'PRO', 'CB', 1),\n",
       " ('H', '96', 'ARG', 'O', 1),\n",
       " ('L', '56', 'PRO', 'CG', 1),\n",
       " ('L', '56', 'PRO', 'CD', 1),\n",
       " ('H', '96', 'ARG', 'CD', 1),\n",
       " ('H', '96', 'ARG', 'NE', 1),\n",
       " ('H', '96', 'ARG', 'CZ', 1),\n",
       " ('L', '32', 'SER', 'OG', 1),\n",
       " ('H', '96', 'ARG', 'NH2', 1),\n",
       " ('L', '56', 'PRO', 'HB3', 1),\n",
       " ('L', '56', 'PRO', 'HD3', 1),\n",
       " ('H', '96', 'ARG', 'HD2', 1),\n",
       " ('H', '52A', 'TRP', 'CG', 1),\n",
       " ('H', '96', 'ARG', 'HD3', 1),\n",
       " ('H', '52A', 'TRP', 'CD2', 1),\n",
       " ('H', '52A', 'TRP', 'CE2', 1),\n",
       " ('H', '52A', 'TRP', 'CE3', 1),\n",
       " ('H', '100E', 'TYR', 'OH', 1),\n",
       " ('H', '97', 'SER', 'HA', 1),\n",
       " ('H', '97', 'SER', 'HB3', 1),\n",
       " ('H', '2', 'VAL', 'HG23', 1),\n",
       " ('H', '98', 'TYR', 'C', 1),\n",
       " ('H', '98', 'TYR', 'CB', 1),\n",
       " ('H', '98', 'TYR', 'CG', 1),\n",
       " ('H', '98', 'TYR', 'CD1', 1),\n",
       " ('H', '98', 'TYR', 'CD2', 1),\n",
       " ('H', '98', 'TYR', 'CE2', 1),\n",
       " ('H', '98', 'TYR', 'CZ', 1),\n",
       " ('L', '50', 'ASP', 'CG', 1),\n",
       " ('H', '98', 'TYR', 'HA', 1),\n",
       " ('H', '98', 'TYR', 'HB2', 1),\n",
       " ('H', '98', 'TYR', 'HB3', 1),\n",
       " ('H', '98', 'TYR', 'HD1', 1),\n",
       " ('H', '98', 'TYR', 'HD2', 1),\n",
       " ('H', '98', 'TYR', 'HE2', 1),\n",
       " ('H', '99', 'VAL', 'N', 1)]"
      ]
     },
     "execution_count": 141,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "buried_ab_ag_interface_res.query(\"idcode == '1adq'\")[\"ab_ag_interface_res\"].values[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [],
   "source": [
    "buried_ab_ag_interface_res_old = pd.read_pickle('data/buried_ab_ag_interface_res_old.pickle')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 166,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_buried_old = pd.read_pickle('data/epitope_buried_old.pickle')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'buried_ab_ag_interface_res_old' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m/home/pedror/IIT/cdr-db/final.ipynb Cell 24'\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell://ssh-remote%2Bbio004/home/pedror/IIT/cdr-db/final.ipynb#ch0000048vscode-remote?line=0'>1</a>\u001b[0m buried_ab_ag_interface_res_old\u001b[39m.\u001b[39msort_values(by\u001b[39m=\u001b[39m[\u001b[39m\"\u001b[39m\u001b[39midcode\u001b[39m\u001b[39m\"\u001b[39m])[:\u001b[39m3\u001b[39m]\n",
      "\u001b[0;31mNameError\u001b[0m: name 'buried_ab_ag_interface_res_old' is not defined"
     ]
    }
   ],
   "source": [
    "buried_ab_ag_interface_res_old.sort_values(by=[\"idcode\"])[:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 129,
   "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>idcode</th>\n",
       "      <th>chainID</th>\n",
       "      <th>chain_type</th>\n",
       "      <th>ab_ag_interface_res</th>\n",
       "      <th>ag_ab_interface_res</th>\n",
       "      <th>chains</th>\n",
       "      <th>hchains</th>\n",
       "      <th>lchains</th>\n",
       "      <th>hcdr1</th>\n",
       "      <th>hcdr2</th>\n",
       "      <th>hcdr3</th>\n",
       "      <th>lcdr1</th>\n",
       "      <th>lcdr2</th>\n",
       "      <th>lcdr3</th>\n",
       "      <th>ab_res</th>\n",
       "      <th>ag_res</th>\n",
       "      <th>incomplete</th>\n",
       "      <th>bothchains</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2388</th>\n",
       "      <td>1adq</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>[(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...</td>\n",
       "      <td>[(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...</td>\n",
       "      <td>(6, 3, 1, 1, 0, 1, 2, 0, [ASP, VAL, PRO, PRO, ...</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>[ASP, VAL, PRO, PRO, ARG, PRO, PRO, ARG, ARG, ...</td>\n",
       "      <td>[SER, SER, SER, ASN, ASN, ASN, ASN, ASN, ASN, ...</td>\n",
       "      <td>False</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>696</th>\n",
       "      <td>1afv</td>\n",
       "      <td>H</td>\n",
       "      <td>H</td>\n",
       "      <td>[(H, 99, TRP, CZ2, 1), (L, 96, LYS, C, 1), (H,...</td>\n",
       "      <td>[(A, 76, GLU, OE2, 1), (A, 102, SER, N, 1), (A...</td>\n",
       "      <td>(8, 7, 0, 0, 0, 3, 0, 0, [TRP, LYS, PHE, TRP, ...</td>\n",
       "      <td>8</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[TRP, LYS, PHE, TRP, TRP, GLU, VAL, VAL, ASN, ...</td>\n",
       "      <td>[GLU, SER, PRO, ALA, ALA, ALA, GLU, GLU, ASP, ...</td>\n",
       "      <td>False</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7068</th>\n",
       "      <td>1ahw</td>\n",
       "      <td>E</td>\n",
       "      <td>H</td>\n",
       "      <td>[(E, 52, ASP, OD1, 1), (E, 52, ASP, HB2, 1), (...</td>\n",
       "      <td>[(F, 152, ILE, CG1, 1), (F, 152, ILE, CD1, 1),...</td>\n",
       "      <td>(14, 7, 4, 4, 0, 1, 1, 5, [ASP, GLU, GLU, ASN,...</td>\n",
       "      <td>14</td>\n",
       "      <td>7</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>[ASP, GLU, GLU, ASN, ASN, ASN, PHE, ILE, ILE, ...</td>\n",
       "      <td>[ILE, ILE, THR, TYR, TYR, TYR, TYR, GLN, GLN, ...</td>\n",
       "      <td>False</td>\n",
       "      <td>21</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     idcode chainID chain_type  \\\n",
       "2388   1adq       H          H   \n",
       "696    1afv       H          H   \n",
       "7068   1ahw       E          H   \n",
       "\n",
       "                                    ab_ag_interface_res  \\\n",
       "2388  [(H, 31, ASP, CG, 1), (H, 99, VAL, CG2, 1), (H...   \n",
       "696   [(H, 99, TRP, CZ2, 1), (L, 96, LYS, C, 1), (H,...   \n",
       "7068  [(E, 52, ASP, OD1, 1), (E, 52, ASP, HB2, 1), (...   \n",
       "\n",
       "                                    ag_ab_interface_res  \\\n",
       "2388  [(A, 253, ILE, HG23, 1), (A, 254, SER, CB, 1),...   \n",
       "696   [(A, 76, GLU, OE2, 1), (A, 102, SER, N, 1), (A...   \n",
       "7068  [(F, 152, ILE, CG1, 1), (F, 152, ILE, CD1, 1),...   \n",
       "\n",
       "                                                 chains  hchains  lchains  \\\n",
       "2388  (6, 3, 1, 1, 0, 1, 2, 0, [ASP, VAL, PRO, PRO, ...        6        3   \n",
       "696   (8, 7, 0, 0, 0, 3, 0, 0, [TRP, LYS, PHE, TRP, ...        8        7   \n",
       "7068  (14, 7, 4, 4, 0, 1, 1, 5, [ASP, GLU, GLU, ASN,...       14        7   \n",
       "\n",
       "      hcdr1  hcdr2  hcdr3  lcdr1  lcdr2  lcdr3  \\\n",
       "2388      1      1      0      1      2      0   \n",
       "696       0      0      0      3      0      0   \n",
       "7068      4      4      0      1      1      5   \n",
       "\n",
       "                                                 ab_res  \\\n",
       "2388  [ASP, VAL, PRO, PRO, ARG, PRO, PRO, ARG, ARG, ...   \n",
       "696   [TRP, LYS, PHE, TRP, TRP, GLU, VAL, VAL, ASN, ...   \n",
       "7068  [ASP, GLU, GLU, ASN, ASN, ASN, PHE, ILE, ILE, ...   \n",
       "\n",
       "                                                 ag_res  incomplete  \\\n",
       "2388  [SER, SER, SER, ASN, ASN, ASN, ASN, ASN, ASN, ...       False   \n",
       "696   [GLU, SER, PRO, ALA, ALA, ALA, GLU, GLU, ASP, ...       False   \n",
       "7068  [ILE, ILE, THR, TYR, TYR, TYR, TYR, GLN, GLN, ...       False   \n",
       "\n",
       "      bothchains  \n",
       "2388           9  \n",
       "696           15  \n",
       "7068          21  "
      ]
     },
     "execution_count": 129,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "buried_ab_ag_interface_res_.sort_values(by=[\"idcode\"])[:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {},
   "outputs": [],
   "source": [
    "buried_ab_ag_interface_res_ = buried_ab_ag_interface_res.query(f\"idcode in {list(set(buried_ab_ag_interface_res.idcode.values) & set(buried_ab_ag_interface_res_old.idcode.values))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 123,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.4178082191780822\n",
      "2.5511756569847854\n"
     ]
    }
   ],
   "source": [
    "# '7mhy', '7mjs', '4xx1', '6wj1', '6q18', '6mph', '6oor', '6bdz'\n",
    "# buried_ab_ag_interface_res.query(\"idcode == '7mhy'\")\n",
    "# set(buried_ab_ag_interface_res.idcode.values) & set(buried_ab_ag_interface_res_old.idcode.values)\n",
    "print(buried_ab_ag_interface_res_['hcdr3'].sum() / buried_ab_ag_interface_res_['hcdr1'].sum())\n",
    "print(buried_ab_ag_interface_res_old['hcdr3'].sum() / buried_ab_ag_interface_res_old['hcdr1'].sum())"
   ]
  }
 ],
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