preprocessing_training.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "####  After running training_and_test_compounds_to_sdf.ipynb the sdf file generated is processed through Padel to provide topological descriptors. The molecular descriptors generated by Padel are saved in \"molecular_descriptors_csv/molecular_descriptors_with_pIC50_values.csv\".\n",
    "#### This notebook reads those descriptors and applies min-max scaling to descriptors. The resultant file is saved in  'molecular_descriptors_csv/min_max_scaled_molecular_descriptors_with_pIC50_values.csv'.\n",
    "#### The scaler data is also saved in 'scaler_data/scaler.dat'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from sklearn.preprocessing import MinMaxScaler\n",
    "import pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read file containing molecular descriptors\n",
    "data_file = \"molecular_descriptors_csv/molecular_descriptors_with_pIC50_values.csv\"\n",
    "csv_df = pd.read_csv(data_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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       "    Unnamed: 0                                               Name  nAcid  \\\n",
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       "4            4  ClC1=CC=C(NC(=O)CSC2=NC=CC(=N2)C2=CC(=NO2)C2=C...      0   \n",
       "..         ...                                                ...    ...   \n",
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       "\n",
       "     ALogP     ALogp2      AMR       apol  naAromAtom  nAromBond  nAtom  ...  \\\n",
       "0   1.8332   3.360622  38.8217  61.657102          23         25     44  ...   \n",
       "1   2.3025   5.301506  48.2354  62.914895          22         24     48  ...   \n",
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       "91  1.5915   2.532872  49.5580  52.395516          15         16     36  ...   \n",
       "92  1.2332   1.520782  52.2965  58.237516          17         17     40  ...   \n",
       "93 -0.3519   0.123834  64.8401  57.631481          11         11     43  ...   \n",
       "\n",
       "       WTPT-1    WTPT-2     WTPT-3    WTPT-4     WTPT-5   WPATH  WPOL  XLogP  \\\n",
       "0   61.601358  2.053379  26.207945  2.543160  12.436456  2949.0  42.0  6.330   \n",
       "1   67.019947  2.030907  34.022386  2.543262  15.595702  3852.0  48.0  5.512   \n",
       "2   65.276625  2.039895  29.438396  2.543325  12.315692  3324.0  48.0  5.515   \n",
       "3   59.520206  2.052421  29.687873  2.543250  15.458889  2712.0  39.0  4.410   \n",
       "4   59.752710  2.060438  23.645955  5.658412  12.395061  2713.0  40.0  6.084   \n",
       "..        ...       ...        ...       ...        ...     ...   ...    ...   \n",
       "89  45.712208  2.077828  14.345409  5.129616   3.515549  1034.0  36.0  4.630   \n",
       "90  45.710723  2.077760  14.357961  5.127368   3.514977  1019.0  37.0  4.092   \n",
       "91  49.706648  2.071110  14.299735  5.122215   3.489699  1455.0  38.0  5.396   \n",
       "92  57.298165  2.046363  22.437376  7.693744   6.565223  2255.0  44.0  4.842   \n",
       "93  53.440335  2.055397  20.275766  7.705829   6.906646  1752.0  42.0  3.420   \n",
       "\n",
       "    Zagreb    values  \n",
       "0    156.0 -0.477121  \n",
       "1    176.0 -1.000000  \n",
       "2    168.0 -1.041393  \n",
       "3    152.0 -1.146128  \n",
       "4    150.0 -1.176091  \n",
       "..     ...       ...  \n",
       "89   124.0  0.022276  \n",
       "90   124.0 -1.049218  \n",
       "91   132.0 -1.371068  \n",
       "92   152.0 -1.099335  \n",
       "93   142.0 -1.243038  \n",
       "\n",
       "[94 rows x 1447 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "csv_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Get smiles of compounds\n",
    "names = csv_df['Name']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Isolate descriptor columns\n",
    "descriptor_df = csv_df.loc[:,'nAcid':'Zagreb']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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       "      <th>WTPT-5</th>\n",
       "      <th>WPATH</th>\n",
       "      <th>WPOL</th>\n",
       "      <th>XLogP</th>\n",
       "      <th>Zagreb</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>1.8332</td>\n",
       "      <td>3.360622</td>\n",
       "      <td>38.8217</td>\n",
       "      <td>61.657102</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>44</td>\n",
       "      <td>30</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>10.727241</td>\n",
       "      <td>61.601358</td>\n",
       "      <td>2.053379</td>\n",
       "      <td>26.207945</td>\n",
       "      <td>2.543160</td>\n",
       "      <td>12.436456</td>\n",
       "      <td>2949.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>6.330</td>\n",
       "      <td>156.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>2.3025</td>\n",
       "      <td>5.301506</td>\n",
       "      <td>48.2354</td>\n",
       "      <td>62.914895</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>48</td>\n",
       "      <td>33</td>\n",
       "      <td>15</td>\n",
       "      <td>...</td>\n",
       "      <td>10.604914</td>\n",
       "      <td>67.019947</td>\n",
       "      <td>2.030907</td>\n",
       "      <td>34.022386</td>\n",
       "      <td>2.543262</td>\n",
       "      <td>15.595702</td>\n",
       "      <td>3852.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>5.512</td>\n",
       "      <td>176.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0</td>\n",
       "      <td>3.4539</td>\n",
       "      <td>11.929425</td>\n",
       "      <td>65.7244</td>\n",
       "      <td>70.371067</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>51</td>\n",
       "      <td>32</td>\n",
       "      <td>19</td>\n",
       "      <td>...</td>\n",
       "      <td>10.157118</td>\n",
       "      <td>65.276625</td>\n",
       "      <td>2.039895</td>\n",
       "      <td>29.438396</td>\n",
       "      <td>2.543325</td>\n",
       "      <td>12.315692</td>\n",
       "      <td>3324.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>5.515</td>\n",
       "      <td>168.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>1.7308</td>\n",
       "      <td>2.995669</td>\n",
       "      <td>46.8983</td>\n",
       "      <td>59.957102</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>43</td>\n",
       "      <td>29</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>10.674533</td>\n",
       "      <td>59.520206</td>\n",
       "      <td>2.052421</td>\n",
       "      <td>29.687873</td>\n",
       "      <td>2.543250</td>\n",
       "      <td>15.458889</td>\n",
       "      <td>2712.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>4.410</td>\n",
       "      <td>152.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>0.3442</td>\n",
       "      <td>0.118474</td>\n",
       "      <td>27.0317</td>\n",
       "      <td>58.045895</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>44</td>\n",
       "      <td>29</td>\n",
       "      <td>15</td>\n",
       "      <td>...</td>\n",
       "      <td>9.592282</td>\n",
       "      <td>59.752710</td>\n",
       "      <td>2.060438</td>\n",
       "      <td>23.645955</td>\n",
       "      <td>5.658412</td>\n",
       "      <td>12.395061</td>\n",
       "      <td>2713.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>6.084</td>\n",
       "      <td>150.0</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",
       "      <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>89</th>\n",
       "      <td>0</td>\n",
       "      <td>1.1237</td>\n",
       "      <td>1.262702</td>\n",
       "      <td>39.2394</td>\n",
       "      <td>47.541930</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>13.092116</td>\n",
       "      <td>45.712208</td>\n",
       "      <td>2.077828</td>\n",
       "      <td>14.345409</td>\n",
       "      <td>5.129616</td>\n",
       "      <td>3.515549</td>\n",
       "      <td>1034.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>4.630</td>\n",
       "      <td>124.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>90</th>\n",
       "      <td>0</td>\n",
       "      <td>0.4479</td>\n",
       "      <td>0.200614</td>\n",
       "      <td>30.9088</td>\n",
       "      <td>44.371930</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>10.219127</td>\n",
       "      <td>45.710723</td>\n",
       "      <td>2.077760</td>\n",
       "      <td>14.357961</td>\n",
       "      <td>5.127368</td>\n",
       "      <td>3.514977</td>\n",
       "      <td>1019.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>4.092</td>\n",
       "      <td>124.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>91</th>\n",
       "      <td>0</td>\n",
       "      <td>1.5915</td>\n",
       "      <td>2.532872</td>\n",
       "      <td>49.5580</td>\n",
       "      <td>52.395516</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>36</td>\n",
       "      <td>24</td>\n",
       "      <td>12</td>\n",
       "      <td>...</td>\n",
       "      <td>12.360093</td>\n",
       "      <td>49.706648</td>\n",
       "      <td>2.071110</td>\n",
       "      <td>14.299735</td>\n",
       "      <td>5.122215</td>\n",
       "      <td>3.489699</td>\n",
       "      <td>1455.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>5.396</td>\n",
       "      <td>132.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>92</th>\n",
       "      <td>0</td>\n",
       "      <td>1.2332</td>\n",
       "      <td>1.520782</td>\n",
       "      <td>52.2965</td>\n",
       "      <td>58.237516</td>\n",
       "      <td>17</td>\n",
       "      <td>17</td>\n",
       "      <td>40</td>\n",
       "      <td>28</td>\n",
       "      <td>12</td>\n",
       "      <td>...</td>\n",
       "      <td>13.048255</td>\n",
       "      <td>57.298165</td>\n",
       "      <td>2.046363</td>\n",
       "      <td>22.437376</td>\n",
       "      <td>7.693744</td>\n",
       "      <td>6.565223</td>\n",
       "      <td>2255.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>4.842</td>\n",
       "      <td>152.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93</th>\n",
       "      <td>0</td>\n",
       "      <td>-0.3519</td>\n",
       "      <td>0.123834</td>\n",
       "      <td>64.8401</td>\n",
       "      <td>57.631481</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>43</td>\n",
       "      <td>26</td>\n",
       "      <td>17</td>\n",
       "      <td>...</td>\n",
       "      <td>11.162801</td>\n",
       "      <td>53.440335</td>\n",
       "      <td>2.055397</td>\n",
       "      <td>20.275766</td>\n",
       "      <td>7.705829</td>\n",
       "      <td>6.906646</td>\n",
       "      <td>1752.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>3.420</td>\n",
       "      <td>142.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>94 rows × 1444 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    nAcid   ALogP     ALogp2      AMR       apol  naAromAtom  nAromBond  \\\n",
       "0       0  1.8332   3.360622  38.8217  61.657102          23         25   \n",
       "1       0  2.3025   5.301506  48.2354  62.914895          22         24   \n",
       "2       0  3.4539  11.929425  65.7244  70.371067          22         24   \n",
       "3       0  1.7308   2.995669  46.8983  59.957102          22         24   \n",
       "4       0  0.3442   0.118474  27.0317  58.045895          23         25   \n",
       "..    ...     ...        ...      ...        ...         ...        ...   \n",
       "89      0  1.1237   1.262702  39.2394  47.541930          15         16   \n",
       "90      0  0.4479   0.200614  30.9088  44.371930          15         16   \n",
       "91      0  1.5915   2.532872  49.5580  52.395516          15         16   \n",
       "92      0  1.2332   1.520782  52.2965  58.237516          17         17   \n",
       "93      0 -0.3519   0.123834  64.8401  57.631481          11         11   \n",
       "\n",
       "    nAtom  nHeavyAtom  nH  ...        AMW     WTPT-1    WTPT-2     WTPT-3  \\\n",
       "0      44          30  14  ...  10.727241  61.601358  2.053379  26.207945   \n",
       "1      48          33  15  ...  10.604914  67.019947  2.030907  34.022386   \n",
       "2      51          32  19  ...  10.157118  65.276625  2.039895  29.438396   \n",
       "3      43          29  14  ...  10.674533  59.520206  2.052421  29.687873   \n",
       "4      44          29  15  ...   9.592282  59.752710  2.060438  23.645955   \n",
       "..    ...         ...  ..  ...        ...        ...       ...        ...   \n",
       "89     32          22  10  ...  13.092116  45.712208  2.077828  14.345409   \n",
       "90     32          22  10  ...  10.219127  45.710723  2.077760  14.357961   \n",
       "91     36          24  12  ...  12.360093  49.706648  2.071110  14.299735   \n",
       "92     40          28  12  ...  13.048255  57.298165  2.046363  22.437376   \n",
       "93     43          26  17  ...  11.162801  53.440335  2.055397  20.275766   \n",
       "\n",
       "      WTPT-4     WTPT-5   WPATH  WPOL  XLogP  Zagreb  \n",
       "0   2.543160  12.436456  2949.0  42.0  6.330   156.0  \n",
       "1   2.543262  15.595702  3852.0  48.0  5.512   176.0  \n",
       "2   2.543325  12.315692  3324.0  48.0  5.515   168.0  \n",
       "3   2.543250  15.458889  2712.0  39.0  4.410   152.0  \n",
       "4   5.658412  12.395061  2713.0  40.0  6.084   150.0  \n",
       "..       ...        ...     ...   ...    ...     ...  \n",
       "89  5.129616   3.515549  1034.0  36.0  4.630   124.0  \n",
       "90  5.127368   3.514977  1019.0  37.0  4.092   124.0  \n",
       "91  5.122215   3.489699  1455.0  38.0  5.396   132.0  \n",
       "92  7.693744   6.565223  2255.0  44.0  4.842   152.0  \n",
       "93  7.705829   6.906646  1752.0  42.0  3.420   142.0  \n",
       "\n",
       "[94 rows x 1444 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "descriptor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>nAcid</th>\n",
       "      <th>ALogP</th>\n",
       "      <th>ALogp2</th>\n",
       "      <th>AMR</th>\n",
       "      <th>apol</th>\n",
       "      <th>naAromAtom</th>\n",
       "      <th>nAromBond</th>\n",
       "      <th>nAtom</th>\n",
       "      <th>nHeavyAtom</th>\n",
       "      <th>nH</th>\n",
       "      <th>...</th>\n",
       "      <th>AMW</th>\n",
       "      <th>WTPT-1</th>\n",
       "      <th>WTPT-2</th>\n",
       "      <th>WTPT-3</th>\n",
       "      <th>WTPT-4</th>\n",
       "      <th>WTPT-5</th>\n",
       "      <th>WPATH</th>\n",
       "      <th>WPOL</th>\n",
       "      <th>XLogP</th>\n",
       "      <th>Zagreb</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>1.8332</td>\n",
       "      <td>3.360622</td>\n",
       "      <td>38.8217</td>\n",
       "      <td>61.657102</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>44</td>\n",
       "      <td>30</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>10.727241</td>\n",
       "      <td>61.601358</td>\n",
       "      <td>2.053379</td>\n",
       "      <td>26.207945</td>\n",
       "      <td>2.543160</td>\n",
       "      <td>12.436456</td>\n",
       "      <td>2949.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>6.330</td>\n",
       "      <td>156.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>2.3025</td>\n",
       "      <td>5.301506</td>\n",
       "      <td>48.2354</td>\n",
       "      <td>62.914895</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>48</td>\n",
       "      <td>33</td>\n",
       "      <td>15</td>\n",
       "      <td>...</td>\n",
       "      <td>10.604914</td>\n",
       "      <td>67.019947</td>\n",
       "      <td>2.030907</td>\n",
       "      <td>34.022386</td>\n",
       "      <td>2.543262</td>\n",
       "      <td>15.595702</td>\n",
       "      <td>3852.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>5.512</td>\n",
       "      <td>176.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0</td>\n",
       "      <td>3.4539</td>\n",
       "      <td>11.929425</td>\n",
       "      <td>65.7244</td>\n",
       "      <td>70.371067</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>51</td>\n",
       "      <td>32</td>\n",
       "      <td>19</td>\n",
       "      <td>...</td>\n",
       "      <td>10.157118</td>\n",
       "      <td>65.276625</td>\n",
       "      <td>2.039895</td>\n",
       "      <td>29.438396</td>\n",
       "      <td>2.543325</td>\n",
       "      <td>12.315692</td>\n",
       "      <td>3324.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>5.515</td>\n",
       "      <td>168.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>1.7308</td>\n",
       "      <td>2.995669</td>\n",
       "      <td>46.8983</td>\n",
       "      <td>59.957102</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>43</td>\n",
       "      <td>29</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>10.674533</td>\n",
       "      <td>59.520206</td>\n",
       "      <td>2.052421</td>\n",
       "      <td>29.687873</td>\n",
       "      <td>2.543250</td>\n",
       "      <td>15.458889</td>\n",
       "      <td>2712.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>4.410</td>\n",
       "      <td>152.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>0.3442</td>\n",
       "      <td>0.118474</td>\n",
       "      <td>27.0317</td>\n",
       "      <td>58.045895</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>44</td>\n",
       "      <td>29</td>\n",
       "      <td>15</td>\n",
       "      <td>...</td>\n",
       "      <td>9.592282</td>\n",
       "      <td>59.752710</td>\n",
       "      <td>2.060438</td>\n",
       "      <td>23.645955</td>\n",
       "      <td>5.658412</td>\n",
       "      <td>12.395061</td>\n",
       "      <td>2713.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>6.084</td>\n",
       "      <td>150.0</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",
       "      <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>89</th>\n",
       "      <td>0</td>\n",
       "      <td>1.1237</td>\n",
       "      <td>1.262702</td>\n",
       "      <td>39.2394</td>\n",
       "      <td>47.541930</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>13.092116</td>\n",
       "      <td>45.712208</td>\n",
       "      <td>2.077828</td>\n",
       "      <td>14.345409</td>\n",
       "      <td>5.129616</td>\n",
       "      <td>3.515549</td>\n",
       "      <td>1034.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>4.630</td>\n",
       "      <td>124.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>90</th>\n",
       "      <td>0</td>\n",
       "      <td>0.4479</td>\n",
       "      <td>0.200614</td>\n",
       "      <td>30.9088</td>\n",
       "      <td>44.371930</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>10.219127</td>\n",
       "      <td>45.710723</td>\n",
       "      <td>2.077760</td>\n",
       "      <td>14.357961</td>\n",
       "      <td>5.127368</td>\n",
       "      <td>3.514977</td>\n",
       "      <td>1019.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>4.092</td>\n",
       "      <td>124.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>91</th>\n",
       "      <td>0</td>\n",
       "      <td>1.5915</td>\n",
       "      <td>2.532872</td>\n",
       "      <td>49.5580</td>\n",
       "      <td>52.395516</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>36</td>\n",
       "      <td>24</td>\n",
       "      <td>12</td>\n",
       "      <td>...</td>\n",
       "      <td>12.360093</td>\n",
       "      <td>49.706648</td>\n",
       "      <td>2.071110</td>\n",
       "      <td>14.299735</td>\n",
       "      <td>5.122215</td>\n",
       "      <td>3.489699</td>\n",
       "      <td>1455.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>5.396</td>\n",
       "      <td>132.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>92</th>\n",
       "      <td>0</td>\n",
       "      <td>1.2332</td>\n",
       "      <td>1.520782</td>\n",
       "      <td>52.2965</td>\n",
       "      <td>58.237516</td>\n",
       "      <td>17</td>\n",
       "      <td>17</td>\n",
       "      <td>40</td>\n",
       "      <td>28</td>\n",
       "      <td>12</td>\n",
       "      <td>...</td>\n",
       "      <td>13.048255</td>\n",
       "      <td>57.298165</td>\n",
       "      <td>2.046363</td>\n",
       "      <td>22.437376</td>\n",
       "      <td>7.693744</td>\n",
       "      <td>6.565223</td>\n",
       "      <td>2255.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>4.842</td>\n",
       "      <td>152.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93</th>\n",
       "      <td>0</td>\n",
       "      <td>-0.3519</td>\n",
       "      <td>0.123834</td>\n",
       "      <td>64.8401</td>\n",
       "      <td>57.631481</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>43</td>\n",
       "      <td>26</td>\n",
       "      <td>17</td>\n",
       "      <td>...</td>\n",
       "      <td>11.162801</td>\n",
       "      <td>53.440335</td>\n",
       "      <td>2.055397</td>\n",
       "      <td>20.275766</td>\n",
       "      <td>7.705829</td>\n",
       "      <td>6.906646</td>\n",
       "      <td>1752.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>3.420</td>\n",
       "      <td>142.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>94 rows × 1119 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    nAcid   ALogP     ALogp2      AMR       apol  naAromAtom  nAromBond  \\\n",
       "0       0  1.8332   3.360622  38.8217  61.657102          23         25   \n",
       "1       0  2.3025   5.301506  48.2354  62.914895          22         24   \n",
       "2       0  3.4539  11.929425  65.7244  70.371067          22         24   \n",
       "3       0  1.7308   2.995669  46.8983  59.957102          22         24   \n",
       "4       0  0.3442   0.118474  27.0317  58.045895          23         25   \n",
       "..    ...     ...        ...      ...        ...         ...        ...   \n",
       "89      0  1.1237   1.262702  39.2394  47.541930          15         16   \n",
       "90      0  0.4479   0.200614  30.9088  44.371930          15         16   \n",
       "91      0  1.5915   2.532872  49.5580  52.395516          15         16   \n",
       "92      0  1.2332   1.520782  52.2965  58.237516          17         17   \n",
       "93      0 -0.3519   0.123834  64.8401  57.631481          11         11   \n",
       "\n",
       "    nAtom  nHeavyAtom  nH  ...        AMW     WTPT-1    WTPT-2     WTPT-3  \\\n",
       "0      44          30  14  ...  10.727241  61.601358  2.053379  26.207945   \n",
       "1      48          33  15  ...  10.604914  67.019947  2.030907  34.022386   \n",
       "2      51          32  19  ...  10.157118  65.276625  2.039895  29.438396   \n",
       "3      43          29  14  ...  10.674533  59.520206  2.052421  29.687873   \n",
       "4      44          29  15  ...   9.592282  59.752710  2.060438  23.645955   \n",
       "..    ...         ...  ..  ...        ...        ...       ...        ...   \n",
       "89     32          22  10  ...  13.092116  45.712208  2.077828  14.345409   \n",
       "90     32          22  10  ...  10.219127  45.710723  2.077760  14.357961   \n",
       "91     36          24  12  ...  12.360093  49.706648  2.071110  14.299735   \n",
       "92     40          28  12  ...  13.048255  57.298165  2.046363  22.437376   \n",
       "93     43          26  17  ...  11.162801  53.440335  2.055397  20.275766   \n",
       "\n",
       "      WTPT-4     WTPT-5   WPATH  WPOL  XLogP  Zagreb  \n",
       "0   2.543160  12.436456  2949.0  42.0  6.330   156.0  \n",
       "1   2.543262  15.595702  3852.0  48.0  5.512   176.0  \n",
       "2   2.543325  12.315692  3324.0  48.0  5.515   168.0  \n",
       "3   2.543250  15.458889  2712.0  39.0  4.410   152.0  \n",
       "4   5.658412  12.395061  2713.0  40.0  6.084   150.0  \n",
       "..       ...        ...     ...   ...    ...     ...  \n",
       "89  5.129616   3.515549  1034.0  36.0  4.630   124.0  \n",
       "90  5.127368   3.514977  1019.0  37.0  4.092   124.0  \n",
       "91  5.122215   3.489699  1455.0  38.0  5.396   132.0  \n",
       "92  7.693744   6.565223  2255.0  44.0  4.842   152.0  \n",
       "93  7.705829   6.906646  1752.0  42.0  3.420   142.0  \n",
       "\n",
       "[94 rows x 1119 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Remove columns with standard deviation = 0\n",
    "descriptor_df = descriptor_df.loc[:, descriptor_df.std() != 0]\n",
    "num_of_samples = len(descriptor_df)\n",
    "processed_descriptor_df = pd.DataFrame()\n",
    "processed_descriptor_df = descriptor_df\n",
    "processed_descriptor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "values_df = csv_df['values']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0    -0.477121\n",
       "1    -1.000000\n",
       "2    -1.041393\n",
       "3    -1.146128\n",
       "4    -1.176091\n",
       "        ...   \n",
       "89    0.022276\n",
       "90   -1.049218\n",
       "91   -1.371068\n",
       "92   -1.099335\n",
       "93   -1.243038\n",
       "Name: values, Length: 94, dtype: float64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "values_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\abhis\\.conda\\envs\\my-rdkit-env\\lib\\site-packages\\ipykernel_launcher.py:1: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  \"\"\"Entry point for launching an IPython kernel.\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>nAcid</th>\n",
       "      <th>ALogP</th>\n",
       "      <th>ALogp2</th>\n",
       "      <th>AMR</th>\n",
       "      <th>apol</th>\n",
       "      <th>naAromAtom</th>\n",
       "      <th>nAromBond</th>\n",
       "      <th>nAtom</th>\n",
       "      <th>nHeavyAtom</th>\n",
       "      <th>nH</th>\n",
       "      <th>...</th>\n",
       "      <th>WTPT-1</th>\n",
       "      <th>WTPT-2</th>\n",
       "      <th>WTPT-3</th>\n",
       "      <th>WTPT-4</th>\n",
       "      <th>WTPT-5</th>\n",
       "      <th>WPATH</th>\n",
       "      <th>WPOL</th>\n",
       "      <th>XLogP</th>\n",
       "      <th>Zagreb</th>\n",
       "      <th>values</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>1.8332</td>\n",
       "      <td>3.360622</td>\n",
       "      <td>38.8217</td>\n",
       "      <td>61.657102</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>44</td>\n",
       "      <td>30</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>61.601358</td>\n",
       "      <td>2.053379</td>\n",
       "      <td>26.207945</td>\n",
       "      <td>2.543160</td>\n",
       "      <td>12.436456</td>\n",
       "      <td>2949.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>6.330</td>\n",
       "      <td>156.0</td>\n",
       "      <td>-0.477121</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>2.3025</td>\n",
       "      <td>5.301506</td>\n",
       "      <td>48.2354</td>\n",
       "      <td>62.914895</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>48</td>\n",
       "      <td>33</td>\n",
       "      <td>15</td>\n",
       "      <td>...</td>\n",
       "      <td>67.019947</td>\n",
       "      <td>2.030907</td>\n",
       "      <td>34.022386</td>\n",
       "      <td>2.543262</td>\n",
       "      <td>15.595702</td>\n",
       "      <td>3852.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>5.512</td>\n",
       "      <td>176.0</td>\n",
       "      <td>-1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0</td>\n",
       "      <td>3.4539</td>\n",
       "      <td>11.929425</td>\n",
       "      <td>65.7244</td>\n",
       "      <td>70.371067</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>51</td>\n",
       "      <td>32</td>\n",
       "      <td>19</td>\n",
       "      <td>...</td>\n",
       "      <td>65.276625</td>\n",
       "      <td>2.039895</td>\n",
       "      <td>29.438396</td>\n",
       "      <td>2.543325</td>\n",
       "      <td>12.315692</td>\n",
       "      <td>3324.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>5.515</td>\n",
       "      <td>168.0</td>\n",
       "      <td>-1.041393</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>1.7308</td>\n",
       "      <td>2.995669</td>\n",
       "      <td>46.8983</td>\n",
       "      <td>59.957102</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>43</td>\n",
       "      <td>29</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>59.520206</td>\n",
       "      <td>2.052421</td>\n",
       "      <td>29.687873</td>\n",
       "      <td>2.543250</td>\n",
       "      <td>15.458889</td>\n",
       "      <td>2712.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>4.410</td>\n",
       "      <td>152.0</td>\n",
       "      <td>-1.146128</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>0.3442</td>\n",
       "      <td>0.118474</td>\n",
       "      <td>27.0317</td>\n",
       "      <td>58.045895</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>44</td>\n",
       "      <td>29</td>\n",
       "      <td>15</td>\n",
       "      <td>...</td>\n",
       "      <td>59.752710</td>\n",
       "      <td>2.060438</td>\n",
       "      <td>23.645955</td>\n",
       "      <td>5.658412</td>\n",
       "      <td>12.395061</td>\n",
       "      <td>2713.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>6.084</td>\n",
       "      <td>150.0</td>\n",
       "      <td>-1.176091</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",
       "      <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>89</th>\n",
       "      <td>0</td>\n",
       "      <td>1.1237</td>\n",
       "      <td>1.262702</td>\n",
       "      <td>39.2394</td>\n",
       "      <td>47.541930</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>45.712208</td>\n",
       "      <td>2.077828</td>\n",
       "      <td>14.345409</td>\n",
       "      <td>5.129616</td>\n",
       "      <td>3.515549</td>\n",
       "      <td>1034.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>4.630</td>\n",
       "      <td>124.0</td>\n",
       "      <td>0.022276</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>90</th>\n",
       "      <td>0</td>\n",
       "      <td>0.4479</td>\n",
       "      <td>0.200614</td>\n",
       "      <td>30.9088</td>\n",
       "      <td>44.371930</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>45.710723</td>\n",
       "      <td>2.077760</td>\n",
       "      <td>14.357961</td>\n",
       "      <td>5.127368</td>\n",
       "      <td>3.514977</td>\n",
       "      <td>1019.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>4.092</td>\n",
       "      <td>124.0</td>\n",
       "      <td>-1.049218</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>91</th>\n",
       "      <td>0</td>\n",
       "      <td>1.5915</td>\n",
       "      <td>2.532872</td>\n",
       "      <td>49.5580</td>\n",
       "      <td>52.395516</td>\n",
       "      <td>15</td>\n",
       "      <td>16</td>\n",
       "      <td>36</td>\n",
       "      <td>24</td>\n",
       "      <td>12</td>\n",
       "      <td>...</td>\n",
       "      <td>49.706648</td>\n",
       "      <td>2.071110</td>\n",
       "      <td>14.299735</td>\n",
       "      <td>5.122215</td>\n",
       "      <td>3.489699</td>\n",
       "      <td>1455.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>5.396</td>\n",
       "      <td>132.0</td>\n",
       "      <td>-1.371068</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>92</th>\n",
       "      <td>0</td>\n",
       "      <td>1.2332</td>\n",
       "      <td>1.520782</td>\n",
       "      <td>52.2965</td>\n",
       "      <td>58.237516</td>\n",
       "      <td>17</td>\n",
       "      <td>17</td>\n",
       "      <td>40</td>\n",
       "      <td>28</td>\n",
       "      <td>12</td>\n",
       "      <td>...</td>\n",
       "      <td>57.298165</td>\n",
       "      <td>2.046363</td>\n",
       "      <td>22.437376</td>\n",
       "      <td>7.693744</td>\n",
       "      <td>6.565223</td>\n",
       "      <td>2255.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>4.842</td>\n",
       "      <td>152.0</td>\n",
       "      <td>-1.099335</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93</th>\n",
       "      <td>0</td>\n",
       "      <td>-0.3519</td>\n",
       "      <td>0.123834</td>\n",
       "      <td>64.8401</td>\n",
       "      <td>57.631481</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>43</td>\n",
       "      <td>26</td>\n",
       "      <td>17</td>\n",
       "      <td>...</td>\n",
       "      <td>53.440335</td>\n",
       "      <td>2.055397</td>\n",
       "      <td>20.275766</td>\n",
       "      <td>7.705829</td>\n",
       "      <td>6.906646</td>\n",
       "      <td>1752.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>3.420</td>\n",
       "      <td>142.0</td>\n",
       "      <td>-1.243038</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>94 rows × 1120 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    nAcid   ALogP     ALogp2      AMR       apol  naAromAtom  nAromBond  \\\n",
       "0       0  1.8332   3.360622  38.8217  61.657102          23         25   \n",
       "1       0  2.3025   5.301506  48.2354  62.914895          22         24   \n",
       "2       0  3.4539  11.929425  65.7244  70.371067          22         24   \n",
       "3       0  1.7308   2.995669  46.8983  59.957102          22         24   \n",
       "4       0  0.3442   0.118474  27.0317  58.045895          23         25   \n",
       "..    ...     ...        ...      ...        ...         ...        ...   \n",
       "89      0  1.1237   1.262702  39.2394  47.541930          15         16   \n",
       "90      0  0.4479   0.200614  30.9088  44.371930          15         16   \n",
       "91      0  1.5915   2.532872  49.5580  52.395516          15         16   \n",
       "92      0  1.2332   1.520782  52.2965  58.237516          17         17   \n",
       "93      0 -0.3519   0.123834  64.8401  57.631481          11         11   \n",
       "\n",
       "    nAtom  nHeavyAtom  nH  ...     WTPT-1    WTPT-2     WTPT-3    WTPT-4  \\\n",
       "0      44          30  14  ...  61.601358  2.053379  26.207945  2.543160   \n",
       "1      48          33  15  ...  67.019947  2.030907  34.022386  2.543262   \n",
       "2      51          32  19  ...  65.276625  2.039895  29.438396  2.543325   \n",
       "3      43          29  14  ...  59.520206  2.052421  29.687873  2.543250   \n",
       "4      44          29  15  ...  59.752710  2.060438  23.645955  5.658412   \n",
       "..    ...         ...  ..  ...        ...       ...        ...       ...   \n",
       "89     32          22  10  ...  45.712208  2.077828  14.345409  5.129616   \n",
       "90     32          22  10  ...  45.710723  2.077760  14.357961  5.127368   \n",
       "91     36          24  12  ...  49.706648  2.071110  14.299735  5.122215   \n",
       "92     40          28  12  ...  57.298165  2.046363  22.437376  7.693744   \n",
       "93     43          26  17  ...  53.440335  2.055397  20.275766  7.705829   \n",
       "\n",
       "       WTPT-5   WPATH  WPOL  XLogP  Zagreb    values  \n",
       "0   12.436456  2949.0  42.0  6.330   156.0 -0.477121  \n",
       "1   15.595702  3852.0  48.0  5.512   176.0 -1.000000  \n",
       "2   12.315692  3324.0  48.0  5.515   168.0 -1.041393  \n",
       "3   15.458889  2712.0  39.0  4.410   152.0 -1.146128  \n",
       "4   12.395061  2713.0  40.0  6.084   150.0 -1.176091  \n",
       "..        ...     ...   ...    ...     ...       ...  \n",
       "89   3.515549  1034.0  36.0  4.630   124.0  0.022276  \n",
       "90   3.514977  1019.0  37.0  4.092   124.0 -1.049218  \n",
       "91   3.489699  1455.0  38.0  5.396   132.0 -1.371068  \n",
       "92   6.565223  2255.0  44.0  4.842   152.0 -1.099335  \n",
       "93   6.906646  1752.0  42.0  3.420   142.0 -1.243038  \n",
       "\n",
       "[94 rows x 1120 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "processed_descriptor_df['values'] = values_df\n",
    "processed_descriptor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Add back the smiles of compounds\n",
    "processed_descriptor_df.insert(0, \"Name\", names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\abhis\\.conda\\envs\\my-rdkit-env\\lib\\site-packages\\pandas\\core\\indexing.py:966: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  self.obj[item] = s\n"
     ]
    },
    {
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       "      <th></th>\n",
       "      <th>Name</th>\n",
       "      <th>nAcid</th>\n",
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       "      <td>0.684211</td>\n",
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       "      <td>0.578947</td>\n",
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       "      <td>0.347355</td>\n",
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       "      <td>0.55</td>\n",
       "      <td>0.234043</td>\n",
       "      <td>0.346154</td>\n",
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       "      <td>0.355826</td>\n",
       "      <td>0.921801</td>\n",
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       "      <td>0.189712</td>\n",
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       "      <td>0.428571</td>\n",
       "      <td>0.606224</td>\n",
       "      <td>0.394737</td>\n",
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       "      <th>90</th>\n",
       "      <td>ClC1=C2C(=O)C(=O)N(CC3=CC4=CC=CC=C4S3)C2=CC=C1</td>\n",
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       "      <td>0.234043</td>\n",
       "      <td>0.346154</td>\n",
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       "      <td>0.355799</td>\n",
       "      <td>0.921312</td>\n",
       "      <td>0.293744</td>\n",
       "      <td>0.161867</td>\n",
       "      <td>0.189681</td>\n",
       "      <td>0.137450</td>\n",
       "      <td>0.446429</td>\n",
       "      <td>0.543042</td>\n",
       "      <td>0.394737</td>\n",
       "      <td>0.420767</td>\n",
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       "    <tr>\n",
       "      <th>91</th>\n",
       "      <td>IC1=CC=C2N(C\\C=C\\C3=CC4=CC=CC=C4S3)C(=O)C(=O)C...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.628181</td>\n",
       "      <td>0.148871</td>\n",
       "      <td>0.478491</td>\n",
       "      <td>0.438914</td>\n",
       "      <td>0.555556</td>\n",
       "      <td>0.55</td>\n",
       "      <td>0.319149</td>\n",
       "      <td>0.423077</td>\n",
       "      <td>...</td>\n",
       "      <td>0.428593</td>\n",
       "      <td>0.873151</td>\n",
       "      <td>0.291892</td>\n",
       "      <td>0.161545</td>\n",
       "      <td>0.188317</td>\n",
       "      <td>0.216407</td>\n",
       "      <td>0.464286</td>\n",
       "      <td>0.696183</td>\n",
       "      <td>0.447368</td>\n",
       "      <td>0.338680</td>\n",
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       "    <tr>\n",
       "      <th>92</th>\n",
       "      <td>ClC1=CC=C(NC(=O)C2=CC=C(CN3C(=O)C(=O)C4=CC(I)=...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.575569</td>\n",
       "      <td>0.089348</td>\n",
       "      <td>0.513294</td>\n",
       "      <td>0.544961</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>0.60</td>\n",
       "      <td>0.404255</td>\n",
       "      <td>0.576923</td>\n",
       "      <td>...</td>\n",
       "      <td>0.566886</td>\n",
       "      <td>0.693921</td>\n",
       "      <td>0.550651</td>\n",
       "      <td>0.322488</td>\n",
       "      <td>0.354284</td>\n",
       "      <td>0.361282</td>\n",
       "      <td>0.571429</td>\n",
       "      <td>0.631122</td>\n",
       "      <td>0.578947</td>\n",
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       "    <tr>\n",
       "      <th>93</th>\n",
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       "      <td>0.0</td>\n",
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       "<p>94 rows × 1121 columns</p>\n",
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      ],
      "text/plain": [
       "                                                 Name  nAcid     ALogP  \\\n",
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       "2   CSC1=C(C(C)=C(S1)C1=NC(C)=CS1)C1=CC=NC(SCC(=O)...    0.0  0.901649   \n",
       "3   CC1=NC(=CS1)C1=NC(=CS1)C1=NC(SCC(=O)NC2=CC=C(C...    0.0  0.648635   \n",
       "4   ClC1=CC=C(NC(=O)CSC2=NC=CC(=N2)C2=CC(=NO2)C2=C...    0.0  0.445032   \n",
       "..                                                ...    ...       ...   \n",
       "89      IC1=CC=C2N(CC3=CC4=CC=CC=C4S3)C(=O)C(=O)C2=C1    0.0  0.559491   \n",
       "90     ClC1=C2C(=O)C(=O)N(CC3=CC4=CC=CC=C4S3)C2=CC=C1    0.0  0.460259   \n",
       "91  IC1=CC=C2N(C\\C=C\\C3=CC4=CC=CC=C4S3)C(=O)C(=O)C...    0.0  0.628181   \n",
       "92  ClC1=CC=C(NC(=O)C2=CC=C(CN3C(=O)C(=O)C4=CC(I)=...    0.0  0.575569   \n",
       "93  IC1=CC=C2N(CC3=CC=C(S3)C(=O)N3CCCCC3)C(=O)C(=O...    0.0  0.342819   \n",
       "\n",
       "      ALogp2       AMR      apol  naAromAtom  nAromBond     nAtom  nHeavyAtom  \\\n",
       "0   0.197552  0.342047  0.607035    1.000000       1.00  0.489362    0.653846   \n",
       "1   0.311700  0.461683  0.629867    0.944444       0.95  0.574468    0.769231   \n",
       "2   0.701501  0.683945  0.765216    0.944444       0.95  0.638298    0.730769   \n",
       "3   0.176089  0.444690  0.576176    0.944444       0.95  0.468085    0.615385   \n",
       "4   0.006875  0.192211  0.541483    1.000000       1.00  0.489362    0.615385   \n",
       "..       ...       ...       ...         ...        ...       ...         ...   \n",
       "89  0.074169  0.347355  0.350809    0.555556       0.55  0.234043    0.346154   \n",
       "90  0.011706  0.241484  0.293265    0.555556       0.55  0.234043    0.346154   \n",
       "91  0.148871  0.478491  0.438914    0.555556       0.55  0.319149    0.423077   \n",
       "92  0.089348  0.513294  0.544961    0.666667       0.60  0.404255    0.576923   \n",
       "93  0.007190  0.672707  0.533960    0.333333       0.30  0.468085    0.500000   \n",
       "\n",
       "    ...    WTPT-1    WTPT-2    WTPT-3    WTPT-4    WTPT-5     WPATH      WPOL  \\\n",
       "0   ...  0.645277  0.744731  0.670546  0.000130  0.671117  0.486961  0.535714   \n",
       "1   ...  0.743987  0.581986  0.919028  0.000137  0.841602  0.650489  0.642857   \n",
       "2   ...  0.712229  0.647073  0.773268  0.000141  0.664601  0.554871  0.642857   \n",
       "3   ...  0.607365  0.737794  0.781200  0.000136  0.834219  0.444042  0.482143   \n",
       "4   ...  0.611601  0.795860  0.589081  0.195103  0.668884  0.444223  0.500000   \n",
       "..  ...       ...       ...       ...       ...       ...       ...       ...   \n",
       "89  ...  0.355826  0.921801  0.293344  0.162008  0.189712  0.140167  0.428571   \n",
       "90  ...  0.355799  0.921312  0.293744  0.161867  0.189681  0.137450  0.446429   \n",
       "91  ...  0.428593  0.873151  0.291892  0.161545  0.188317  0.216407  0.464286   \n",
       "92  ...  0.566886  0.693921  0.550651  0.322488  0.354284  0.361282  0.571429   \n",
       "93  ...  0.496609  0.759352  0.481916  0.323244  0.372708  0.270192  0.535714   \n",
       "\n",
       "       XLogP    Zagreb    values  \n",
       "0   0.805872  0.605263  0.566680  \n",
       "1   0.709806  0.736842  0.433320  \n",
       "2   0.710159  0.684211  0.422763  \n",
       "3   0.580388  0.578947  0.396050  \n",
       "4   0.776982  0.565789  0.388408  \n",
       "..       ...       ...       ...  \n",
       "89  0.606224  0.394737  0.694051  \n",
       "90  0.543042  0.394737  0.420767  \n",
       "91  0.696183  0.447368  0.338680  \n",
       "92  0.631122  0.578947  0.407985  \n",
       "93  0.464122  0.513158  0.371334  \n",
       "\n",
       "[94 rows x 1121 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# min max scaling of columns.\n",
    "scaler = MinMaxScaler()\n",
    "scaled_values = scaler.fit_transform(processed_descriptor_df.loc[:,'nAcid':'values'])\n",
    "processed_descriptor_df.loc[:,1:] = scaled_values\n",
    "processed_descriptor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Save scaler for future use during inference\n",
    "pickle.dump(scaler,open('scaler_data/scaler.dat','wb'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "#  Save min max scaled molecular descriptors as a csv file\n",
    "processed_descriptor_df.to_csv('molecular_descriptors_csv/min_max_scaled_molecular_descriptors_with_pIC50_values.csv')"
   ]
  }
 ],
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