data_processor.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import sys, os\n",
    "import time\n",
    "import multiprocessing\n",
    "from itertools import repeat, product"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "f_euclid_dist = lambda a,b: np.linalg.norm(a-b)\n",
    "\n",
    "def f_h_step(x, a):\n",
    "    return 1 if (x<=a) else 0\n",
    "\n",
    "f_y = lambda k : -np.log10(k)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Y Data Processor"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "id              2pcb\n",
      "1               2.80\n",
      "2               1993\n",
      "k            Kd=10uM\n",
      "4                 //\n",
      "5           2pcb.pdf\n",
      "6          (104-mer)\n",
      "7         cytochrome\n",
      "8                 c,\n",
      "9        Ka=10^5M-1,\n",
      "10          Kd=10-5M\n",
      "11              None\n",
      "12              None\n",
      "13              None\n",
      "14              None\n",
      "15              None\n",
      "16              None\n",
      "17              None\n",
      "18              None\n",
      "19              None\n",
      "20              None\n",
      "21              None\n",
      "22              None\n",
      "23              None\n",
      "24              None\n",
      "25              None\n",
      "26              None\n",
      "27              None\n",
      "28              None\n",
      "29              None\n",
      "30              None\n",
      "31              None\n",
      "32              None\n",
      "33              None\n",
      "34              None\n",
      "35              None\n",
      "36              None\n",
      "37              None\n",
      "log_y              5\n",
      "Name: 9, dtype: object\n",
      "2416\n"
     ]
    }
   ],
   "source": [
    "'''\n",
    "Create dataframes of log_10^y\n",
    "'''\n",
    "path = 'C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Dataset/PP/index/INDEX_general_PP.2018'\n",
    "mol_units = {'uM':1.e-6, 'pM':1.e-12, 'fM':1.e-15, 'nM':1.e-9, 'mM':1.e-3}\n",
    "\n",
    "#load the index file\n",
    "l = []\n",
    "with open(path, 'r') as f:\n",
    "    for line in f:\n",
    "        if not line.startswith('#'):\n",
    "            clean_line = line.rstrip()\n",
    "            l.append((line.rstrip()).split())\n",
    "df_idx = (pd.DataFrame(l)).rename(columns={0:'id',3:'k'})\n",
    "#print(df_idx)\n",
    "\n",
    "#generate the -log_10k values\n",
    "op_tokens = ['=','~','>','<']\n",
    "logys = np.zeros(df_idx.shape[0])\n",
    "for i in range(df_idx.shape[0]):\n",
    "    string = df_idx.loc[i]['k']\n",
    "    for s in string:\n",
    "        if s in op_tokens:\n",
    "            split_str = string.split(s)\n",
    "            break\n",
    "    logys[i] = f_y( float(split_str[-1][:-2]) * mol_units[split_str[-1][-2:]] )\n",
    "df_idx[\"log_y\"] = logys\n",
    "\n",
    "print(df_idx.loc[9])\n",
    "print(len(df_idx))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Complex Data Processor"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2416\n",
      "C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Dataset/PP/1a3b.ent.pdb\n"
     ]
    }
   ],
   "source": [
    "'''\n",
    "files loader\n",
    "'''\n",
    "path = 'C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Dataset/PP'\n",
    "\n",
    "\n",
    "complex_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))]\n",
    "print(len(complex_files))\n",
    "\n",
    "test_file = path+'/'+complex_files[2]\n",
    "print(test_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['ATOM', '2242', 'N', 'GLY', 'I', '9', '20.469', '-13.494', '37.284', '1.00', '107.45', 'N']\n"
     ]
    },
    {
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       "      <th></th>\n",
       "      <th>record</th>\n",
       "      <th>1</th>\n",
       "      <th>2</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>ALA</td>\n",
       "      <td>L</td>\n",
       "      <td>1B</td>\n",
       "      <td>15.110</td>\n",
       "      <td>18.115</td>\n",
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       "      <td>1.00</td>\n",
       "      <td>36.99</td>\n",
       "      <td>N</td>\n",
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       "      <td>ATOM</td>\n",
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       "      <td>ALA</td>\n",
       "      <td>L</td>\n",
       "      <td>1B</td>\n",
       "      <td>15.151</td>\n",
       "      <td>19.655</td>\n",
       "      <td>15.324</td>\n",
       "      <td>1.00</td>\n",
       "      <td>44.33</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>3</td>\n",
       "      <td>C</td>\n",
       "      <td>ALA</td>\n",
       "      <td>L</td>\n",
       "      <td>1B</td>\n",
       "      <td>16.619</td>\n",
       "      <td>19.913</td>\n",
       "      <td>15.465</td>\n",
       "      <td>1.00</td>\n",
       "      <td>31.21</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>4</td>\n",
       "      <td>O</td>\n",
       "      <td>ALA</td>\n",
       "      <td>L</td>\n",
       "      <td>1B</td>\n",
       "      <td>17.199</td>\n",
       "      <td>20.722</td>\n",
       "      <td>14.728</td>\n",
       "      <td>1.00</td>\n",
       "      <td>27.87</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>5</td>\n",
       "      <td>CB</td>\n",
       "      <td>ALA</td>\n",
       "      <td>L</td>\n",
       "      <td>1B</td>\n",
       "      <td>14.328</td>\n",
       "      <td>19.790</td>\n",
       "      <td>16.582</td>\n",
       "      <td>1.00</td>\n",
       "      <td>36.57</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>6</td>\n",
       "      <td>N</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>17.075</td>\n",
       "      <td>19.131</td>\n",
       "      <td>16.396</td>\n",
       "      <td>1.00</td>\n",
       "      <td>24.26</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>7</td>\n",
       "      <td>CA</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>18.455</td>\n",
       "      <td>18.973</td>\n",
       "      <td>16.762</td>\n",
       "      <td>1.00</td>\n",
       "      <td>24.64</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>8</td>\n",
       "      <td>C</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>18.725</td>\n",
       "      <td>17.483</td>\n",
       "      <td>16.620</td>\n",
       "      <td>1.00</td>\n",
       "      <td>18.66</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>9</td>\n",
       "      <td>O</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>19.822</td>\n",
       "      <td>16.999</td>\n",
       "      <td>16.911</td>\n",
       "      <td>1.00</td>\n",
       "      <td>19.27</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>10</td>\n",
       "      <td>CB</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>18.645</td>\n",
       "      <td>19.446</td>\n",
       "      <td>18.202</td>\n",
       "      <td>1.00</td>\n",
       "      <td>31.66</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>11</td>\n",
       "      <td>CG</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>20.085</td>\n",
       "      <td>19.313</td>\n",
       "      <td>18.682</td>\n",
       "      <td>1.00</td>\n",
       "      <td>39.01</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>12</td>\n",
       "      <td>OD1</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>21.043</td>\n",
       "      <td>19.254</td>\n",
       "      <td>17.822</td>\n",
       "      <td>1.00</td>\n",
       "      <td>60.26</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>13</td>\n",
       "      <td>OD2</td>\n",
       "      <td>ASP</td>\n",
       "      <td>L</td>\n",
       "      <td>1A</td>\n",
       "      <td>20.339</td>\n",
       "      <td>19.261</td>\n",
       "      <td>19.944</td>\n",
       "      <td>1.00</td>\n",
       "      <td>57.76</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>14</td>\n",
       "      <td>N</td>\n",
       "      <td>CYS</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>17.664</td>\n",
       "      <td>16.833</td>\n",
       "      <td>16.160</td>\n",
       "      <td>1.00</td>\n",
       "      <td>17.75</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>15</td>\n",
       "      <td>CA</td>\n",
       "      <td>CYS</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>17.614</td>\n",
       "      <td>15.384</td>\n",
       "      <td>15.950</td>\n",
       "      <td>1.00</td>\n",
       "      <td>18.84</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>16</td>\n",
       "      <td>C</td>\n",
       "      <td>CYS</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>18.695</td>\n",
       "      <td>14.923</td>\n",
       "      <td>14.970</td>\n",
       "      <td>1.00</td>\n",
       "      <td>15.87</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>17</td>\n",
       "      <td>O</td>\n",
       "      <td>CYS</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>19.015</td>\n",
       "      <td>15.618</td>\n",
       "      <td>13.998</td>\n",
       "      <td>1.00</td>\n",
       "      <td>14.39</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>18</td>\n",
       "      <td>CB</td>\n",
       "      <td>CYS</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>16.251</td>\n",
       "      <td>14.985</td>\n",
       "      <td>15.367</td>\n",
       "      <td>1.00</td>\n",
       "      <td>20.41</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>19</td>\n",
       "      <td>SG</td>\n",
       "      <td>CYS</td>\n",
       "      <td>L</td>\n",
       "      <td>1</td>\n",
       "      <td>16.089</td>\n",
       "      <td>15.371</td>\n",
       "      <td>13.593</td>\n",
       "      <td>1.00</td>\n",
       "      <td>18.36</td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>20</td>\n",
       "      <td>N</td>\n",
       "      <td>GLY</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>19.224</td>\n",
       "      <td>13.755</td>\n",
       "      <td>15.285</td>\n",
       "      <td>1.00</td>\n",
       "      <td>15.56</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>21</td>\n",
       "      <td>CA</td>\n",
       "      <td>GLY</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>20.212</td>\n",
       "      <td>13.059</td>\n",
       "      <td>14.445</td>\n",
       "      <td>1.00</td>\n",
       "      <td>11.86</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>22</td>\n",
       "      <td>C</td>\n",
       "      <td>GLY</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>21.631</td>\n",
       "      <td>13.651</td>\n",
       "      <td>14.541</td>\n",
       "      <td>1.00</td>\n",
       "      <td>16.01</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>23</td>\n",
       "      <td>O</td>\n",
       "      <td>GLY</td>\n",
       "      <td>L</td>\n",
       "      <td>2</td>\n",
       "      <td>22.536</td>\n",
       "      <td>13.255</td>\n",
       "      <td>13.796</td>\n",
       "      <td>1.00</td>\n",
       "      <td>15.28</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>24</td>\n",
       "      <td>N</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>21.824</td>\n",
       "      <td>14.595</td>\n",
       "      <td>15.437</td>\n",
       "      <td>1.00</td>\n",
       "      <td>15.22</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>25</td>\n",
       "      <td>CA</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>23.158</td>\n",
       "      <td>15.198</td>\n",
       "      <td>15.651</td>\n",
       "      <td>1.00</td>\n",
       "      <td>13.04</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>26</td>\n",
       "      <td>C</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>23.665</td>\n",
       "      <td>14.745</td>\n",
       "      <td>17.026</td>\n",
       "      <td>1.00</td>\n",
       "      <td>13.60</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>27</td>\n",
       "      <td>O</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>23.179</td>\n",
       "      <td>15.204</td>\n",
       "      <td>18.066</td>\n",
       "      <td>1.00</td>\n",
       "      <td>18.09</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>28</td>\n",
       "      <td>CB</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>23.066</td>\n",
       "      <td>16.728</td>\n",
       "      <td>15.581</td>\n",
       "      <td>1.00</td>\n",
       "      <td>14.72</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>29</td>\n",
       "      <td>CG</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>22.591</td>\n",
       "      <td>17.248</td>\n",
       "      <td>14.217</td>\n",
       "      <td>1.00</td>\n",
       "      <td>21.82</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>30</td>\n",
       "      <td>CD1</td>\n",
       "      <td>LEU</td>\n",
       "      <td>L</td>\n",
       "      <td>3</td>\n",
       "      <td>22.354</td>\n",
       "      <td>18.761</td>\n",
       "      <td>14.200</td>\n",
       "      <td>1.00</td>\n",
       "      <td>17.76</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\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>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2298</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2299</td>\n",
       "      <td>CA</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>16</td>\n",
       "      <td>14.774</td>\n",
       "      <td>1.309</td>\n",
       "      <td>43.626</td>\n",
       "      <td>1.00</td>\n",
       "      <td>83.01</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2300</td>\n",
       "      <td>C</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>16</td>\n",
       "      <td>14.250</td>\n",
       "      <td>2.707</td>\n",
       "      <td>43.822</td>\n",
       "      <td>1.00</td>\n",
       "      <td>89.61</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2301</td>\n",
       "      <td>O</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>16</td>\n",
       "      <td>13.741</td>\n",
       "      <td>3.039</td>\n",
       "      <td>44.895</td>\n",
       "      <td>1.00</td>\n",
       "      <td>96.34</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2301</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2302</td>\n",
       "      <td>N</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>14.321</td>\n",
       "      <td>3.603</td>\n",
       "      <td>42.873</td>\n",
       "      <td>1.00</td>\n",
       "      <td>95.67</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2302</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2303</td>\n",
       "      <td>CA</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>13.623</td>\n",
       "      <td>4.882</td>\n",
       "      <td>42.887</td>\n",
       "      <td>1.00</td>\n",
       "      <td>99.81</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2303</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2304</td>\n",
       "      <td>C</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>12.562</td>\n",
       "      <td>4.746</td>\n",
       "      <td>41.800</td>\n",
       "      <td>1.00</td>\n",
       "      <td>102.28</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2304</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2305</td>\n",
       "      <td>O</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>11.548</td>\n",
       "      <td>5.458</td>\n",
       "      <td>41.800</td>\n",
       "      <td>1.00</td>\n",
       "      <td>103.18</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2305</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2306</td>\n",
       "      <td>CB</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>14.519</td>\n",
       "      <td>6.061</td>\n",
       "      <td>42.540</td>\n",
       "      <td>1.00</td>\n",
       "      <td>103.54</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2306</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2307</td>\n",
       "      <td>CG</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>15.431</td>\n",
       "      <td>6.477</td>\n",
       "      <td>43.692</td>\n",
       "      <td>1.00</td>\n",
       "      <td>105.06</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2307</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2308</td>\n",
       "      <td>CD</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>16.734</td>\n",
       "      <td>5.684</td>\n",
       "      <td>43.726</td>\n",
       "      <td>1.00</td>\n",
       "      <td>105.09</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2308</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2309</td>\n",
       "      <td>OE1</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>16.897</td>\n",
       "      <td>4.680</td>\n",
       "      <td>42.933</td>\n",
       "      <td>1.00</td>\n",
       "      <td>105.93</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2309</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2310</td>\n",
       "      <td>OE2</td>\n",
       "      <td>GLU</td>\n",
       "      <td>I</td>\n",
       "      <td>17</td>\n",
       "      <td>17.669</td>\n",
       "      <td>6.017</td>\n",
       "      <td>44.548</td>\n",
       "      <td>1.00</td>\n",
       "      <td>106.34</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2310</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2311</td>\n",
       "      <td>N</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>12.900</td>\n",
       "      <td>3.800</td>\n",
       "      <td>40.927</td>\n",
       "      <td>1.00</td>\n",
       "      <td>103.19</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2311</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2312</td>\n",
       "      <td>CA</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>12.083</td>\n",
       "      <td>3.376</td>\n",
       "      <td>39.786</td>\n",
       "      <td>1.00</td>\n",
       "      <td>103.03</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2312</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2313</td>\n",
       "      <td>C</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>11.566</td>\n",
       "      <td>1.953</td>\n",
       "      <td>40.077</td>\n",
       "      <td>1.00</td>\n",
       "      <td>104.38</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2313</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2314</td>\n",
       "      <td>O</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>10.420</td>\n",
       "      <td>1.763</td>\n",
       "      <td>40.499</td>\n",
       "      <td>1.00</td>\n",
       "      <td>105.64</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2314</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2315</td>\n",
       "      <td>CB</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>12.925</td>\n",
       "      <td>3.424</td>\n",
       "      <td>38.503</td>\n",
       "      <td>1.00</td>\n",
       "      <td>100.75</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2315</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2316</td>\n",
       "      <td>CG</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>14.176</td>\n",
       "      <td>4.300</td>\n",
       "      <td>38.645</td>\n",
       "      <td>1.00</td>\n",
       "      <td>99.09</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2316</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2317</td>\n",
       "      <td>CD1</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>14.101</td>\n",
       "      <td>5.687</td>\n",
       "      <td>38.438</td>\n",
       "      <td>1.00</td>\n",
       "      <td>99.38</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2317</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2318</td>\n",
       "      <td>CD2</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>15.399</td>\n",
       "      <td>3.714</td>\n",
       "      <td>38.986</td>\n",
       "      <td>1.00</td>\n",
       "      <td>99.20</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2318</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2319</td>\n",
       "      <td>CE1</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>15.249</td>\n",
       "      <td>6.482</td>\n",
       "      <td>38.584</td>\n",
       "      <td>1.00</td>\n",
       "      <td>98.81</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2319</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2320</td>\n",
       "      <td>CE2</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>16.543</td>\n",
       "      <td>4.507</td>\n",
       "      <td>39.136</td>\n",
       "      <td>1.00</td>\n",
       "      <td>98.84</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2320</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2321</td>\n",
       "      <td>CZ</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>16.469</td>\n",
       "      <td>5.891</td>\n",
       "      <td>38.937</td>\n",
       "      <td>1.00</td>\n",
       "      <td>98.61</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2321</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2322</td>\n",
       "      <td>OH</td>\n",
       "      <td>TYR</td>\n",
       "      <td>I</td>\n",
       "      <td>18</td>\n",
       "      <td>17.581</td>\n",
       "      <td>6.659</td>\n",
       "      <td>39.089</td>\n",
       "      <td>1.00</td>\n",
       "      <td>96.67</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2322</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2323</td>\n",
       "      <td>N</td>\n",
       "      <td>LEU</td>\n",
       "      <td>I</td>\n",
       "      <td>19</td>\n",
       "      <td>12.427</td>\n",
       "      <td>0.963</td>\n",
       "      <td>39.863</td>\n",
       "      <td>1.00</td>\n",
       "      <td>107.80</td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2323</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2324</td>\n",
       "      <td>CA</td>\n",
       "      <td>LEU</td>\n",
       "      <td>I</td>\n",
       "      <td>19</td>\n",
       "      <td>12.087</td>\n",
       "      <td>-0.457</td>\n",
       "      <td>40.135</td>\n",
       "      <td>1.00</td>\n",
       "      <td>109.88</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2324</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2325</td>\n",
       "      <td>C</td>\n",
       "      <td>LEU</td>\n",
       "      <td>I</td>\n",
       "      <td>19</td>\n",
       "      <td>12.269</td>\n",
       "      <td>-0.739</td>\n",
       "      <td>41.619</td>\n",
       "      <td>1.00</td>\n",
       "      <td>112.34</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2325</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2326</td>\n",
       "      <td>O</td>\n",
       "      <td>LEU</td>\n",
       "      <td>I</td>\n",
       "      <td>19</td>\n",
       "      <td>11.858</td>\n",
       "      <td>0.008</td>\n",
       "      <td>42.525</td>\n",
       "      <td>1.00</td>\n",
       "      <td>113.15</td>\n",
       "      <td>O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2326</th>\n",
       "      <td>ATOM</td>\n",
       "      <td>2327</td>\n",
       "      <td>CB</td>\n",
       "      <td>LEU</td>\n",
       "      <td>I</td>\n",
       "      <td>19</td>\n",
       "      <td>13.000</td>\n",
       "      <td>-1.382</td>\n",
       "      <td>39.328</td>\n",
       "      <td>1.00</td>\n",
       "      <td>114.04</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2327</th>\n",
       "      <td>TER</td>\n",
       "      <td>2328</td>\n",
       "      <td>LEU</td>\n",
       "      <td>I</td>\n",
       "      <td>19</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2328 rows × 12 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     record     1    2    3   4     5  x_coor  y_coor  z_coor     9      10  \\\n",
       "0      ATOM     1    N  ALA   L    1B  15.110  18.115  15.087  1.00   36.99   \n",
       "1      ATOM     2   CA  ALA   L    1B  15.151  19.655  15.324  1.00   44.33   \n",
       "2      ATOM     3    C  ALA   L    1B  16.619  19.913  15.465  1.00   31.21   \n",
       "3      ATOM     4    O  ALA   L    1B  17.199  20.722  14.728  1.00   27.87   \n",
       "4      ATOM     5   CB  ALA   L    1B  14.328  19.790  16.582  1.00   36.57   \n",
       "5      ATOM     6    N  ASP   L    1A  17.075  19.131  16.396  1.00   24.26   \n",
       "6      ATOM     7   CA  ASP   L    1A  18.455  18.973  16.762  1.00   24.64   \n",
       "7      ATOM     8    C  ASP   L    1A  18.725  17.483  16.620  1.00   18.66   \n",
       "8      ATOM     9    O  ASP   L    1A  19.822  16.999  16.911  1.00   19.27   \n",
       "9      ATOM    10   CB  ASP   L    1A  18.645  19.446  18.202  1.00   31.66   \n",
       "10     ATOM    11   CG  ASP   L    1A  20.085  19.313  18.682  1.00   39.01   \n",
       "11     ATOM    12  OD1  ASP   L    1A  21.043  19.254  17.822  1.00   60.26   \n",
       "12     ATOM    13  OD2  ASP   L    1A  20.339  19.261  19.944  1.00   57.76   \n",
       "13     ATOM    14    N  CYS   L     1  17.664  16.833  16.160  1.00   17.75   \n",
       "14     ATOM    15   CA  CYS   L     1  17.614  15.384  15.950  1.00   18.84   \n",
       "15     ATOM    16    C  CYS   L     1  18.695  14.923  14.970  1.00   15.87   \n",
       "16     ATOM    17    O  CYS   L     1  19.015  15.618  13.998  1.00   14.39   \n",
       "17     ATOM    18   CB  CYS   L     1  16.251  14.985  15.367  1.00   20.41   \n",
       "18     ATOM    19   SG  CYS   L     1  16.089  15.371  13.593  1.00   18.36   \n",
       "19     ATOM    20    N  GLY   L     2  19.224  13.755  15.285  1.00   15.56   \n",
       "20     ATOM    21   CA  GLY   L     2  20.212  13.059  14.445  1.00   11.86   \n",
       "21     ATOM    22    C  GLY   L     2  21.631  13.651  14.541  1.00   16.01   \n",
       "22     ATOM    23    O  GLY   L     2  22.536  13.255  13.796  1.00   15.28   \n",
       "23     ATOM    24    N  LEU   L     3  21.824  14.595  15.437  1.00   15.22   \n",
       "24     ATOM    25   CA  LEU   L     3  23.158  15.198  15.651  1.00   13.04   \n",
       "25     ATOM    26    C  LEU   L     3  23.665  14.745  17.026  1.00   13.60   \n",
       "26     ATOM    27    O  LEU   L     3  23.179  15.204  18.066  1.00   18.09   \n",
       "27     ATOM    28   CB  LEU   L     3  23.066  16.728  15.581  1.00   14.72   \n",
       "28     ATOM    29   CG  LEU   L     3  22.591  17.248  14.217  1.00   21.82   \n",
       "29     ATOM    30  CD1  LEU   L     3  22.354  18.761  14.200  1.00   17.76   \n",
       "...     ...   ...  ...  ...  ..   ...     ...     ...     ...   ...     ...   \n",
       "2298   ATOM  2299   CA  GLU   I    16  14.774   1.309  43.626  1.00   83.01   \n",
       "2299   ATOM  2300    C  GLU   I    16  14.250   2.707  43.822  1.00   89.61   \n",
       "2300   ATOM  2301    O  GLU   I    16  13.741   3.039  44.895  1.00   96.34   \n",
       "2301   ATOM  2302    N  GLU   I    17  14.321   3.603  42.873  1.00   95.67   \n",
       "2302   ATOM  2303   CA  GLU   I    17  13.623   4.882  42.887  1.00   99.81   \n",
       "2303   ATOM  2304    C  GLU   I    17  12.562   4.746  41.800  1.00  102.28   \n",
       "2304   ATOM  2305    O  GLU   I    17  11.548   5.458  41.800  1.00  103.18   \n",
       "2305   ATOM  2306   CB  GLU   I    17  14.519   6.061  42.540  1.00  103.54   \n",
       "2306   ATOM  2307   CG  GLU   I    17  15.431   6.477  43.692  1.00  105.06   \n",
       "2307   ATOM  2308   CD  GLU   I    17  16.734   5.684  43.726  1.00  105.09   \n",
       "2308   ATOM  2309  OE1  GLU   I    17  16.897   4.680  42.933  1.00  105.93   \n",
       "2309   ATOM  2310  OE2  GLU   I    17  17.669   6.017  44.548  1.00  106.34   \n",
       "2310   ATOM  2311    N  TYR   I    18  12.900   3.800  40.927  1.00  103.19   \n",
       "2311   ATOM  2312   CA  TYR   I    18  12.083   3.376  39.786  1.00  103.03   \n",
       "2312   ATOM  2313    C  TYR   I    18  11.566   1.953  40.077  1.00  104.38   \n",
       "2313   ATOM  2314    O  TYR   I    18  10.420   1.763  40.499  1.00  105.64   \n",
       "2314   ATOM  2315   CB  TYR   I    18  12.925   3.424  38.503  1.00  100.75   \n",
       "2315   ATOM  2316   CG  TYR   I    18  14.176   4.300  38.645  1.00   99.09   \n",
       "2316   ATOM  2317  CD1  TYR   I    18  14.101   5.687  38.438  1.00   99.38   \n",
       "2317   ATOM  2318  CD2  TYR   I    18  15.399   3.714  38.986  1.00   99.20   \n",
       "2318   ATOM  2319  CE1  TYR   I    18  15.249   6.482  38.584  1.00   98.81   \n",
       "2319   ATOM  2320  CE2  TYR   I    18  16.543   4.507  39.136  1.00   98.84   \n",
       "2320   ATOM  2321   CZ  TYR   I    18  16.469   5.891  38.937  1.00   98.61   \n",
       "2321   ATOM  2322   OH  TYR   I    18  17.581   6.659  39.089  1.00   96.67   \n",
       "2322   ATOM  2323    N  LEU   I    19  12.427   0.963  39.863  1.00  107.80   \n",
       "2323   ATOM  2324   CA  LEU   I    19  12.087  -0.457  40.135  1.00  109.88   \n",
       "2324   ATOM  2325    C  LEU   I    19  12.269  -0.739  41.619  1.00  112.34   \n",
       "2325   ATOM  2326    O  LEU   I    19  11.858   0.008  42.525  1.00  113.15   \n",
       "2326   ATOM  2327   CB  LEU   I    19  13.000  -1.382  39.328  1.00  114.04   \n",
       "2327    TER  2328  LEU    I  19  None    None    None    None  None    None   \n",
       "\n",
       "     atom_type  \n",
       "0            N  \n",
       "1            C  \n",
       "2            C  \n",
       "3            O  \n",
       "4            C  \n",
       "5            N  \n",
       "6            C  \n",
       "7            C  \n",
       "8            O  \n",
       "9            C  \n",
       "10           C  \n",
       "11           O  \n",
       "12           O  \n",
       "13           N  \n",
       "14           C  \n",
       "15           C  \n",
       "16           O  \n",
       "17           C  \n",
       "18           S  \n",
       "19           N  \n",
       "20           C  \n",
       "21           C  \n",
       "22           O  \n",
       "23           N  \n",
       "24           C  \n",
       "25           C  \n",
       "26           O  \n",
       "27           C  \n",
       "28           C  \n",
       "29           C  \n",
       "...        ...  \n",
       "2298         C  \n",
       "2299         C  \n",
       "2300         O  \n",
       "2301         N  \n",
       "2302         C  \n",
       "2303         C  \n",
       "2304         O  \n",
       "2305         C  \n",
       "2306         C  \n",
       "2307         C  \n",
       "2308         O  \n",
       "2309         O  \n",
       "2310         N  \n",
       "2311         C  \n",
       "2312         C  \n",
       "2313         O  \n",
       "2314         C  \n",
       "2315         C  \n",
       "2316         C  \n",
       "2317         C  \n",
       "2318         C  \n",
       "2319         C  \n",
       "2320         C  \n",
       "2321         O  \n",
       "2322         N  \n",
       "2323         C  \n",
       "2324         C  \n",
       "2325         O  \n",
       "2326         C  \n",
       "2327      None  \n",
       "\n",
       "[2328 rows x 12 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'''\n",
    "atom dataframe generator\n",
    "'''\n",
    "\n",
    "l =[]\n",
    "with open(test_file, 'r') as f:\n",
    "    for line in f:\n",
    "        if line.startswith('ATOM') or line.startswith('TER'):\n",
    "            clean_line = (line.rstrip()).split()\n",
    "            #check for alignment mistakes within data, a row with spacing alignment error has 11 length after splitted by whitespace\n",
    "            if len(clean_line) == 11:\n",
    "                #split the 2nd last column by the 4th index (this inference is according to PDB file formatting)\n",
    "                split = [clean_line[-2][:4], clean_line[-2][4:]]\n",
    "                clean_line[-2] = split[1]\n",
    "                clean_line.insert(-2, split[0])\n",
    "            l.append(clean_line)\n",
    "df_atoms = (pd.DataFrame(l)).rename(columns={0:'record', 6:'x_coor', 7:'y_coor', 8:'z_coor', 11:'atom_type'})\n",
    "\n",
    "'''\n",
    "print(len(l[2314]))\n",
    "spl = [l[2314][-2][:4], l[2314][-2][4:]]\n",
    "l[2314][-2] = spl[1]\n",
    "l[2314].insert(-2, spl[0])\n",
    "l[2314].insert(-2, l[2314][-2][4:])\n",
    "print(l[2314])\n",
    "'''\n",
    "print(l[2241])\n",
    "\n",
    "df_atoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[222, 2240, 2327]\n",
      "[    record    1    2    3  4    5  x_coor  y_coor  z_coor     9     10  \\\n",
      "0     ATOM    1    N  ALA  L   1B  15.110  18.115  15.087  1.00  36.99   \n",
      "1     ATOM    2   CA  ALA  L   1B  15.151  19.655  15.324  1.00  44.33   \n",
      "2     ATOM    3    C  ALA  L   1B  16.619  19.913  15.465  1.00  31.21   \n",
      "3     ATOM    4    O  ALA  L   1B  17.199  20.722  14.728  1.00  27.87   \n",
      "4     ATOM    5   CB  ALA  L   1B  14.328  19.790  16.582  1.00  36.57   \n",
      "5     ATOM    6    N  ASP  L   1A  17.075  19.131  16.396  1.00  24.26   \n",
      "6     ATOM    7   CA  ASP  L   1A  18.455  18.973  16.762  1.00  24.64   \n",
      "7     ATOM    8    C  ASP  L   1A  18.725  17.483  16.620  1.00  18.66   \n",
      "8     ATOM    9    O  ASP  L   1A  19.822  16.999  16.911  1.00  19.27   \n",
      "9     ATOM   10   CB  ASP  L   1A  18.645  19.446  18.202  1.00  31.66   \n",
      "10    ATOM   11   CG  ASP  L   1A  20.085  19.313  18.682  1.00  39.01   \n",
      "11    ATOM   12  OD1  ASP  L   1A  21.043  19.254  17.822  1.00  60.26   \n",
      "12    ATOM   13  OD2  ASP  L   1A  20.339  19.261  19.944  1.00  57.76   \n",
      "13    ATOM   14    N  CYS  L    1  17.664  16.833  16.160  1.00  17.75   \n",
      "14    ATOM   15   CA  CYS  L    1  17.614  15.384  15.950  1.00  18.84   \n",
      "15    ATOM   16    C  CYS  L    1  18.695  14.923  14.970  1.00  15.87   \n",
      "16    ATOM   17    O  CYS  L    1  19.015  15.618  13.998  1.00  14.39   \n",
      "17    ATOM   18   CB  CYS  L    1  16.251  14.985  15.367  1.00  20.41   \n",
      "18    ATOM   19   SG  CYS  L    1  16.089  15.371  13.593  1.00  18.36   \n",
      "19    ATOM   20    N  GLY  L    2  19.224  13.755  15.285  1.00  15.56   \n",
      "20    ATOM   21   CA  GLY  L    2  20.212  13.059  14.445  1.00  11.86   \n",
      "21    ATOM   22    C  GLY  L    2  21.631  13.651  14.541  1.00  16.01   \n",
      "22    ATOM   23    O  GLY  L    2  22.536  13.255  13.796  1.00  15.28   \n",
      "23    ATOM   24    N  LEU  L    3  21.824  14.595  15.437  1.00  15.22   \n",
      "24    ATOM   25   CA  LEU  L    3  23.158  15.198  15.651  1.00  13.04   \n",
      "25    ATOM   26    C  LEU  L    3  23.665  14.745  17.026  1.00  13.60   \n",
      "26    ATOM   27    O  LEU  L    3  23.179  15.204  18.066  1.00  18.09   \n",
      "27    ATOM   28   CB  LEU  L    3  23.066  16.728  15.581  1.00  14.72   \n",
      "28    ATOM   29   CG  LEU  L    3  22.591  17.248  14.217  1.00  21.82   \n",
      "29    ATOM   30  CD1  LEU  L    3  22.354  18.761  14.200  1.00  17.76   \n",
      "..     ...  ...  ...  ... ..  ...     ...     ...     ...   ...    ...   \n",
      "192   ATOM  193   CG  GLU  L  14H  33.633   5.786   1.305  1.00  18.90   \n",
      "193   ATOM  194   CD  GLU  L  14H  34.787   5.025   1.958  1.00  22.63   \n",
      "194   ATOM  195  OE1  GLU  L  14H  34.658   3.773   2.237  1.00  26.74   \n",
      "195   ATOM  196  OE2  GLU  L  14H  35.892   5.637   2.225  1.00  27.63   \n",
      "196   ATOM  197    N  SER  L  14I  29.147   4.452   0.362  1.00  16.78   \n",
      "197   ATOM  198   CA  SER  L  14I  28.137   3.594  -0.293  1.00  16.80   \n",
      "198   ATOM  199    C  SER  L  14I  27.028   4.439  -0.951  1.00  18.15   \n",
      "199   ATOM  200    O  SER  L  14I  26.282   3.958  -1.815  1.00  21.21   \n",
      "200   ATOM  201   CB  SER  L  14I  27.510   2.638   0.722  1.00  19.97   \n",
      "201   ATOM  202   OG  SER  L  14I  26.590   3.335   1.543  1.00  18.99   \n",
      "202   ATOM  203    N  TYR  L  14J  26.928   5.691  -0.526  1.00  15.76   \n",
      "203   ATOM  204   CA  TYR  L  14J  25.943   6.642  -1.091  1.00  15.57   \n",
      "204   ATOM  205    C  TYR  L  14J  26.551   7.269  -2.345  1.00  28.81   \n",
      "205   ATOM  206    O  TYR  L  14J  27.097   8.382  -2.303  1.00  24.65   \n",
      "206   ATOM  207   CB  TYR  L  14J  25.615   7.733  -0.071  1.00  16.05   \n",
      "207   ATOM  208   CG  TYR  L  14J  25.177   7.178   1.286  1.00  20.15   \n",
      "208   ATOM  209  CD1  TYR  L  14J  24.620   5.895   1.378  1.00  16.24   \n",
      "209   ATOM  210  CD2  TYR  L  14J  25.333   7.956   2.439  1.00  17.86   \n",
      "210   ATOM  211  CE1  TYR  L  14J  24.223   5.392   2.624  1.00  16.50   \n",
      "211   ATOM  212  CE2  TYR  L  14J  24.937   7.453   3.684  1.00  21.41   \n",
      "212   ATOM  213   CZ  TYR  L  14J  24.383   6.170   3.777  1.00  20.60   \n",
      "213   ATOM  214   OH  TYR  L  14J  24.000   5.682   4.988  1.00  17.01   \n",
      "214   ATOM  215    N  ILE  L  14K  26.423   6.523  -3.423  1.00  32.15   \n",
      "215   ATOM  216   CA  ILE  L  14K  27.045   6.862  -4.707  1.00  41.36   \n",
      "216   ATOM  217    C  ILE  L  14K  26.127   7.552  -5.693  1.00  50.46   \n",
      "217   ATOM  218    O  ILE  L  14K  25.837   8.782  -5.482  1.00  59.53   \n",
      "218   ATOM  219   CB  ILE  L  14K  27.517   5.586  -5.400  1.00  42.46   \n",
      "219   ATOM  220  CG1  ILE  L  14K  26.382   4.582  -5.613  1.00  41.28   \n",
      "220   ATOM  221  CG2  ILE  L  14K  28.595   4.841  -4.610  1.00  41.66   \n",
      "221   ATOM  222  CD1  ILE  L  14K  26.818   3.339  -6.388  1.00  48.00   \n",
      "\n",
      "    atom_type  \n",
      "0           N  \n",
      "1           C  \n",
      "2           C  \n",
      "3           O  \n",
      "4           C  \n",
      "5           N  \n",
      "6           C  \n",
      "7           C  \n",
      "8           O  \n",
      "9           C  \n",
      "10          C  \n",
      "11          O  \n",
      "12          O  \n",
      "13          N  \n",
      "14          C  \n",
      "15          C  \n",
      "16          O  \n",
      "17          C  \n",
      "18          S  \n",
      "19          N  \n",
      "20          C  \n",
      "21          C  \n",
      "22          O  \n",
      "23          N  \n",
      "24          C  \n",
      "25          C  \n",
      "26          O  \n",
      "27          C  \n",
      "28          C  \n",
      "29          C  \n",
      "..        ...  \n",
      "192         C  \n",
      "193         C  \n",
      "194         O  \n",
      "195         O  \n",
      "196         N  \n",
      "197         C  \n",
      "198         C  \n",
      "199         O  \n",
      "200         C  \n",
      "201         O  \n",
      "202         N  \n",
      "203         C  \n",
      "204         C  \n",
      "205         O  \n",
      "206         C  \n",
      "207         C  \n",
      "208         C  \n",
      "209         C  \n",
      "210         C  \n",
      "211         C  \n",
      "212         C  \n",
      "213         O  \n",
      "214         N  \n",
      "215         C  \n",
      "216         C  \n",
      "217         O  \n",
      "218         C  \n",
      "219         C  \n",
      "220         C  \n",
      "221         C  \n",
      "\n",
      "[222 rows x 12 columns],      record     1    2    3  4    5  x_coor   y_coor  z_coor     9     10  \\\n",
      "223    ATOM   224    N  ILE  H   16  23.509   -8.759  17.618  1.00  13.87   \n",
      "224    ATOM   225   CA  ILE  H   16  24.222   -8.566  16.338  1.00  17.31   \n",
      "225    ATOM   226    C  ILE  H   16  25.343   -9.603  16.140  1.00  21.27   \n",
      "226    ATOM   227    O  ILE  H   16  26.142   -9.866  17.049  1.00  22.18   \n",
      "227    ATOM   228   CB  ILE  H   16  24.941   -7.190  16.272  1.00  17.58   \n",
      "228    ATOM   229  CG1  ILE  H   16  24.026   -6.019  16.636  1.00  19.35   \n",
      "229    ATOM   230  CG2  ILE  H   16  25.493   -6.870  14.882  1.00  17.10   \n",
      "230    ATOM   231  CD1  ILE  H   16  22.922   -5.778  15.604  1.00  18.51   \n",
      "231    ATOM   232    N  VAL  H   17  25.380  -10.156  14.933  1.00  18.56   \n",
      "232    ATOM   233   CA  VAL  H   17  26.403  -11.145  14.533  1.00  22.11   \n",
      "233    ATOM   234    C  VAL  H   17  27.427  -10.496  13.600  1.00  21.49   \n",
      "234    ATOM   235    O  VAL  H   17  27.069   -9.821  12.628  1.00  24.33   \n",
      "235    ATOM   236   CB  VAL  H   17  25.768  -12.309  13.760  1.00  21.79   \n",
      "236    ATOM   237  CG1  VAL  H   17  26.774  -13.407  13.396  1.00  19.15   \n",
      "237    ATOM   238  CG2  VAL  H   17  24.652  -13.010  14.533  1.00  21.58   \n",
      "238    ATOM   239    N  GLU  H   18  28.685  -10.711  13.923  1.00  18.88   \n",
      "239    ATOM   240   CA  GLU  H   18  29.806  -10.207  13.114  1.00  25.46   \n",
      "240    ATOM   241    C  GLU  H   18  29.855   -8.680  13.092  1.00  22.52   \n",
      "241    ATOM   242    O  GLU  H   18  30.229   -8.066  12.081  1.00  23.39   \n",
      "242    ATOM   243   CB  GLU  H   18  29.670  -10.696  11.674  1.00  29.84   \n",
      "243    ATOM   244   CG  GLU  H   18  29.946  -12.193  11.525  1.00  44.50   \n",
      "244    ATOM   245   CD  GLU  H   18  31.418  -12.550  11.731  1.00  44.13   \n",
      "245    ATOM   246  OE1  GLU  H   18  32.337  -11.864  11.141  1.00  41.85   \n",
      "246    ATOM   247  OE2  GLU  H   18  31.742  -13.538  12.496  1.00  54.70   \n",
      "247    ATOM   248    N  GLY  H   19  29.475   -8.107  14.208  1.00  21.97   \n",
      "248    ATOM   249   CA  GLY  H   19  29.515   -6.656  14.401  1.00  18.80   \n",
      "249    ATOM   250    C  GLY  H   19  30.774   -6.326  15.195  1.00  24.60   \n",
      "250    ATOM   251    O  GLY  H   19  31.743   -7.096  15.203  1.00  24.88   \n",
      "251    ATOM   252    N  SER  H   20  30.731   -5.192  15.846  1.00  17.04   \n",
      "252    ATOM   253   CA  SER  H   20  31.832   -4.728  16.699  1.00  24.35   \n",
      "...     ...   ...  ...  ... ..  ...     ...      ...     ...   ...    ...   \n",
      "2210   ATOM  2211  CG2  ILE  H  242   4.015   13.259  18.095  1.00  28.50   \n",
      "2211   ATOM  2212  CD1  ILE  H  242   5.627   10.820  17.187  1.00  39.11   \n",
      "2212   ATOM  2213    N  ASP  H  243   0.561   13.283  17.103  1.00  30.67   \n",
      "2213   ATOM  2214   CA  ASP  H  243  -0.249   14.494  16.929  1.00  34.20   \n",
      "2214   ATOM  2215    C  ASP  H  243  -1.497   14.430  17.815  1.00  40.26   \n",
      "2215   ATOM  2216    O  ASP  H  243  -1.868   15.412  18.473  1.00  41.31   \n",
      "2216   ATOM  2217   CB  ASP  H  243  -0.675   14.639  15.469  1.00  34.26   \n",
      "2217   ATOM  2218   CG  ASP  H  243   0.374   15.356  14.618  1.00  39.66   \n",
      "2218   ATOM  2219  OD1  ASP  H  243   1.513   15.675  15.133  1.00  39.85   \n",
      "2219   ATOM  2220  OD2  ASP  H  243   0.121   15.639  13.385  1.00  44.25   \n",
      "2220   ATOM  2221    N  GLN  H  244  -2.122   13.267  17.821  1.00  38.97   \n",
      "2221   ATOM  2222   CA  GLN  H  244  -3.355   13.055  18.591  1.00  37.56   \n",
      "2222   ATOM  2223    C  GLN  H  244  -3.074   12.832  20.074  1.00  39.15   \n",
      "2223   ATOM  2224    O  GLN  H  244  -3.907   13.145  20.938  1.00  36.14   \n",
      "2224   ATOM  2225   CB  GLN  H  244  -4.120   11.812  18.108  1.00  39.99   \n",
      "2225   ATOM  2226   CG  GLN  H  244  -5.313   11.468  19.018  1.00  60.51   \n",
      "2226   ATOM  2227   CD  GLN  H  244  -6.212   10.353  18.466  1.00  67.63   \n",
      "2227   ATOM  2228  OE1  GLN  H  244  -7.245   10.041  19.063  1.00  79.46   \n",
      "2228   ATOM  2229  NE2  GLN  H  244  -5.882    9.725  17.354  1.00  59.10   \n",
      "2229   ATOM  2230    N  PHE  H  245  -1.902   12.309  20.382  1.00  39.35   \n",
      "2230   ATOM  2231   CA  PHE  H  245  -1.626   11.944  21.768  1.00  35.62   \n",
      "2231   ATOM  2232    C  PHE  H  245  -0.374   12.572  22.394  1.00  37.76   \n",
      "2232   ATOM  2233    O  PHE  H  245  -0.271   12.253  23.634  1.00  43.62   \n",
      "2233   ATOM  2234   CB  PHE  H  245  -1.474   10.412  21.894  1.00  37.76   \n",
      "2234   ATOM  2235   CG  PHE  H  245  -2.736    9.598  21.498  1.00  49.16   \n",
      "2235   ATOM  2236  CD1  PHE  H  245  -3.870    9.567  22.335  1.00  45.21   \n",
      "2236   ATOM  2237  CD2  PHE  H  245  -2.762    8.865  20.298  1.00  46.89   \n",
      "2237   ATOM  2238  CE1  PHE  H  245  -5.003    8.809  21.973  1.00  60.62   \n",
      "2238   ATOM  2239  CE2  PHE  H  245  -3.890    8.109  19.941  1.00  51.13   \n",
      "2239   ATOM  2240   CZ  PHE  H  245  -5.009    8.079  20.778  1.00  51.75   \n",
      "\n",
      "     atom_type  \n",
      "223          N  \n",
      "224          C  \n",
      "225          C  \n",
      "226          O  \n",
      "227          C  \n",
      "228          C  \n",
      "229          C  \n",
      "230          C  \n",
      "231          N  \n",
      "232          C  \n",
      "233          C  \n",
      "234          O  \n",
      "235          C  \n",
      "236          C  \n",
      "237          C  \n",
      "238          N  \n",
      "239          C  \n",
      "240          C  \n",
      "241          O  \n",
      "242          C  \n",
      "243          C  \n",
      "244          C  \n",
      "245          O  \n",
      "246          O  \n",
      "247          N  \n",
      "248          C  \n",
      "249          C  \n",
      "250          O  \n",
      "251          N  \n",
      "252          C  \n",
      "...        ...  \n",
      "2210         C  \n",
      "2211         C  \n",
      "2212         N  \n",
      "2213         C  \n",
      "2214         C  \n",
      "2215         O  \n",
      "2216         C  \n",
      "2217         C  \n",
      "2218         O  \n",
      "2219         O  \n",
      "2220         N  \n",
      "2221         C  \n",
      "2222         C  \n",
      "2223         O  \n",
      "2224         C  \n",
      "2225         C  \n",
      "2226         C  \n",
      "2227         O  \n",
      "2228         N  \n",
      "2229         N  \n",
      "2230         C  \n",
      "2231         C  \n",
      "2232         O  \n",
      "2233         C  \n",
      "2234         C  \n",
      "2235         C  \n",
      "2236         C  \n",
      "2237         C  \n",
      "2238         C  \n",
      "2239         C  \n",
      "\n",
      "[2017 rows x 12 columns],      record     1    2    3  4   5  x_coor   y_coor  z_coor     9      10  \\\n",
      "2241   ATOM  2242    N  GLY  I   9  20.469  -13.494  37.284  1.00  107.45   \n",
      "2242   ATOM  2243   CA  GLY  I   9  21.843  -13.276  37.701  1.00   97.24   \n",
      "2243   ATOM  2244    C  GLY  I   9  22.610  -12.484  36.651  1.00   89.03   \n",
      "2244   ATOM  2245    O  GLY  I   9  23.651  -11.877  36.944  1.00   90.34   \n",
      "2245   ATOM  2246    N  ASP  I  10  22.053  -12.530  35.473  1.00   78.89   \n",
      "2246   ATOM  2247   CA  ASP  I  10  22.600  -11.875  34.289  1.00   65.99   \n",
      "2247   ATOM  2248    C  ASP  I  10  22.689  -10.354  34.475  1.00   55.66   \n",
      "2248   ATOM  2249    O  ASP  I  10  23.751   -9.747  34.286  1.00   52.55   \n",
      "2249   ATOM  2250   CB  ASP  I  10  21.674  -12.146  33.113  1.00   72.25   \n",
      "2250   ATOM  2251   CG  ASP  I  10  20.208  -12.174  33.543  1.00   79.86   \n",
      "2251   ATOM  2252  OD1  ASP  I  10  19.820  -11.451  34.541  1.00   87.91   \n",
      "2252   ATOM  2253  OD2  ASP  I  10  19.363  -12.916  32.917  1.00   89.50   \n",
      "2253   ATOM  2254    N  PHE  I  11  21.563   -9.766  34.847  1.00   44.85   \n",
      "2254   ATOM  2255   CA  PHE  I  11  21.446   -8.300  34.967  1.00   39.46   \n",
      "2255   ATOM  2256    C  PHE  I  11  21.579   -7.789  36.395  1.00   44.02   \n",
      "2256   ATOM  2257    O  PHE  I  11  21.024   -8.370  37.339  1.00   37.12   \n",
      "2257   ATOM  2258   CB  PHE  I  11  20.083   -7.837  34.473  1.00   37.89   \n",
      "2258   ATOM  2259   CG  PHE  I  11  19.985   -7.885  32.960  1.00   32.68   \n",
      "2259   ATOM  2260  CD1  PHE  I  11  19.538   -9.050  32.336  1.00   33.41   \n",
      "2260   ATOM  2261  CD2  PHE  I  11  20.352   -6.768  32.206  1.00   31.63   \n",
      "2261   ATOM  2262  CE1  PHE  I  11  19.460   -9.100  30.941  1.00   41.62   \n",
      "2262   ATOM  2263  CE2  PHE  I  11  20.274   -6.816  30.813  1.00   35.75   \n",
      "2263   ATOM  2264   CZ  PHE  I  11  19.828   -7.983  30.179  1.00   45.76   \n",
      "2264   ATOM  2265    N  GLU  I  12  22.317   -6.693  36.472  1.00   33.10   \n",
      "2265   ATOM  2266   CA  GLU  I  12  22.532   -5.964  37.719  1.00   36.77   \n",
      "2266   ATOM  2267    C  GLU  I  12  21.244   -5.217  38.049  1.00   34.39   \n",
      "2267   ATOM  2268    O  GLU  I  12  20.573   -4.683  37.153  1.00   34.40   \n",
      "2268   ATOM  2269   CB  GLU  I  12  23.688   -4.973  37.569  1.00   28.11   \n",
      "2269   ATOM  2270   CG  GLU  I  12  23.865   -4.084  38.803  1.00   35.95   \n",
      "2270   ATOM  2271   CD  GLU  I  12  25.075   -3.153  38.709  1.00   42.81   \n",
      "...     ...   ...  ...  ... ..  ..     ...      ...     ...   ...     ...   \n",
      "2297   ATOM  2298    N  GLU  I  16  16.194    1.159  43.373  1.00   74.73   \n",
      "2298   ATOM  2299   CA  GLU  I  16  14.774    1.309  43.626  1.00   83.01   \n",
      "2299   ATOM  2300    C  GLU  I  16  14.250    2.707  43.822  1.00   89.61   \n",
      "2300   ATOM  2301    O  GLU  I  16  13.741    3.039  44.895  1.00   96.34   \n",
      "2301   ATOM  2302    N  GLU  I  17  14.321    3.603  42.873  1.00   95.67   \n",
      "2302   ATOM  2303   CA  GLU  I  17  13.623    4.882  42.887  1.00   99.81   \n",
      "2303   ATOM  2304    C  GLU  I  17  12.562    4.746  41.800  1.00  102.28   \n",
      "2304   ATOM  2305    O  GLU  I  17  11.548    5.458  41.800  1.00  103.18   \n",
      "2305   ATOM  2306   CB  GLU  I  17  14.519    6.061  42.540  1.00  103.54   \n",
      "2306   ATOM  2307   CG  GLU  I  17  15.431    6.477  43.692  1.00  105.06   \n",
      "2307   ATOM  2308   CD  GLU  I  17  16.734    5.684  43.726  1.00  105.09   \n",
      "2308   ATOM  2309  OE1  GLU  I  17  16.897    4.680  42.933  1.00  105.93   \n",
      "2309   ATOM  2310  OE2  GLU  I  17  17.669    6.017  44.548  1.00  106.34   \n",
      "2310   ATOM  2311    N  TYR  I  18  12.900    3.800  40.927  1.00  103.19   \n",
      "2311   ATOM  2312   CA  TYR  I  18  12.083    3.376  39.786  1.00  103.03   \n",
      "2312   ATOM  2313    C  TYR  I  18  11.566    1.953  40.077  1.00  104.38   \n",
      "2313   ATOM  2314    O  TYR  I  18  10.420    1.763  40.499  1.00  105.64   \n",
      "2314   ATOM  2315   CB  TYR  I  18  12.925    3.424  38.503  1.00  100.75   \n",
      "2315   ATOM  2316   CG  TYR  I  18  14.176    4.300  38.645  1.00   99.09   \n",
      "2316   ATOM  2317  CD1  TYR  I  18  14.101    5.687  38.438  1.00   99.38   \n",
      "2317   ATOM  2318  CD2  TYR  I  18  15.399    3.714  38.986  1.00   99.20   \n",
      "2318   ATOM  2319  CE1  TYR  I  18  15.249    6.482  38.584  1.00   98.81   \n",
      "2319   ATOM  2320  CE2  TYR  I  18  16.543    4.507  39.136  1.00   98.84   \n",
      "2320   ATOM  2321   CZ  TYR  I  18  16.469    5.891  38.937  1.00   98.61   \n",
      "2321   ATOM  2322   OH  TYR  I  18  17.581    6.659  39.089  1.00   96.67   \n",
      "2322   ATOM  2323    N  LEU  I  19  12.427    0.963  39.863  1.00  107.80   \n",
      "2323   ATOM  2324   CA  LEU  I  19  12.087   -0.457  40.135  1.00  109.88   \n",
      "2324   ATOM  2325    C  LEU  I  19  12.269   -0.739  41.619  1.00  112.34   \n",
      "2325   ATOM  2326    O  LEU  I  19  11.858    0.008  42.525  1.00  113.15   \n",
      "2326   ATOM  2327   CB  LEU  I  19  13.000   -1.382  39.328  1.00  114.04   \n",
      "\n",
      "     atom_type  \n",
      "2241         N  \n",
      "2242         C  \n",
      "2243         C  \n",
      "2244         O  \n",
      "2245         N  \n",
      "2246         C  \n",
      "2247         C  \n",
      "2248         O  \n",
      "2249         C  \n",
      "2250         C  \n",
      "2251         O  \n",
      "2252         O  \n",
      "2253         N  \n",
      "2254         C  \n",
      "2255         C  \n",
      "2256         O  \n",
      "2257         C  \n",
      "2258         C  \n",
      "2259         C  \n",
      "2260         C  \n",
      "2261         C  \n",
      "2262         C  \n",
      "2263         C  \n",
      "2264         N  \n",
      "2265         C  \n",
      "2266         C  \n",
      "2267         O  \n",
      "2268         C  \n",
      "2269         C  \n",
      "2270         C  \n",
      "...        ...  \n",
      "2297         N  \n",
      "2298         C  \n",
      "2299         C  \n",
      "2300         O  \n",
      "2301         N  \n",
      "2302         C  \n",
      "2303         C  \n",
      "2304         O  \n",
      "2305         C  \n",
      "2306         C  \n",
      "2307         C  \n",
      "2308         O  \n",
      "2309         O  \n",
      "2310         N  \n",
      "2311         C  \n",
      "2312         C  \n",
      "2313         O  \n",
      "2314         C  \n",
      "2315         C  \n",
      "2316         C  \n",
      "2317         C  \n",
      "2318         C  \n",
      "2319         C  \n",
      "2320         C  \n",
      "2321         O  \n",
      "2322         N  \n",
      "2323         C  \n",
      "2324         C  \n",
      "2325         O  \n",
      "2326         C  \n",
      "\n",
      "[86 rows x 12 columns]]\n"
     ]
    }
   ],
   "source": [
    "'''\n",
    "split dataframes based on chains ended by \"TER\"\n",
    "'''\n",
    "l_df = []\n",
    "last_idx = 0\n",
    "for idx in df_atoms.index[df_atoms['record'] == 'TER'].tolist():\n",
    "    l_df.append(df_atoms.iloc[last_idx:idx])\n",
    "    last_idx = idx+1\n",
    "\n",
    "print(df_atoms.index[df_atoms['record'] == 'TER'].tolist())\n",
    "print(l_df)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'x_vector' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-7-b9b98d90e66c>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m     53\u001b[0m             x_vector += protein_interaction(l_df[i], l_df[j], atom_types)'''\n\u001b[0;32m     54\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 55\u001b[1;33m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'value of x vector (R^N) = '\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mx_vector\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     56\u001b[0m \u001b[0mend_time\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mtime\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtime\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     57\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'time elapsed ='\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mend_time\u001b[0m\u001b[1;33m-\u001b[0m\u001b[0mcurr_time\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mNameError\u001b[0m: name 'x_vector' is not defined"
     ]
    }
   ],
   "source": [
    "'''\n",
    "calculate the combination of euclidian distance and heaviside step between chains in a protein, \n",
    "e.g chains=[A,B,C,D], hence the interactions are: [[A-B],[A-C],[A-D],[B-C],[B-D],[C-D]]\n",
    "\n",
    "'atom_types' are the type of atoms used for calculation\n",
    "'cutoff' is the distance cutoff between atoms for heaviside step function (in Angstrom)\n",
    "'''\n",
    "\n",
    "'''a = l_df[0].loc[l_df[0]['atom_type'] == 'N']\n",
    "print(float(a.iloc[1]['x_coor'])*2)\n",
    "print(a.shape)'''\n",
    "\n",
    "atom_types = ['C','N','O','F','P','S','Cl','Br','I']\n",
    "#atom_types = ['C','N','O','S']\n",
    "cutoff = 12\n",
    "\n",
    "def protein_interaction(df_protein_A, df_protein_B, atom_types, cutoff):\n",
    "    type_len = len(atom_types)\n",
    "    x_vector = np.zeros(type_len**2)\n",
    "    idx = 0\n",
    "    for a_type in atom_types:\n",
    "        for b_type in atom_types:\n",
    "            #calculate the interaction of each atoms:\n",
    "            sum_interaction = 0\n",
    "            a_atoms = df_protein_A.loc[df_protein_A['atom_type'] == a_type]\n",
    "            b_atoms = df_protein_B.loc[df_protein_B['atom_type'] == b_type]\n",
    "            for i in range(a_atoms.shape[0]):\n",
    "                for j in range(b_atoms.shape[0]):\n",
    "                    #get the (x,y,z):\n",
    "                    a_atom = a_atoms.iloc[i]\n",
    "                    b_atom = b_atoms.iloc[j]\n",
    "                    a_coord = np.array([float(a_atom['x_coor']), float(a_atom['y_coor']), float(a_atom['z_coor'])]) \n",
    "                    b_coord = np.array([float(b_atom['x_coor']), float(b_atom['y_coor']), float(b_atom['z_coor'])])\n",
    "                    #calculate the euclidean distance and heaviside step value:\n",
    "                    sum_interaction += f_h_step(x=f_euclid_dist(a_coord, b_coord), a=cutoff) \n",
    "            x_vector[idx] = sum_interaction\n",
    "            idx+=1\n",
    "            print(x_vector)\n",
    "    return x_vector\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "curr_time = time.time()\n",
    "\n",
    "'''x_vector = np.zeros(len(atom_types)**2)\n",
    "length = len(l_df)\n",
    "for i in range(length):\n",
    "    for j in range(length):\n",
    "        if j>i:\n",
    "            #sum each chain interaction values:\n",
    "            print('protein chain :', i, j)\n",
    "            x_vector += protein_interaction(l_df[i], l_df[j], atom_types)'''\n",
    "\n",
    "print('value of x vector (R^N) = ', x_vector)\n",
    "end_time = time.time()\n",
    "print('time elapsed =',end_time-curr_time)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'2mj5.ent.pdb', '2mjw.ent.pdb', '2mkc.ent.pdb', '2mlx.ent.pdb', '2mly.ent.pdb', '2mlz.ent.pdb', '2mnu.ent.pdb', '2mp0.ent.pdb', '2mre.ent.pdb', '2mro.ent.pdb', '2mta.ent.pdb', '2mur.ent.pdb', '2mv7.ent.pdb', '2mws.ent.pdb', '2mzd.ent.pdb', '2n01.ent.pdb', '2n13.ent.pdb', '2n1d.ent.pdb', '2n2h.ent.pdb', '2n73.ent.pdb', '2n8j.ent.pdb', '2nbv.ent.pdb', '2noj.ent.pdb', '2nqd.ent.pdb', '2nup.ent.pdb', '2nut.ent.pdb', '2nyy.ent.pdb', '2nyz.ent.pdb', '2nz1.ent.pdb', '2nz9.ent.pdb', '2o3b.ent.pdb', '2o8v.ent.pdb', '2o98.ent.pdb', '2odg.ent.pdb', '2ody.ent.pdb', '2oin.ent.pdb', '2oje.ent.pdb', '2omt.ent.pdb', '2omu.ent.pdb', '2omv.ent.pdb', '2omw.ent.pdb', '2omx.ent.pdb', '2omy.ent.pdb', '2omz.ent.pdb', '2onl.ent.pdb', '2oob.ent.pdb', '2oor.ent.pdb', '2oqj.ent.pdb', '2ot3.ent.pdb', '2ot8.ent.pdb', '2otk.ent.pdb', '2oul.ent.pdb', '2oza.ent.pdb', '2p1l.ent.pdb', '2p3f.ent.pdb', '2p42.ent.pdb', '2p43.ent.pdb', '2p44.ent.pdb', '2p45.ent.pdb', '2p46.ent.pdb', '2p47.ent.pdb', '2p48.ent.pdb', '2p49.ent.pdb', '2p4a.ent.pdb', '2p5e.ent.pdb', '2p5t.ent.pdb', '2p8q.ent.pdb', '2pcb.ent.pdb', '2pcc.ent.pdb', '2phe.ent.pdb', '2pjy.ent.pdb', '2pkg.ent.pdb', '2pms.ent.pdb', '2pon.ent.pdb', '2pop.ent.pdb', '2psm.ent.pdb', '2ptc.ent.pdb', '2ptt.ent.pdb', '2pw8.ent.pdb', '2px9.ent.pdb', '2pye.ent.pdb', '2q0o.ent.pdb', '2q5d.ent.pdb', '2q7n.ent.pdb', '2qc1.ent.pdb', '2qej.ent.pdb', '2qho.ent.pdb', '2qiy.ent.pdb', '2qj9.ent.pdb', '2qja.ent.pdb', '2qjb.ent.pdb', '2qna.ent.pdb', '2qr0.ent.pdb', '2qur.ent.pdb', '2qxv.ent.pdb', '2r0k.ent.pdb', '2r0l.ent.pdb', '2r56.ent.pdb', '2r9p.ent.pdb', '2ra3.ent.pdb', '2rf9.ent.pdb', '2rgn.ent.pdb', '2rmk.ent.pdb', '2rms.ent.pdb', '2rnr.ent.pdb', '2roz.ent.pdb', '2rr3.ent.pdb', '2ru4.ent.pdb', '2ruk.ent.pdb', '2rvb.ent.pdb', '2sic.ent.pdb', '2sni.ent.pdb', '2tgp.ent.pdb', '2uuy.ent.pdb', '2uwe.ent.pdb', '2uxn.ent.pdb', '2uyz.ent.pdb', '2uzi.ent.pdb', '2v1d.ent.pdb', '2v2w.ent.pdb', '2v3b.ent.pdb', '2v4z.ent.pdb', '2v51.ent.pdb', '2v52.ent.pdb', '2v5q.ent.pdb', '2v6x.ent.pdb', '2v8s.ent.pdb', '2v9t.ent.pdb', '2vay.ent.pdb', '2vda.ent.pdb', '2vdb.ent.pdb', '2ve7.ent.pdb', '2ver.ent.pdb', '2vfx.ent.pdb', '2vir.ent.pdb', '2vis.ent.pdb', '2vlj.ent.pdb', '2vln.ent.pdb', '2vlo.ent.pdb', '2vlp.ent.pdb', '2vlq.ent.pdb', '2vlr.ent.pdb', '2vof.ent.pdb', '2vog.ent.pdb', '2voh.ent.pdb', '2voi.ent.pdb', '2vsm.ent.pdb', '2vwe.ent.pdb', '2vxq.ent.pdb', '2vxs.ent.pdb', '2vxt.ent.pdb', '2vyr.ent.pdb', '2w19.ent.pdb', '2w2m.ent.pdb', '2w2n.ent.pdb', '2w2x.ent.pdb', '2w80.ent.pdb', '2w81.ent.pdb', '2w83.ent.pdb', '2w84.ent.pdb', '2w8b.ent.pdb', '2w9e.ent.pdb', '2wbj.ent.pdb', '2wby.ent.pdb', '2wd5.ent.pdb', '2wel.ent.pdb', '2wfx.ent.pdb', '2wg3.ent.pdb', '2wg4.ent.pdb', '2wh6.ent.pdb', '2wii.ent.pdb', '2wjv.ent.pdb', '2wo2.ent.pdb', '2wo3.ent.pdb', '2wp0.ent.pdb', '2wp3.ent.pdb', '2wpt.ent.pdb', '2wqz.ent.pdb', '2wss.ent.pdb', '2wub.ent.pdb', '2wuc.ent.pdb', '2wus.ent.pdb', '2wvw.ent.pdb', '2wwk.ent.pdb', '2wwx.ent.pdb', '2wx0.ent.pdb', '2wy2.ent.pdb', '2wy3.ent.pdb', '2wy8.ent.pdb', '2x1w.ent.pdb', '2x1x.ent.pdb', '2x2d.ent.pdb', '2x89.ent.pdb', '2x9a.ent.pdb', '2xa0.ent.pdb', '2xb6.ent.pdb', '2xbb.ent.pdb', '2xdf.ent.pdb', '2xgy.ent.pdb', '2xhe.ent.pdb', '2xns.ent.pdb', '2xpx.ent.pdb', '2xqb.ent.pdb', '2xqr.ent.pdb', '2xqw.ent.pdb', '2xra.ent.pdb', '2xtj.ent.pdb', '2xtt.ent.pdb', '2xzd.ent.pdb', '2xze.ent.pdb', '2y0b.ent.pdb', '2y48.ent.pdb', '2y5b.ent.pdb', '2y6t.ent.pdb', '2y8s.ent.pdb', '2y8t.ent.pdb', '2y9m.ent.pdb', '2ybr.ent.pdb', '2ygg.ent.pdb', '2yj1.ent.pdb', '2ypl.ent.pdb', '2ypv.ent.pdb', '2yq7.ent.pdb', '2yvj.ent.pdb', '2z34.ent.pdb', '2z3q.ent.pdb', '2z3r.ent.pdb', '2z58.ent.pdb', '2z7f.ent.pdb', '2z8v.ent.pdb', '2z8w.ent.pdb', '2za4.ent.pdb', '2zvk.ent.pdb', '2zvn.ent.pdb', '2zvo.ent.pdb', '2zxx.ent.pdb', '3a4s.ent.pdb', '3a67.ent.pdb', '3a6b.ent.pdb', '3a6c.ent.pdb', '3aa0.ent.pdb', '3aa6.ent.pdb', '3aaa.ent.pdb', '3ajb.ent.pdb', '3alz.ent.pdb', '3aon.ent.pdb', '3au4.ent.pdb', '3ay4.ent.pdb', '3b08.ent.pdb', '3b23.ent.pdb', '3b2u.ent.pdb', '3b2v.ent.pdb', '3b4v.ent.pdb', '3b9f.ent.pdb', '3bdy.ent.pdb', '3be1.ent.pdb', '3beg.ent.pdb', '3bg4.ent.pdb', '3bgf.ent.pdb', '3bh6.ent.pdb', '3bik.ent.pdb', '3biw.ent.pdb', '3bk3.ent.pdb', '3bky.ent.pdb', '3blh.ent.pdb', '3bn3.ent.pdb', '3bow.ent.pdb', '3bp8.ent.pdb', '3bpl.ent.pdb', '3bpn.ent.pdb', '3bpo.ent.pdb', '3brt.ent.pdb', '3brv.ent.pdb', '3bs5.ent.pdb', '3bx1.ent.pdb', '3bzd.ent.pdb', '3c09.ent.pdb', '3c4m.ent.pdb', '3c4o.ent.pdb', '3c4p.ent.pdb', '3c59.ent.pdb', '3c5t.ent.pdb', '3c66.ent.pdb', '3c8k.ent.pdb', '3c9a.ent.pdb', '3ch5.ent.pdb', '3chw.ent.pdb', '3cqc.ent.pdb', '3cqg.ent.pdb', '3cqx.ent.pdb', '3crk.ent.pdb', '3cx6.ent.pdb', '3cx7.ent.pdb', '3cx8.ent.pdb', '3d1m.ent.pdb', '3d2u.ent.pdb', '3d39.ent.pdb', '3d3v.ent.pdb', '3d5o.ent.pdb', '3d5r.ent.pdb', '3d5s.ent.pdb', '3d7t.ent.pdb', '3d7u.ent.pdb', '3da7.ent.pdb', '3dbh.ent.pdb', '3dbl.ent.pdb', '3dbr.ent.pdb', '3dco.ent.pdb', '3ddc.ent.pdb', '3dgc.ent.pdb', '3di2.ent.pdb', '3di3.ent.pdb', '3dmm.ent.pdb', '3doe.ent.pdb', '3dvg.ent.pdb', '3dvm.ent.pdb', '3dvn.ent.pdb', '3dvu.ent.pdb', '3dxa.ent.pdb', '3dxc.ent.pdb', '3dxd.ent.pdb', '3dxe.ent.pdb', '3e1z.ent.pdb', '3e2h.ent.pdb', '3e2k.ent.pdb', '3e2l.ent.pdb', '3e2u.ent.pdb', '3e3q.ent.pdb', '3eab.ent.pdb', '3eba.ent.pdb', '3ech.ent.pdb', '3eg5.ent.pdb', '3egg.ent.pdb', '3ehu.ent.pdb', '3eiq.ent.pdb', '3ejh.ent.pdb', '3ejj.ent.pdb', '3eo1.ent.pdb', '3eoa.ent.pdb', '3eob.ent.pdb', '3eoy.ent.pdb', '3etb.ent.pdb', '3ew3.ent.pdb', '3f1p.ent.pdb', '3f4y.ent.pdb', '3f50.ent.pdb', '3f5c.ent.pdb', '3f7p.ent.pdb', '3ff7.ent.pdb', '3ff8.ent.pdb', '3ffc.ent.pdb', '3fhc.ent.pdb', '3fie.ent.pdb', '3fii.ent.pdb', '3fju.ent.pdb', '3fku.ent.pdb', '3fp6.ent.pdb', '3fpu.ent.pdb', '3fsh.ent.pdb', '3fxd.ent.pdb', '3g3a.ent.pdb', '3g3b.ent.pdb', '3g6d.ent.pdb', '3g6j.ent.pdb', '3g7a.ent.pdb', '3g7z.ent.pdb', '3g9v.ent.pdb', '3g9w.ent.pdb', '3gb8.ent.pdb', '3gc3.ent.pdb', '3gd1.ent.pdb', '3gj3.ent.pdb', '3gj4.ent.pdb', '3gj5.ent.pdb', '3gj6.ent.pdb', '3gj7.ent.pdb', '3gj8.ent.pdb', '3gjf.ent.pdb', '3gjn.ent.pdb', '3gmw.ent.pdb', '3gni.ent.pdb', '3gqi.ent.pdb', '3gs2.ent.pdb', '3gsn.ent.pdb', '3gty.ent.pdb', '3gxu.ent.pdb', '3h2u.ent.pdb', '3h2v.ent.pdb', '3h3g.ent.pdb', '3h3p.ent.pdb', '3h42.ent.pdb', '3h6g.ent.pdb', '3h6s.ent.pdb', '3h7b.ent.pdb', '3h8d.ent.pdb', '3h8k.ent.pdb', '3h9h.ent.pdb', '3hae.ent.pdb', '3hct.ent.pdb', '3hcu.ent.pdb', '3he6.ent.pdb', '3he7.ent.pdb', '3hg0.ent.pdb', '3hh2.ent.pdb', '3hi1.ent.pdb', '3hi6.ent.pdb', '3ho5.ent.pdb', '3hpw.ent.pdb', '3htu.ent.pdb', '3hug.ent.pdb', '3huj.ent.pdb', '3ia3.ent.pdb', '3idb.ent.pdb', '3idc.ent.pdb', '3idx.ent.pdb', '3idy.ent.pdb', '3ifq.ent.pdb', '3im4.ent.pdb', '3inb.ent.pdb', '3iol.ent.pdb', '3it8.ent.pdb', '3iu3.ent.pdb', '3ixa.ent.pdb', '3ixe.ent.pdb', '3ixs.ent.pdb', '3ixt.ent.pdb', '3jrm.ent.pdb', '3jse.ent.pdb', '3jsv.ent.pdb', '3jtl.ent.pdb', '3jvf.ent.pdb', '3jza.ent.pdb', '3k1r.ent.pdb', '3k2m.ent.pdb', '3k2u.ent.pdb', '3k3q.ent.pdb', '3k6g.ent.pdb', '3k75.ent.pdb', '3k8p.ent.pdb', '3k9m.ent.pdb', '3kbt.ent.pdb', '3kj0.ent.pdb', '3kj1.ent.pdb', '3kj2.ent.pdb', '3kls.ent.pdb', '3knb.ent.pdb', '3kpr.ent.pdb', '3kps.ent.pdb', '3kr3.ent.pdb', '3kuc.ent.pdb', '3kud.ent.pdb', '3kv4.ent.pdb', '3kw5.ent.pdb', '3kxf.ent.pdb', '3kyi.ent.pdb', '3kz0.ent.pdb', '3kz1.ent.pdb', '3l33.ent.pdb', '3l5n.ent.pdb', '3l5w.ent.pdb', '3l5x.ent.pdb', '3l89.ent.pdb', '3l95.ent.pdb', '3l9j.ent.pdb', '3laq.ent.pdb', '3lb6.ent.pdb', '3lb8.ent.pdb', '3lbx.ent.pdb', '3lev.ent.pdb', '3lh2.ent.pdb', '3lhp.ent.pdb', '3lk2.ent.pdb', '3lk3.ent.pdb', '3lk4.ent.pdb', '3lms.ent.pdb', '3lqa.ent.pdb', '3m0a.ent.pdb', '3m18.ent.pdb', '3m63.ent.pdb', '3m9d.ent.pdb', '3ma2.ent.pdb', '3ma9.ent.pdb', '3mac.ent.pdb', '3mc0.ent.pdb', '3mca.ent.pdb', '3me2.ent.pdb', '3mhp.ent.pdb', '3mj7.ent.pdb', '3mj9.ent.pdb', '3mjh.ent.pdb', '3mv7.ent.pdb', '3mv8.ent.pdb', '3mv9.ent.pdb', '3mxw.ent.pdb', '3mzg.ent.pdb', '3mzw.ent.pdb', '3n00.ent.pdb', '3n06.ent.pdb', '3n0p.ent.pdb', '3n4i.ent.pdb', '3n85.ent.pdb', '3ncb.ent.pdb', '3ncc.ent.pdb', '3nfp.ent.pdb', '3ngb.ent.pdb', '3nh7.ent.pdb', '3noc.ent.pdb', '3nog.ent.pdb', '3nps.ent.pdb', '3npz.ent.pdb', '3nvn.ent.pdb', '3nvq.ent.pdb', '3o34.ent.pdb', '3o40.ent.pdb', '3o43.ent.pdb', '3o4o.ent.pdb', '3o5t.ent.pdb', '3o6b.ent.pdb', '3o6f.ent.pdb', '3o6q.ent.pdb', '3o8x.ent.pdb', '3o9w.ent.pdb', '3oak.ent.pdb', '3oed.ent.pdb', '3ogo.ent.pdb', '3ohm.ent.pdb', '3oiq.ent.pdb', '3oj2.ent.pdb', '3ojm.ent.pdb', '3oky.ent.pdb', '3ol2.ent.pdb', '3olm.ent.pdb', '3ona.ent.pdb', '3onl.ent.pdb', '3onw.ent.pdb', '3opz.ent.pdb', '3orv.ent.pdb', '3osl.ent.pdb', '3oun.ent.pdb', '3ouw.ent.pdb', '3oux.ent.pdb', '3owt.ent.pdb', '3oxu.ent.pdb', '3p0y.ent.pdb', '3p11.ent.pdb', '3p6z.ent.pdb', '3p71.ent.pdb', '3p8m.ent.pdb', '3p92.ent.pdb', '3p95.ent.pdb', '3p9w.ent.pdb', '3pbp.ent.pdb', '3pl6.ent.pdb', '3pmh.ent.pdb', '3pnr.ent.pdb', '3pp4.ent.pdb', '3pvm.ent.pdb', '3q1s.ent.pdb', '3q3g.ent.pdb', '3q4f.ent.pdb', '3q9n.ent.pdb', '3q9u.ent.pdb', '3qbq.ent.pdb', '3qbr.ent.pdb', '3qbt.ent.pdb', '3qbv.ent.pdb', '3qc8.ent.pdb', '3qdg.ent.pdb', '3qdj.ent.pdb', '3qdm.ent.pdb', '3qeq.ent.pdb', '3qht.ent.pdb', '3qhy.ent.pdb', '3qi2.ent.pdb', '3qib.ent.pdb', '3qiu.ent.pdb', '3qiw.ent.pdb', '3qlu.ent.pdb', '3qml.ent.pdb', '3qq8.ent.pdb', '3qs7.ent.pdb', '3qsk.ent.pdb', '3qt2.ent.pdb', '3qtl.ent.pdb', '3qux.ent.pdb', '3quy.ent.pdb', '3quz.ent.pdb', '3qwo.ent.pdb', '3qwq.ent.pdb', '3qwr.ent.pdb', '3r0l.ent.pdb', '3r1g.ent.pdb', '3r2x.ent.pdb', '3r4d.ent.pdb', '3r85.ent.pdb', '3r9a.ent.pdb', '3rbb.ent.pdb', '3rdt.ent.pdb', '3rdz.ent.pdb', '3rea.ent.pdb', '3reb.ent.pdb', '3rgf.ent.pdb', '3rgv.ent.pdb', '3rk3.ent.pdb', '3rkd.ent.pdb', '3ro2.ent.pdb', '3rpg.ent.pdb', '3rt0.ent.pdb', '3rtq.ent.pdb', '3ru8.ent.pdb', '3rug.ent.pdb', '3rvv.ent.pdb', '3rvw.ent.pdb', '3ry6.ent.pdb', '3rzc.ent.pdb', '3rzw.ent.pdb', '3s2k.ent.pdb', '3s4s.ent.pdb', '3s5l.ent.pdb', '3s8v.ent.pdb', '3scm.ent.pdb', '3sda.ent.pdb', '3sdc.ent.pdb', '3sdd.ent.pdb', '3sdy.ent.pdb', '3sf4.ent.pdb', '3sgb.ent.pdb', '3sgk.ent.pdb', '3sip.ent.pdb', '3sja.ent.pdb', '3sjd.ent.pdb', '3sjh.ent.pdb', '3sjv.ent.pdb', '3skj.ent.pdb', '3sku.ent.pdb', '3so3.ent.pdb', '3sqo.ent.pdb', '3sri.ent.pdb', '3ssb.ent.pdb', '3sua.ent.pdb', '3swp.ent.pdb', '3syn.ent.pdb', '3t04.ent.pdb', '3t0y.ent.pdb', '3t1q.ent.pdb', '3t2n.ent.pdb', '3t4a.ent.pdb', '3t6g.ent.pdb', '3tac.ent.pdb', '3tei.ent.pdb', '3tg1.ent.pdb', '3tgk.ent.pdb', '3thm.ent.pdb', '3tje.ent.pdb', '3tjz.ent.pdb', '3tkl.ent.pdb', '3tl8.ent.pdb', '3tn0.ent.pdb', '3tnf.ent.pdb', '3to4.ent.pdb', '3tq7.ent.pdb', '3tsr.ent.pdb', '3tu3.ent.pdb', '3tvj.ent.pdb', '3tvm.ent.pdb', '3twi.ent.pdb', '3tz1.ent.pdb', '3u1j.ent.pdb', '3u43.ent.pdb', '3u82.ent.pdb', '3u8x.ent.pdb', '3u9d.ent.pdb', '3u9z.ent.pdb', '3uai.ent.pdb', '3uaj.ent.pdb', '3uc0.ent.pdb', '3uez.ent.pdb', '3uir.ent.pdb', '3ujg.ent.pdb', '3ukw.ent.pdb', '3ukx.ent.pdb', '3ukz.ent.pdb', '3ul0.ent.pdb', '3ul1.ent.pdb', '3ul4.ent.pdb', '3ula.ent.pdb', '3uts.ent.pdb', '3ux9.ent.pdb', '3uyo.ent.pdb', '3uyp.ent.pdb', '3uz0.ent.pdb', '3uze.ent.pdb', '3uzq.ent.pdb', '3uzv.ent.pdb', '3v1c.ent.pdb', '3v3k.ent.pdb', '3v4y.ent.pdb', '3v62.ent.pdb', '3v6b.ent.pdb', '3v6o.ent.pdb', '3v6z.ent.pdb', '3v96.ent.pdb', '3ve0.ent.pdb', '3vep.ent.pdb', '3vfm.ent.pdb', '3vfn.ent.pdb', '3vfo.ent.pdb', '3vfp.ent.pdb', '3vfr.ent.pdb', '3vfs.ent.pdb', '3vft.ent.pdb', '3vfu.ent.pdb', '3vfv.ent.pdb', '3vfw.ent.pdb', '3vg9.ent.pdb', '3vh8.ent.pdb', '3vhx.ent.pdb', '3vpj.ent.pdb', '3vux.ent.pdb', '3vv2.ent.pdb', '3vwj.ent.pdb', '3vwk.ent.pdb', '3vxr.ent.pdb', '3vxs.ent.pdb', '3vxu.ent.pdb', '3vyr.ent.pdb', '3vys.ent.pdb', '3vza.ent.pdb', '3w2d.ent.pdb', '3w6j.ent.pdb', '3w8h.ent.pdb', '3w8i.ent.pdb', '3w9e.ent.pdb', '3wa0.ent.pdb', '3wa5.ent.pdb', '3wd5.ent.pdb', '3wdg.ent.pdb', '3wih.ent.pdb', '3wkn.ent.pdb', '3wkt.ent.pdb', '3wn5.ent.pdb', '3wn7.ent.pdb', '3wo3.ent.pdb', '3wo4.ent.pdb', '3wqb.ent.pdb', '3wrx.ent.pdb', '3wry.ent.pdb', '3wwk.ent.pdb', '3wwn.ent.pdb', '3wwq.ent.pdb', '3zet.ent.pdb', '3zeu.ent.pdb', '3zia.ent.pdb', '3zjy.ent.pdb', '3zkq.ent.pdb', '3znz.ent.pdb', '3zo0.ent.pdb', '3zrz.ent.pdb', '3zs8.ent.pdb', '3zs9.ent.pdb', '3zu7.ent.pdb', '3zuv.ent.pdb', '3zv0.ent.pdb', '3zwh.ent.pdb', '3zwl.ent.pdb', '3zwz.ent.pdb', '3zyi.ent.pdb', '3zyj.ent.pdb', '4a1s.ent.pdb', '4a1u.ent.pdb', '4a49.ent.pdb', '4a94.ent.pdb', '4aei.ent.pdb', '4afq.ent.pdb', '4afz.ent.pdb', '4ag2.ent.pdb', '4al8.ent.pdb', '4ala.ent.pdb', '4am0.ent.pdb', '4an7.ent.pdb', '4aoq.ent.pdb', '4aor.ent.pdb', '4ap2.ent.pdb', '4apf.ent.pdb', '4apx.ent.pdb', '4aqe.ent.pdb', '4asw.ent.pdb', '4auo.ent.pdb', '4auq.ent.pdb', '4awx.ent.pdb', '4ayd.ent.pdb', '4aye.ent.pdb', '4ayi.ent.pdb', '4b0m.ent.pdb', '4b1v.ent.pdb', '4b1x.ent.pdb', '4b1y.ent.pdb', '4b93.ent.pdb', '4bd9.ent.pdb', '4bfi.ent.pdb', '4bj5.ent.pdb', '4bkl.ent.pdb', '4bkx.ent.pdb', '4boh.ent.pdb', '4bpk.ent.pdb', '4bpx.ent.pdb', '4bq6.ent.pdb', '4bqd.ent.pdb', '4bru.ent.pdb', '4brw.ent.pdb', '4bsr.ent.pdb', '4bwq.ent.pdb', '4bxl.ent.pdb', '4bxz.ent.pdb', '4byf.ent.pdb', '4c1n.ent.pdb', '4c2a.ent.pdb', '4c2b.ent.pdb', '4c4k.ent.pdb', '4c4p.ent.pdb', '4c5g.ent.pdb', '4c7n.ent.pdb', '4c99.ent.pdb', '4c9b.ent.pdb', '4cc4.ent.pdb', '4cdk.ent.pdb', '4cj0.ent.pdb', '4cj1.ent.pdb', '4cj2.ent.pdb', '4cmh.ent.pdb', '4cmm.ent.pdb', '4cni.ent.pdb', '4ct0.ent.pdb', '4cu4.ent.pdb', '4cvw.ent.pdb', '4d0g.ent.pdb', '4d0n.ent.pdb', '4d2g.ent.pdb', '4d9q.ent.pdb', '4d9r.ent.pdb', '4day.ent.pdb', '4dbg.ent.pdb', '4dck.ent.pdb', '4dcn.ent.pdb', '4dg4.ent.pdb', '4dge.ent.pdb', '4dgi.ent.pdb', '4dh2.ent.pdb', '4di3.ent.pdb', '4did.ent.pdb', '4dj9.ent.pdb', '4djz.ent.pdb', '4dkd.ent.pdb', '4dke.ent.pdb', '4dkf.ent.pdb', '4dm6.ent.pdb', '4dm8.ent.pdb', '4dn4.ent.pdb', '4doh.ent.pdb', '4doq.ent.pdb', '4dpg.ent.pdb', '4dra.ent.pdb', '4drb.ent.pdb', '4drx.ent.pdb', '4ds8.ent.pdb', '4dt1.ent.pdb', '4dtg.ent.pdb', '4dvg.ent.pdb', '4dx8.ent.pdb', '4dxa.ent.pdb', '4dzu.ent.pdb', '4dzv.ent.pdb', '4e05.ent.pdb', '4e41.ent.pdb', '4e42.ent.pdb', '4eah.ent.pdb', '4edw.ent.pdb', '4eee.ent.pdb', '4eef.ent.pdb', '4ehq.ent.pdb', '4ei5.ent.pdb', '4eig.ent.pdb', '4eiz.ent.pdb', '4ekc.ent.pdb', '4ekd.ent.pdb', '4elm.ent.pdb', '4en3.ent.pdb', '4eo5.ent.pdb', '4eoz.ent.pdb', '4eqa.ent.pdb', '4ers.ent.pdb', '4etp.ent.pdb', '4etq.ent.pdb', '4etw.ent.pdb', '4euk.ent.pdb', '4exp.ent.pdb', '4f0a.ent.pdb', '4f0z.ent.pdb', '4f37.ent.pdb', '4f38.ent.pdb', '4f3f.ent.pdb', '4f48.ent.pdb', '4f6r.ent.pdb', '4f9l.ent.pdb', '4f9p.ent.pdb', '4fao.ent.pdb', '4ffy.ent.pdb', '4ffz.ent.pdb', '4fq0.ent.pdb', '4fqi.ent.pdb', '4fqj.ent.pdb', '4fqr.ent.pdb', '4fqv.ent.pdb', '4fqy.ent.pdb', '4ft4.ent.pdb', '4ftg.ent.pdb', '4fxg.ent.pdb', '4fza.ent.pdb', '4fzv.ent.pdb', '4g01.ent.pdb', '4g35.ent.pdb', '4g3y.ent.pdb', '4g4s.ent.pdb', '4g59.ent.pdb', '4g6f.ent.pdb', '4g6j.ent.pdb', '4g6m.ent.pdb', '4g6u.ent.pdb', '4g6v.ent.pdb', '4g8a.ent.pdb', '4g8g.ent.pdb', '4g9f.ent.pdb', '4gaf.ent.pdb', '4geh.ent.pdb', '4geq.ent.pdb', '4gg6.ent.pdb', '4gh7.ent.pdb', '4gi3.ent.pdb', '4giq.ent.pdb', '4gko.ent.pdb', '4gla.ent.pdb', '4glv.ent.pdb', '4gms.ent.pdb', '4gn3.ent.pdb', '4gn4.ent.pdb', '4gn5.ent.pdb', '4gnk.ent.pdb', '4grl.ent.pdb', '4gu0.ent.pdb', '4gur.ent.pdb', '4gxu.ent.pdb', '4h1l.ent.pdb', '4h2s.ent.pdb', '4h2w.ent.pdb', '4h3p.ent.pdb', '4h5s.ent.pdb', '4h6j.ent.pdb', '4h88.ent.pdb', '4hcn.ent.pdb', '4hcp.ent.pdb', '4hdo.ent.pdb', '4hdq.ent.pdb', '4hem.ent.pdb', '4hep.ent.pdb', '4hff.ent.pdb', '4hfk.ent.pdb', '4hgk.ent.pdb', '4hgm.ent.pdb', '4hh3.ent.pdb', '4hix.ent.pdb', '4hj0.ent.pdb', '4hjj.ent.pdb', '4hkj.ent.pdb', '4hkx.ent.pdb', '4hlz.ent.pdb', '4hmy.ent.pdb', '4hnj.ent.pdb', '4hrl.ent.pdb', '4hsa.ent.pdb', '4hx3.ent.pdb', '4i0c.ent.pdb', '4i18.ent.pdb', '4i2x.ent.pdb', '4i3r.ent.pdb', '4i6l.ent.pdb', '4i77.ent.pdb', '4i9x.ent.pdb', '4ic7.ent.pdb', '4idj.ent.pdb', '4ihh.ent.pdb', '4ihl.ent.pdb', '4iiq.ent.pdb', '4ij3.ent.pdb', '4ika.ent.pdb', '4ilg.ent.pdb', '4ilw.ent.pdb', '4imy.ent.pdb', '4iof.ent.pdb', '4iop.ent.pdb', '4ios.ent.pdb', '4iu3.ent.pdb', '4iw4.ent.pdb', '4iyp.ent.pdb', '4j2l.ent.pdb', '4j2y.ent.pdb', '4j32.ent.pdb', '4j4p.ent.pdb', '4j6g.ent.pdb', '4jan.ent.pdb', '4jb8.ent.pdb', '4je4.ent.pdb', '4jeg.ent.pdb', '4jeh.ent.pdb', '4jeu.ent.pdb', '4jgh.ent.pdb', '4jkp.ent.pdb', '4jlr.ent.pdb', '4jmf.ent.pdb', '4jo6.ent.pdb', '4jpk.ent.pdb', '4jra.ent.pdb', '4jrx.ent.pdb', '4jry.ent.pdb', '4js0.ent.pdb', '4jw2.ent.pdb', '4jw3.ent.pdb', '4jzj.ent.pdb', '4jzw.ent.pdb', '4k0a.ent.pdb', '4k1r.ent.pdb', '4k24.ent.pdb', '4k2u.ent.pdb', '4k3j.ent.pdb', '4k5a.ent.pdb', '4k5b.ent.pdb', '4k71.ent.pdb', '4k81.ent.pdb', '4k94.ent.pdb', '4k9e.ent.pdb', '4ka2.ent.pdb', '4kbb.ent.pdb', '4kdi.ent.pdb', '4kfz.ent.pdb', '4kgg.ent.pdb', '4kgq.ent.pdb', '4kht.ent.pdb', '4khx.ent.pdb', '4kjy.ent.pdb', '4kp3.ent.pdb', '4kr0.ent.pdb', '4krl.ent.pdb', '4kro.ent.pdb', '4krp.ent.pdb', '4ksd.ent.pdb', '4kt1.ent.pdb', '4kt3.ent.pdb', '4kt5.ent.pdb', '4kv5.ent.pdb', '4kvg.ent.pdb', '4kvn.ent.pdb', '4kxz.ent.pdb', '4l0p.ent.pdb', '4l67.ent.pdb', '4lad.ent.pdb', '4leo.ent.pdb', '4lgp.ent.pdb', '4lgr.ent.pdb', '4liq.ent.pdb', '4llo.ent.pdb', '4lmq.ent.pdb', '4ln0.ent.pdb', '4lqf.ent.pdb', '4lqw.ent.pdb', '4lrx.ent.pdb', '4lrz.ent.pdb', '4lu5.ent.pdb', '4lxr.ent.pdb', '4lyl.ent.pdb', '4lzx.ent.pdb', '4m0w.ent.pdb', '4m1g.ent.pdb', '4m1l.ent.pdb', '4m38.ent.pdb', '4m5f.ent.pdb', '4m5z.ent.pdb', '4m62.ent.pdb', '4m6b.ent.pdb', '4m8q.ent.pdb', '4may.ent.pdb', '4mhh.ent.pdb', '4mhj.ent.pdb', '4mi8.ent.pdb', '4mit.ent.pdb', '4mjs.ent.pdb', '4ml7.ent.pdb', '4mne.ent.pdb', '4mp0.ent.pdb', '4mqv.ent.pdb', '4mqw.ent.pdb', '4mrt.ent.pdb', '4msm.ent.pdb', '4myw.ent.pdb', '4n7v.ent.pdb', '4n7z.ent.pdb', '4n8c.ent.pdb', '4n8v.ent.pdb', '4n9g.ent.pdb', '4naw.ent.pdb', '4ne9.ent.pdb', '4nee.ent.pdb', '4ng2.ent.pdb', '4niq.ent.pdb', '4nl9.ent.pdb', '4nm3.ent.pdb', '4nm8.ent.pdb', '4nn6.ent.pdb', '4noo.ent.pdb', '4np4.ent.pdb', '4nqw.ent.pdb', '4nso.ent.pdb', '4nst.ent.pdb', '4nu1.ent.pdb', '4nzl.ent.pdb', '4nzw.ent.pdb', '4o1q.ent.pdb', '4o27.ent.pdb', '4od2.ent.pdb', '4odx.ent.pdb', '4ofy.ent.pdb', '4ojk.ent.pdb', '4ol0.ent.pdb', '4ons.ent.pdb', '4oqt.ent.pdb', '4ov6.ent.pdb', '4ovn.ent.pdb', '4oyd.ent.pdb', '4ozf.ent.pdb', '4ozg.ent.pdb', '4ozh.ent.pdb', '4ozi.ent.pdb', '4p1n.ent.pdb', '4p23.ent.pdb', '4p2c.ent.pdb', '4p2o.ent.pdb', '4p2q.ent.pdb', '4p2r.ent.pdb', '4p3y.ent.pdb', '4p46.ent.pdb', '4p59.ent.pdb', '4p5t.ent.pdb', '4p6i.ent.pdb', '4p9h.ent.pdb', '4pas.ent.pdb', '4pbv.ent.pdb', '4pbw.ent.pdb', '4pbz.ent.pdb', '4pc0.ent.pdb', '4peq.ent.pdb', '4per.ent.pdb', '4pgj.ent.pdb', '4pj2.ent.pdb', '4pj5.ent.pdb', '4pj7.ent.pdb', '4pj8.ent.pdb', '4pj9.ent.pdb', '4pja.ent.pdb', '4pjb.ent.pdb', '4pjc.ent.pdb', '4pjd.ent.pdb', '4pje.ent.pdb', '4pjf.ent.pdb', '4pjg.ent.pdb', '4pjh.ent.pdb', '4pjx.ent.pdb', '4pl8.ent.pdb', '4plo.ent.pdb', '4pou.ent.pdb', '4pp8.ent.pdb', '4pqt.ent.pdb', '4ps4.ent.pdb', '4pvz.ent.pdb', '4pw9.ent.pdb', '4pwx.ent.pdb', '4py8.ent.pdb', '4pz6.ent.pdb', '4q5e.ent.pdb', '4q5u.ent.pdb', '4q96.ent.pdb', '4qci.ent.pdb', '4qd2.ent.pdb', '4qlb.ent.pdb', '4qlp.ent.pdb', '4qnp.ent.pdb', '4qrp.ent.pdb', '4qt8.ent.pdb', '4qti.ent.pdb', '4qxa.ent.pdb', '4qzv.ent.pdb', '4r2g.ent.pdb', '4r8g.ent.pdb', '4r8i.ent.pdb', '4r8w.ent.pdb', '4ra0.ent.pdb', '4rdq.ent.pdb', '4re1.ent.pdb', '4rey.ent.pdb', '4rgm.ent.pdb', '4rgo.ent.pdb', '4rjf.ent.pdb', '4rs1.ent.pdb', '4rt6.ent.pdb', '4rws.ent.pdb', '4rwt.ent.pdb', '4s0s.ent.pdb', '4s3o.ent.pdb', '4thn.ent.pdb', '4tq0.ent.pdb', '4tq1.ent.pdb', '4u0q.ent.pdb', '4u2x.ent.pdb', '4u30.ent.pdb', '4u32.ent.pdb', '4u3j.ent.pdb', '4u4c.ent.pdb', '4u5w.ent.pdb', '4u6h.ent.pdb', '4u6v.ent.pdb', '4u97.ent.pdb', '4udm.ent.pdb', '4uem.ent.pdb', '4uf1.ent.pdb', '4ui0.ent.pdb', '4ui1.ent.pdb', '4uu9.ent.pdb', '4uuz.ent.pdb', '4uwq.ent.pdb', '4uwx.ent.pdb', '4uyp.ent.pdb', '4uyq.ent.pdb', '4v0m.ent.pdb', '4v0n.ent.pdb', '4v0o.ent.pdb', '4v2c.ent.pdb', '4v3k.ent.pdb', '4w4l.ent.pdb', '4w4o.ent.pdb', '4w6w.ent.pdb', '4w6x.ent.pdb', '4w6y.ent.pdb', '4wb2.ent.pdb', '4wem.ent.pdb', '4wen.ent.pdb', '4weu.ent.pdb', '4wfd.ent.pdb', '4wnd.ent.pdb', '4wnn.ent.pdb', '4wo4.ent.pdb', '4wuu.ent.pdb', '4wv1.ent.pdb', '4wwi.ent.pdb', '4x33.ent.pdb', '4x4m.ent.pdb', '4x7d.ent.pdb', '4x7e.ent.pdb', '4x7f.ent.pdb', '4x7s.ent.pdb', '4xhj.ent.pdb', '4xhu.ent.pdb', '4xi5.ent.pdb', '4xkh.ent.pdb', '4xkl.ent.pdb', '4xl1.ent.pdb', '4xl5.ent.pdb', '4xlw.ent.pdb', '4xnm.ent.pdb', '4xoi.ent.pdb', '4xr8.ent.pdb', '4xvp.ent.pdb', '4xwj.ent.pdb', '4xxb.ent.pdb', '4y5o.ent.pdb', '4y61.ent.pdb', '4ybl.ent.pdb', '4yc7.ent.pdb', '4ydh.ent.pdb', '4yeb.ent.pdb', '4yh7.ent.pdb', '4yiq.ent.pdb', '4yiz.ent.pdb', '4yj4.ent.pdb', '4yk4.ent.pdb', '4yl8.ent.pdb', '4yn0.ent.pdb', '4yoc.ent.pdb', '4ypg.ent.pdb', '4ypi.ent.pdb', '4yvq.ent.pdb', '4ywc.ent.pdb', '4yyp.ent.pdb', '4z2m.ent.pdb', '4z5r.ent.pdb', '4z80.ent.pdb', '4z8l.ent.pdb', '4z9k.ent.pdb', '4z9v.ent.pdb', '4zak.ent.pdb', '4zff.ent.pdb', '4zfg.ent.pdb', '4zfo.ent.pdb', '4zgm.ent.pdb', '4zgq.ent.pdb', '4zgy.ent.pdb', '4zi2.ent.pdb', '4zi3.ent.pdb', '4zii.ent.pdb', '4zk9.ent.pdb', '4zkc.ent.pdb', '4zlt.ent.pdb', '4zpt.ent.pdb', '4zqu.ent.pdb', '4zrj.ent.pdb', '4zrk.ent.pdb', '4zrp.ent.pdb', '4zs6.ent.pdb', '4zs7.ent.pdb', '4zv4.ent.pdb', '4zw2.ent.pdb', '5a3i.ent.pdb', '5a6w.ent.pdb', '5aam.ent.pdb', '5aaw.ent.pdb', '5abv.ent.pdb', '5agw.ent.pdb', '5agx.ent.pdb', '5ajj.ent.pdb', '5ajk.ent.pdb', '5anm.ent.pdb', '5aoq.ent.pdb', '5ayr.ent.pdb', '5ays.ent.pdb', '5b3h.ent.pdb', '5b64.ent.pdb', '5b71.ent.pdb', '5b75.ent.pdb', '5b76.ent.pdb', '5b77.ent.pdb', '5b78.ent.pdb', '5bn5.ent.pdb', '5bnq.ent.pdb', '5bo1.ent.pdb', '5boz.ent.pdb', '5bqe.ent.pdb', '5brm.ent.pdb', '5bt1.ent.pdb', '5bvp.ent.pdb', '5bw7.ent.pdb', '5bw8.ent.pdb', '5c07.ent.pdb', '5c08.ent.pdb', '5c09.ent.pdb', '5c0a.ent.pdb', '5c0b.ent.pdb', '5c0c.ent.pdb', '5c0n.ent.pdb', 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'5mj3.ent.pdb', '5mjy.ent.pdb', '5mk0.ent.pdb', '5ml9.ent.pdb', '5mn2.ent.pdb', '5mtj.ent.pdb', '5mtm.ent.pdb', '5mtn.ent.pdb', '5mu3.ent.pdb', '5mv8.ent.pdb', '5mv9.ent.pdb', '5my6.ent.pdb', '5n4w.ent.pdb', '5n88.ent.pdb', '5nan.ent.pdb', '5ngv.ent.pdb', '5nh3.ent.pdb', '5nhu.ent.pdb', '5nnp.ent.pdb', '5npo.ent.pdb', '5nqf.ent.pdb', '5nqg.ent.pdb', '5nt7.ent.pdb', '5nus.ent.pdb', '5nvk.ent.pdb', '5nvl.ent.pdb', '5nvm.ent.pdb', '5nvn.ent.pdb', '5nwm.ent.pdb', '5o03.ent.pdb', '5o05.ent.pdb', '5o0w.ent.pdb', '5o2s.ent.pdb', '5o2t.ent.pdb', '5o2u.ent.pdb', '5o4e.ent.pdb', '5o74.ent.pdb', '5o76.ent.pdb', '5oaq.ent.pdb', '5oc7.ent.pdb', '5odw.ent.pdb', '5ohm.ent.pdb', '5ohp.ent.pdb', '5omb.ent.pdb', '5omm.ent.pdb', '5omn.ent.pdb', '5ona.ent.pdb', '5oo6.ent.pdb', '5oob.ent.pdb', '5osh.ent.pdb', '5ovw.ent.pdb', '5sv3.ent.pdb', '5sws.ent.pdb', '5swz.ent.pdb', '5sx4.ent.pdb', '5sx5.ent.pdb', '5sxp.ent.pdb', '5sy8.ent.pdb', '5szh.ent.pdb', '5szi.ent.pdb', '5szj.ent.pdb', '5szk.ent.pdb', '5t0f.ent.pdb', '5t1d.ent.pdb', '5t29.ent.pdb', '5t5b.ent.pdb', '5t5f.ent.pdb', '5t5w.ent.pdb', '5t6l.ent.pdb', '5tar.ent.pdb', '5te4.ent.pdb', '5te6.ent.pdb', '5te7.ent.pdb', '5tez.ent.pdb', '5tfw.ent.pdb', '5tgh.ent.pdb', '5th9.ent.pdb', '5thp.ent.pdb', '5tl6.ent.pdb', '5tl7.ent.pdb', '5toj.ent.pdb', '5tp6.ent.pdb', '5tru.ent.pdb', '5tte.ent.pdb', '5tuv.ent.pdb', '5tvq.ent.pdb', '5twa.ent.pdb', '5tz2.ent.pdb', '5tzn.ent.pdb', '5tzp.ent.pdb', '5tzq.ent.pdb', '5tzt.ent.pdb', '5u4k.ent.pdb', '5u4y.ent.pdb', '5u52.ent.pdb', '5ua4.ent.pdb', '5ufe.ent.pdb', '5ufq.ent.pdb', '5uk5.ent.pdb', '5un5.ent.pdb', '5un7.ent.pdb', '5upk.ent.pdb', '5uq3.ent.pdb', '5ush.ent.pdb', '5usl.ent.pdb', '5uul.ent.pdb', '5uwh.ent.pdb', '5uwo.ent.pdb', '5uwq.ent.pdb', '5uws.ent.pdb', '5uwu.ent.pdb', '5uzu.ent.pdb', '5v52.ent.pdb', '5v5g.ent.pdb', '5v5h.ent.pdb', '5v5i.ent.pdb', '5v5v.ent.pdb', '5v62.ent.pdb', '5v69.ent.pdb', '5v6a.ent.pdb', '5vag.ent.pdb', '5vcb.ent.pdb', '5vey.ent.pdb', '5vkl.ent.pdb', '5vko.ent.pdb', '5vmm.ent.pdb', '5vob.ent.pdb', '5vpg.ent.pdb', '5vpl.ent.pdb', '5vt9.ent.pdb', '5vwx.ent.pdb', '5vwy.ent.pdb', '5vx0.ent.pdb', '5vx2.ent.pdb', '5vx3.ent.pdb', '5vxz.ent.pdb', '5vz4.ent.pdb', '5w0k.ent.pdb', '5w3x.ent.pdb', '5w6g.ent.pdb', '5w8t.ent.pdb', '5wb7.ent.pdb', '5wb8.ent.pdb', '5wgg.ent.pdb', '5wko.ent.pdb', '5wos.ent.pdb', '5wql.ent.pdb', '5wrv.ent.pdb', '5wt9.ent.pdb', '5wuj.ent.pdb', '5wux.ent.pdb', '5wvo.ent.pdb', '5wy2.ent.pdb', '5x0w.ent.pdb', '5x4l.ent.pdb', '5x60.ent.pdb', '5xbf.ent.pdb', '5xco.ent.pdb', '5xeq.ent.pdb', '5xfs.ent.pdb', '5xjg.ent.pdb', '5xku.ent.pdb', '5xot.ent.pdb', '5xov.ent.pdb', '5xsq.ent.pdb', '5xv8.ent.pdb', '5xxy.ent.pdb', '5y11.ent.pdb', '5y1z.ent.pdb', '5y4r.ent.pdb', '6amb.ent.pdb', '6atk.ent.pdb', '6azz.ent.pdb', '6b08.ent.pdb', '6b0a.ent.pdb', '6b0e.ent.pdb', '6b0g.ent.pdb', '6b0s.ent.pdb', '6b12.ent.pdb', '6b3s.ent.pdb', '6b6u.ent.pdb', '6b9j.ent.pdb', '6ba6.ent.pdb', '6bit.ent.pdb']\n",
      "protein chain : 0 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
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      "protein chain : 1 2\n"
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      "[4088.  645. 1112.    0.    0.    0.    0.    0.    0. 1144.  180.  323.\n",
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      "    0.    0.    0.    0.    0.    0.    0.    0.    0.   48.    8.   15.\n",
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      "    0.    0.    0.    0.    0.    0.    0.    0.    0.]\n",
      "value of x vector (R^N) =  {'id': '1a3b.ent.pdb', 'x_vector': array([1.3854e+04, 3.3330e+03, 3.6180e+03, 0.0000e+00, 0.0000e+00,\n",
      "       1.2200e+02, 0.0000e+00, 0.0000e+00, 0.0000e+00, 3.5360e+03,\n",
      "       8.5400e+02, 9.5400e+02, 0.0000e+00, 0.0000e+00, 3.1000e+01,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 4.0920e+03, 1.0330e+03,\n",
      "       1.0860e+03, 0.0000e+00, 0.0000e+00, 3.6000e+01, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       1.6800e+02, 4.0000e+01, 4.4000e+01, 0.0000e+00, 0.0000e+00,\n",
      "       2.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n",
      "       0.0000e+00])}\n",
      "time elapsed = 137.37900042533875 seconds\n"
     ]
    }
   ],
   "source": [
    "'''\n",
    "multiple protein data processor calculation,\n",
    "do the steps of file loading until vector processing.\n",
    "uses parallelization (soon)\n",
    "'''\n",
    "\n",
    "def minus(x, y):\n",
    "    return x-y\n",
    "\n",
    "list(map(minus, [1,2,3], repeat(2)))\n",
    "\n",
    "sample_files = complex_files[0:5]\n",
    "\n",
    "########################################\n",
    "\n",
    "def data_processing(path,id_name, atom_types, cutoff):\n",
    "    #dataframe loader:\n",
    "    path_file = path+'/'+id_name\n",
    "    l =[]\n",
    "    with open(path_file, 'r') as f:\n",
    "        for line in f:\n",
    "            if line.startswith('ATOM') or line.startswith('TER'):\n",
    "                clean_line = (line.rstrip()).split()\n",
    "                #check for alignment mistakes within data, a row with spacing alignment error has 11 length after splitted by whitespace\n",
    "                if len(clean_line) == 11:\n",
    "                    #split the 2nd last column by the 4th index (this inference is according to PDB file formatting)\n",
    "                    split = [clean_line[-2][:4], clean_line[-2][4:]]\n",
    "                    clean_line[-2] = split[1]\n",
    "                    clean_line.insert(-2, split[0])\n",
    "                l.append(clean_line)\n",
    "    df_atoms = (pd.DataFrame(l)).rename(columns={0:'record', 6:'x_coor', 7:'y_coor', 8:'z_coor', 11:'atom_type'})\n",
    "    \n",
    "    #dataframe splitter:\n",
    "    l_df = []\n",
    "    last_idx = 0\n",
    "    for idx in df_atoms.index[df_atoms['record'] == 'TER'].tolist():\n",
    "        l_df.append(df_atoms.iloc[last_idx:idx])\n",
    "        last_idx = idx+1\n",
    "        \n",
    "    #vector calculation:\n",
    "    x_vector = np.zeros(len(atom_types)**2)\n",
    "    length = len(l_df)\n",
    "    for i in range(length):\n",
    "        for j in range(length):\n",
    "            if j>i:\n",
    "                #sum each chain interaction values:\n",
    "                print('protein chain :', i, j)\n",
    "                x_vector += protein_interaction(l_df[i], l_df[j], atom_types, cutoff)\n",
    "    return {'id':id_name, 'x_vector':x_vector}\n",
    "\n",
    "\n",
    "path = 'C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Dataset/PP'\n",
    "id_file = complex_files[2]\n",
    "atom_types = ['C','N','O','F','P','S','Cl','Br','I']\n",
    "cutoff = 12\n",
    "\n",
    "print(complex_files)\n",
    "curr_time = time.time()\n",
    "x_vector = data_processing(path, id_file, atom_types, cutoff)\n",
    "print('value of x vector (R^N) = ', x_vector)\n",
    "end_time = time.time()\n",
    "print('time elapsed =',end_time-curr_time,'seconds')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(180320,)\n",
      "time elapsed = 1.0159235000610352 seconds\n"
     ]
    }
   ],
   "source": [
    "'''\n",
    "multiprocessing on interaction calculation\n",
    "'''\n",
    "def protein_interaction_mp(df_protein_A, df_protein_B, atom_types, cutoff):\n",
    "    type_len = len(atom_types)\n",
    "    x_vector = np.zeros(type_len**2)\n",
    "    idx = 0\n",
    "    for a_type in atom_types:\n",
    "        for b_type in atom_types:\n",
    "            #calculate the interaction of each atoms:\n",
    "            sum_interaction = 0\n",
    "            a_atoms = df_protein_A.loc[df_protein_A['atom_type'] == a_type].to_dict('records')\n",
    "            b_atoms = df_protein_B.loc[df_protein_B['atom_type'] == b_type].to_dict('records')\n",
    "            a_coords = np.array([[a_atom['x_coor'], a_atom['y_coor'], a_atom['z_coor']] for a_atom in a_atoms], dtype=float)\n",
    "            b_coords = np.array([[b_atom['x_coor'], b_atom['y_coor'], b_atom['z_coor']] for b_atom in b_atoms], dtype=float)\n",
    "            \n",
    "            \n",
    "            for i in range(a_atoms.shape[0]):\n",
    "                for j in range(b_atoms.shape[0]):\n",
    "                    #get the (x,y,z):\n",
    "                    a_atom = a_atoms.iloc[i]\n",
    "                    b_atom = b_atoms.iloc[j]\n",
    "                    a_coord = np.array([float(a_atom['x_coor']), float(a_atom['y_coor']), float(a_atom['z_coor'])]) \n",
    "                    b_coord = np.array([float(b_atom['x_coor']), float(b_atom['y_coor']), float(b_atom['z_coor'])])\n",
    "                    #calculate the euclidean distance and heaviside step value:\n",
    "                    sum_interaction += f_h_step(x=f_euclid_dist(a_coord, b_coord), a=cutoff) \n",
    "            x_vector[idx] = sum_interaction\n",
    "            idx+=1\n",
    "            print(x_vector)\n",
    "    return x_vector\n",
    "\n",
    "def f_euc_mp(params):\n",
    "    return np.linalg.norm(params[0]-params[1])\n",
    "\n",
    "a = l_df[0].loc[l_df[0]['atom_type'] == 'C'].to_dict('records')\n",
    "b = l_df[1].loc[l_df[1]['atom_type'] == 'C'].to_dict('records')\n",
    "a_c = np.array([[a_['x_coor'], a_['y_coor'], a_['z_coor']] for a_ in a], dtype=float)\n",
    "b_c = np.array([[b_['x_coor'], b_['y_coor'], b_['z_coor']] for b_ in b], dtype=float)\n",
    "paramlist = list(product(a_c, b_c))\n",
    "pool = multiprocessing.Pool(processes=6)\n",
    "\n",
    "start_time = time.time()\n",
    "euclid_dists = map(f_euc_mp, paramlist)\n",
    "\n",
    "#print(list(euclid_dists)[0:100], len(paramlist))\n",
    "a = list(euclid_dists)\n",
    "print(np.array(a).shape)\n",
    "end_time = time.time()\n",
    "print('time elapsed =',end_time-start_time,'seconds')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# -*- coding: utf-8 -*-\n",
    "\"\"\"\n",
    "Spyder Editor\n",
    "\n",
    "This is a temporary script file.\n",
    "\"\"\"\n",
    "\n",
    "#!/usr/bin/env python3\n",
    "import itertools\n",
    "import multiprocessing\n",
    "#Generate values for each parameter\n",
    "a = range(10)\n",
    "b = range(10)\n",
    "c = range(10)\n",
    "d = range(10)\n",
    "\n",
    "#Generate a list of tuples where each tuple is a combination of parameters.\n",
    "#The list will contain all possible combinations of parameters.\n",
    "paramlist = list(itertools.product(a,b,c,d))\n",
    "\n",
    "#A function which will process a tuple of parameters\n",
    "def func(params):\n",
    "  a = params[0]\n",
    "  b = params[1]\n",
    "  c = params[2]\n",
    "  d = params[3]\n",
    "  return a*b*c*d\n",
    "\n",
    "if __name__ == '__main__':\n",
    "    #Generate processes equal to the number of cores\n",
    "    pool = multiprocessing.Pool()\n",
    "    \n",
    "    #Distribute the parameter sets evenly across the cores\n",
    "    res  = pool.map(func,paramlist)\n",
    "    print(res)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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