tutorial3.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Part 3 Descriptor Calculation and Dataset Preparation\n",
    "* https://github.com/dataprofessor/bioinformatics_freecodecamp/blob/main/CDD_ML_Part_3_Acetylcholinesterase_Descriptor_Dataset_Preparation.ipynb\n",
    "* https://youtu.be/jBlTQjcKuaY?t=2905\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
    "#! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n",
    "     "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('./data/bioactivity_data_2class_pIC50.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "      <th>bioactivity_class</th>\n",
       "      <th>MW</th>\n",
       "      <th>LogP</th>\n",
       "      <th>NumHDonors</th>\n",
       "      <th>NumHAcceptors</th>\n",
       "      <th>standard_value_norm</th>\n",
       "      <th>pIC50</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2</td>\n",
       "      <td>CHEMBL185698</td>\n",
       "      <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
       "      <td>13500.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>421.190</td>\n",
       "      <td>2.66050</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>13500.0</td>\n",
       "      <td>4.869666</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>3</td>\n",
       "      <td>CHEMBL426082</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
       "      <td>13110.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>293.347</td>\n",
       "      <td>3.63080</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>13110.0</td>\n",
       "      <td>4.882397</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>5</td>\n",
       "      <td>CHEMBL365134</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c(Br)cccc21</td>\n",
       "      <td>980.0</td>\n",
       "      <td>active</td>\n",
       "      <td>372.243</td>\n",
       "      <td>4.39330</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>980.0</td>\n",
       "      <td>6.008774</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>7</td>\n",
       "      <td>CHEMBL190743</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccc(I)cc21</td>\n",
       "      <td>950.0</td>\n",
       "      <td>active</td>\n",
       "      <td>419.243</td>\n",
       "      <td>4.23540</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>950.0</td>\n",
       "      <td>6.022276</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>8</td>\n",
       "      <td>CHEMBL365469</td>\n",
       "      <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2cccc(Cl)c21</td>\n",
       "      <td>11200.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>327.792</td>\n",
       "      <td>4.28420</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>11200.0</td>\n",
       "      <td>4.950782</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113</th>\n",
       "      <td>128</td>\n",
       "      <td>CHEMBL2146517</td>\n",
       "      <td>COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...</td>\n",
       "      <td>10600.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>338.359</td>\n",
       "      <td>3.40102</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>10600.0</td>\n",
       "      <td>4.974694</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114</th>\n",
       "      <td>129</td>\n",
       "      <td>CHEMBL187460</td>\n",
       "      <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
       "      <td>10100.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>296.366</td>\n",
       "      <td>3.44330</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>10100.0</td>\n",
       "      <td>4.995679</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115</th>\n",
       "      <td>130</td>\n",
       "      <td>CHEMBL363535</td>\n",
       "      <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
       "      <td>11500.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>276.291</td>\n",
       "      <td>4.09564</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>11500.0</td>\n",
       "      <td>4.939302</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>131</td>\n",
       "      <td>CHEMBL227075</td>\n",
       "      <td>Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1</td>\n",
       "      <td>10700.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>278.307</td>\n",
       "      <td>3.29102</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>10700.0</td>\n",
       "      <td>4.970616</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117</th>\n",
       "      <td>132</td>\n",
       "      <td>CHEMBL45830</td>\n",
       "      <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
       "      <td>78900.0</td>\n",
       "      <td>inactive</td>\n",
       "      <td>282.383</td>\n",
       "      <td>4.10530</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>78900.0</td>\n",
       "      <td>4.102923</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>118 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Unnamed: 0 molecule_chembl_id  \\\n",
       "0             2       CHEMBL185698   \n",
       "1             3       CHEMBL426082   \n",
       "2             5       CHEMBL365134   \n",
       "3             7       CHEMBL190743   \n",
       "4             8       CHEMBL365469   \n",
       "..          ...                ...   \n",
       "113         128      CHEMBL2146517   \n",
       "114         129       CHEMBL187460   \n",
       "115         130       CHEMBL363535   \n",
       "116         131       CHEMBL227075   \n",
       "117         132        CHEMBL45830   \n",
       "\n",
       "                                      canonical_smiles  standard_value  \\\n",
       "0              O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21         13500.0   \n",
       "1                  O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21         13110.0   \n",
       "2              O=C1C(=O)N(Cc2cc3ccccc3s2)c2c(Br)cccc21           980.0   \n",
       "3               O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccc(I)cc21           950.0   \n",
       "4              O=C1C(=O)N(Cc2cc3ccccc3s2)c2cccc(Cl)c21         11200.0   \n",
       "..                                                 ...             ...   \n",
       "113  COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...         10600.0   \n",
       "114        C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C         10100.0   \n",
       "115             Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12         11500.0   \n",
       "116      Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1         10700.0   \n",
       "117             CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C         78900.0   \n",
       "\n",
       "    bioactivity_class       MW     LogP  NumHDonors  NumHAcceptors  \\\n",
       "0            inactive  421.190  2.66050         0.0            4.0   \n",
       "1            inactive  293.347  3.63080         0.0            3.0   \n",
       "2              active  372.243  4.39330         0.0            3.0   \n",
       "3              active  419.243  4.23540         0.0            3.0   \n",
       "4            inactive  327.792  4.28420         0.0            3.0   \n",
       "..                ...      ...      ...         ...            ...   \n",
       "113          inactive  338.359  3.40102         0.0            5.0   \n",
       "114          inactive  296.366  3.44330         0.0            3.0   \n",
       "115          inactive  276.291  4.09564         0.0            3.0   \n",
       "116          inactive  278.307  3.29102         0.0            3.0   \n",
       "117          inactive  282.383  4.10530         0.0            2.0   \n",
       "\n",
       "     standard_value_norm     pIC50  \n",
       "0                13500.0  4.869666  \n",
       "1                13110.0  4.882397  \n",
       "2                  980.0  6.008774  \n",
       "3                  950.0  6.022276  \n",
       "4                11200.0  4.950782  \n",
       "..                   ...       ...  \n",
       "113              10600.0  4.974694  \n",
       "114              10100.0  4.995679  \n",
       "115              11500.0  4.939302  \n",
       "116              10700.0  4.970616  \n",
       "117              78900.0  4.102923  \n",
       "\n",
       "[118 rows x 11 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Unnamed: 0', 'molecule_chembl_id', 'canonical_smiles',\n",
       "       'standard_value', 'bioactivity_class', 'MW', 'LogP', 'NumHDonors',\n",
       "       'NumHAcceptors', 'standard_value_norm', 'pIC50'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_selected = df[['canonical_smiles', 'molecule_chembl_id']]\n",
    "df_selected.to_csv('./data/molecule.smi', sep='\\t', index=False, header=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21\tCHEMBL185698\n",
      "O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21\tCHEMBL426082\n",
      "O=C1C(=O)N(Cc2cc3ccccc3s2)c2c(Br)cccc21\tCHEMBL365134\n",
      "O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccc(I)cc21\tCHEMBL190743\n",
      "O=C1C(=O)N(Cc2cc3ccccc3s2)c2cccc(Cl)c21\tCHEMBL365469\n"
     ]
    }
   ],
   "source": [
    "! cat ./data/molecule.smi | head -5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "118\n"
     ]
    }
   ],
   "source": [
    "! cat ./data/molecule.smi | wc -l"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculate fingerprint descriptors\n",
    "#### Calculate PaDEL descriptors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "java -Xms1G -Xmx1G -Djava.awt.headless=true -jar ./PaDEL-Descriptor/PaDEL-Descriptor.jar -removesalt -standardizenitro -fingerprints -descriptortypes ./PaDEL-Descriptor/PubchemFingerprinter.xml -dir ./ -file descriptors_output.csv\n"
     ]
    }
   ],
   "source": [
    "! cat padel.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL185698 in molecule.smi (1/118). \n",
      "Processing CHEMBL426082 in molecule.smi (2/118). \n",
      "Processing CHEMBL365134 in molecule.smi (3/118). \n",
      "Processing CHEMBL190743 in molecule.smi (4/118). \n",
      "Processing CHEMBL365469 in molecule.smi (5/118). \n",
      "Processing CHEMBL188983 in molecule.smi (6/118). \n",
      "Processing CHEMBL191575 in molecule.smi (7/118). \n",
      "Processing CHEMBL370923 in molecule.smi (8/118). \n",
      "Processing CHEMBL194398 in molecule.smi (9/118). \n",
      "Processing CHEMBL196635 in molecule.smi (10/118). \n",
      "Processing CHEMBL209287 in molecule.smi (11/118). \n",
      "Processing CHEMBL358279 in molecule.smi (12/118). \n",
      "Processing CHEMBL379727 in molecule.smi (14/118). Average speed: 0.72 s/mol.\n",
      "Processing CHEMBL348660 in molecule.smi (13/118). Average speed: 1.27 s/mol.\n",
      "Processing CHEMBL210525 in molecule.smi (15/118). Average speed: 0.50 s/mol.\n",
      "Processing CHEMBL148483 in molecule.smi (16/118). Average speed: 0.37 s/mol.\n",
      "Processing CHEMBL118596 in molecule.smi (17/118). Average speed: 0.32 s/mol.\n",
      "Processing CHEMBL210146 in molecule.smi (18/118). Average speed: 0.27 s/mol.\n",
      "Processing CHEMBL210146 in molecule.smi (19/118). Average speed: 0.23 s/mol.\n",
      "Processing CHEMBL207458 in molecule.smi (20/118). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL207458 in molecule.smi (21/118). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL207484 in molecule.smi (22/118). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL207484 in molecule.smi (23/118). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL207207 in molecule.smi (24/118). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL207207 in molecule.smi (25/118). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL210487 in molecule.smi (26/118). Average speed: 0.14 s/mol.\n",
      "Processing CHEMBL210487 in molecule.smi (27/118). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL380470 in molecule.smi (28/118). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL380470 in molecule.smi (29/118). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL210612 in molecule.smi (31/118). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL210612 in molecule.smi (30/118). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL209667 in molecule.smi (32/118). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL209667 in molecule.smi (33/118). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL210097 in molecule.smi (34/118). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL210097 in molecule.smi (35/118). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL378674 in molecule.smi (36/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL378674 in molecule.smi (37/118). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL210216 in molecule.smi (38/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL210195 in molecule.smi (40/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL210216 in molecule.smi (39/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL210195 in molecule.smi (41/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL210437 in molecule.smi (42/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL210437 in molecule.smi (43/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL378677 in molecule.smi (44/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL378677 in molecule.smi (45/118). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL210972 in molecule.smi (46/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210972 in molecule.smi (47/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210145 in molecule.smi (48/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210145 in molecule.smi (49/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL377225 in molecule.smi (50/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL377225 in molecule.smi (51/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210823 in molecule.smi (52/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL210823 in molecule.smi (53/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL207381 in molecule.smi (54/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL207381 in molecule.smi (55/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210511 in molecule.smi (56/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210511 in molecule.smi (57/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210632 in molecule.smi (58/118). Average speed: 0.09 s/mol.\n",
      "Processing CHEMBL210632 in molecule.smi (59/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL210497 in molecule.smi (60/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL210497 in molecule.smi (61/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL208584 in molecule.smi (62/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL208584 in molecule.smi (63/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL208763 in molecule.smi (64/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL208763 in molecule.smi (65/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL209227 in molecule.smi (66/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL209227 in molecule.smi (67/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL210092 in molecule.smi (68/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL210092 in molecule.smi (69/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL377150 in molecule.smi (70/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL377150 in molecule.smi (71/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL212454 in molecule.smi (72/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL380403 in molecule.smi (73/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL212504 in molecule.smi (74/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL211969 in molecule.smi (75/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL384739 in molecule.smi (76/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL215732 in molecule.smi (77/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL212240 in molecule.smi (78/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL215397 in molecule.smi (80/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL377253 in molecule.smi (79/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL378342 in molecule.smi (81/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL212190 in molecule.smi (82/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL378700 in molecule.smi (83/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL212019 in molecule.smi (84/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL212399 in molecule.smi (85/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL215733 in molecule.smi (86/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL375130 in molecule.smi (87/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL214372 in molecule.smi (88/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL212218 in molecule.smi (89/118). Average speed: 0.08 s/mol.\n",
      "Processing CHEMBL222840 in molecule.smi (90/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL222769 in molecule.smi (91/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL222735 in molecule.smi (92/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL222628 in molecule.smi (93/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL222893 in molecule.smi (94/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL225515 in molecule.smi (95/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL222234 in molecule.smi (96/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL426898 in molecule.smi (97/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL187266 in molecule.smi (98/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL2146517 in molecule.smi (100/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL215254 in molecule.smi (99/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL187460 in molecule.smi (101/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL363535 in molecule.smi (102/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL227075 in molecule.smi (103/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL45830 in molecule.smi (104/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL215254 in molecule.smi (105/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL187460 in molecule.smi (106/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL45830 in molecule.smi (107/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL215254 in molecule.smi (108/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL187460 in molecule.smi (109/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL363535 in molecule.smi (110/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL45830 in molecule.smi (111/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL187266 in molecule.smi (112/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL215254 in molecule.smi (113/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL2146517 in molecule.smi (114/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL187460 in molecule.smi (115/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL363535 in molecule.smi (116/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL227075 in molecule.smi (117/118). Average speed: 0.07 s/mol.\n",
      "Processing CHEMBL45830 in molecule.smi (118/118). Average speed: 0.07 s/mol.\n",
      "Descriptor calculation completed in 7.817 secs . Average speed: 0.07 s/mol.\n"
     ]
    }
   ],
   "source": [
    "! bash padel.sh"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Preparing the X and Y data matrices"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_X = pd.read_csv('descriptors_output.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Name</th>\n",
       "      <th>PubchemFP0</th>\n",
       "      <th>PubchemFP1</th>\n",
       "      <th>PubchemFP2</th>\n",
       "      <th>PubchemFP3</th>\n",
       "      <th>PubchemFP4</th>\n",
       "      <th>PubchemFP5</th>\n",
       "      <th>PubchemFP6</th>\n",
       "      <th>PubchemFP7</th>\n",
       "      <th>PubchemFP8</th>\n",
       "      <th>...</th>\n",
       "      <th>PubchemFP871</th>\n",
       "      <th>PubchemFP872</th>\n",
       "      <th>PubchemFP873</th>\n",
       "      <th>PubchemFP874</th>\n",
       "      <th>PubchemFP875</th>\n",
       "      <th>PubchemFP876</th>\n",
       "      <th>PubchemFP877</th>\n",
       "      <th>PubchemFP878</th>\n",
       "      <th>PubchemFP879</th>\n",
       "      <th>PubchemFP880</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL209287</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL190743</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL185698</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL370923</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL188983</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    <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>113</th>\n",
       "      <td>CHEMBL187266</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114</th>\n",
       "      <td>CHEMBL215254</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115</th>\n",
       "      <td>CHEMBL227075</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>CHEMBL2146517</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117</th>\n",
       "      <td>CHEMBL363535</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>118 rows × 882 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              Name  PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  \\\n",
       "0     CHEMBL209287           1           1           0           0   \n",
       "1     CHEMBL190743           1           1           0           0   \n",
       "2     CHEMBL185698           1           1           0           0   \n",
       "3     CHEMBL370923           1           1           1           0   \n",
       "4     CHEMBL188983           1           1           0           0   \n",
       "..             ...         ...         ...         ...         ...   \n",
       "113   CHEMBL187266           1           1           1           0   \n",
       "114   CHEMBL215254           1           1           1           0   \n",
       "115   CHEMBL227075           1           1           0           0   \n",
       "116  CHEMBL2146517           1           1           1           0   \n",
       "117   CHEMBL363535           1           1           0           0   \n",
       "\n",
       "     PubchemFP4  PubchemFP5  PubchemFP6  PubchemFP7  PubchemFP8  ...  \\\n",
       "0             0           0           0           0           0  ...   \n",
       "1             0           0           0           0           0  ...   \n",
       "2             0           0           0           0           0  ...   \n",
       "3             0           0           0           0           0  ...   \n",
       "4             0           0           0           0           0  ...   \n",
       "..          ...         ...         ...         ...         ...  ...   \n",
       "113           0           0           0           0           0  ...   \n",
       "114           0           0           0           0           0  ...   \n",
       "115           0           0           0           0           0  ...   \n",
       "116           0           0           0           0           0  ...   \n",
       "117           0           0           0           0           0  ...   \n",
       "\n",
       "     PubchemFP871  PubchemFP872  PubchemFP873  PubchemFP874  PubchemFP875  \\\n",
       "0               0             0             0             0             0   \n",
       "1               0             0             0             0             0   \n",
       "2               0             0             0             0             0   \n",
       "3               0             0             0             0             0   \n",
       "4               0             0             0             0             0   \n",
       "..            ...           ...           ...           ...           ...   \n",
       "113             0             0             0             0             0   \n",
       "114             0             0             0             0             0   \n",
       "115             0             0             0             0             0   \n",
       "116             0             0             0             0             0   \n",
       "117             0             0             0             0             0   \n",
       "\n",
       "     PubchemFP876  PubchemFP877  PubchemFP878  PubchemFP879  PubchemFP880  \n",
       "0               0             0             0             0             0  \n",
       "1               0             0             0             0             0  \n",
       "2               0             0             0             0             0  \n",
       "3               0             0             0             0             0  \n",
       "4               0             0             0             0             0  \n",
       "..            ...           ...           ...           ...           ...  \n",
       "113             0             0             0             0             0  \n",
       "114             0             0             0             0             0  \n",
       "115             0             0             0             0             0  \n",
       "116             0             0             0             0             0  \n",
       "117             0             0             0             0             0  \n",
       "\n",
       "[118 rows x 882 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>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>113</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>118 rows × 881 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  PubchemFP5  \\\n",
       "0             1           1           0           0           0           0   \n",
       "1             1           1           0           0           0           0   \n",
       "2             1           1           0           0           0           0   \n",
       "3             1           1           1           0           0           0   \n",
       "4             1           1           0           0           0           0   \n",
       "..          ...         ...         ...         ...         ...         ...   \n",
       "113           1           1           1           0           0           0   \n",
       "114           1           1           1           0           0           0   \n",
       "115           1           1           0           0           0           0   \n",
       "116           1           1           1           0           0           0   \n",
       "117           1           1           0           0           0           0   \n",
       "\n",
       "     PubchemFP6  PubchemFP7  PubchemFP8  PubchemFP9  ...  PubchemFP871  \\\n",
       "0             0           0           0           1  ...             0   \n",
       "1             0           0           0           1  ...             0   \n",
       "2             0           0           0           1  ...             0   \n",
       "3             0           0           0           1  ...             0   \n",
       "4             0           0           0           1  ...             0   \n",
       "..          ...         ...         ...         ...  ...           ...   \n",
       "113           0           0           0           1  ...             0   \n",
       "114           0           0           0           1  ...             0   \n",
       "115           0           0           0           1  ...             0   \n",
       "116           0           0           0           1  ...             0   \n",
       "117           0           0           0           1  ...             0   \n",
       "\n",
       "     PubchemFP872  PubchemFP873  PubchemFP874  PubchemFP875  PubchemFP876  \\\n",
       "0               0             0             0             0             0   \n",
       "1               0             0             0             0             0   \n",
       "2               0             0             0             0             0   \n",
       "3               0             0             0             0             0   \n",
       "4               0             0             0             0             0   \n",
       "..            ...           ...           ...           ...           ...   \n",
       "113             0             0             0             0             0   \n",
       "114             0             0             0             0             0   \n",
       "115             0             0             0             0             0   \n",
       "116             0             0             0             0             0   \n",
       "117             0             0             0             0             0   \n",
       "\n",
       "     PubchemFP877  PubchemFP878  PubchemFP879  PubchemFP880  \n",
       "0               0             0             0             0  \n",
       "1               0             0             0             0  \n",
       "2               0             0             0             0  \n",
       "3               0             0             0             0  \n",
       "4               0             0             0             0  \n",
       "..            ...           ...           ...           ...  \n",
       "113             0             0             0             0  \n",
       "114             0             0             0             0  \n",
       "115             0             0             0             0  \n",
       "116             0             0             0             0  \n",
       "117             0             0             0             0  \n",
       "\n",
       "[118 rows x 881 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_X = df_X.drop(columns=['Name'])\n",
    "df_X"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Y variable\n",
    "#### Convert IC50 to pIC50"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0      4.869666\n",
       "1      4.882397\n",
       "2      6.008774\n",
       "3      6.022276\n",
       "4      4.950782\n",
       "         ...   \n",
       "113    4.974694\n",
       "114    4.995679\n",
       "115    4.939302\n",
       "116    4.970616\n",
       "117    4.102923\n",
       "Name: pIC50, Length: 118, dtype: float64"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_Y = df['pIC50']\n",
    "df_Y"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Combing X and Y variable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>PubchemFP0</th>\n",
       "      <th>PubchemFP1</th>\n",
       "      <th>PubchemFP2</th>\n",
       "      <th>PubchemFP3</th>\n",
       "      <th>PubchemFP4</th>\n",
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       "      <th>PubchemFP8</th>\n",
       "      <th>PubchemFP9</th>\n",
       "      <th>...</th>\n",
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       "      <th>PubchemFP873</th>\n",
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       "      <th>PubchemFP876</th>\n",
       "      <th>PubchemFP877</th>\n",
       "      <th>PubchemFP878</th>\n",
       "      <th>PubchemFP879</th>\n",
       "      <th>PubchemFP880</th>\n",
       "      <th>pIC50</th>\n",
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       "  </thead>\n",
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       "      <th>1</th>\n",
       "      <td>1</td>\n",
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       "      <td>4.882397</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
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       "      <td>0</td>\n",
       "      <td>6.008774</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
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       "    <tr>\n",
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       "      <td>1</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4.995679</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4.939302</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4.970616</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4.102923</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>118 rows × 882 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  PubchemFP5  \\\n",
       "0             1           1           0           0           0           0   \n",
       "1             1           1           0           0           0           0   \n",
       "2             1           1           0           0           0           0   \n",
       "3             1           1           1           0           0           0   \n",
       "4             1           1           0           0           0           0   \n",
       "..          ...         ...         ...         ...         ...         ...   \n",
       "113           1           1           1           0           0           0   \n",
       "114           1           1           1           0           0           0   \n",
       "115           1           1           0           0           0           0   \n",
       "116           1           1           1           0           0           0   \n",
       "117           1           1           0           0           0           0   \n",
       "\n",
       "     PubchemFP6  PubchemFP7  PubchemFP8  PubchemFP9  ...  PubchemFP872  \\\n",
       "0             0           0           0           1  ...             0   \n",
       "1             0           0           0           1  ...             0   \n",
       "2             0           0           0           1  ...             0   \n",
       "3             0           0           0           1  ...             0   \n",
       "4             0           0           0           1  ...             0   \n",
       "..          ...         ...         ...         ...  ...           ...   \n",
       "113           0           0           0           1  ...             0   \n",
       "114           0           0           0           1  ...             0   \n",
       "115           0           0           0           1  ...             0   \n",
       "116           0           0           0           1  ...             0   \n",
       "117           0           0           0           1  ...             0   \n",
       "\n",
       "     PubchemFP873  PubchemFP874  PubchemFP875  PubchemFP876  PubchemFP877  \\\n",
       "0               0             0             0             0             0   \n",
       "1               0             0             0             0             0   \n",
       "2               0             0             0             0             0   \n",
       "3               0             0             0             0             0   \n",
       "4               0             0             0             0             0   \n",
       "..            ...           ...           ...           ...           ...   \n",
       "113             0             0             0             0             0   \n",
       "114             0             0             0             0             0   \n",
       "115             0             0             0             0             0   \n",
       "116             0             0             0             0             0   \n",
       "117             0             0             0             0             0   \n",
       "\n",
       "     PubchemFP878  PubchemFP879  PubchemFP880     pIC50  \n",
       "0               0             0             0  4.869666  \n",
       "1               0             0             0  4.882397  \n",
       "2               0             0             0  6.008774  \n",
       "3               0             0             0  6.022276  \n",
       "4               0             0             0  4.950782  \n",
       "..            ...           ...           ...       ...  \n",
       "113             0             0             0  4.974694  \n",
       "114             0             0             0  4.995679  \n",
       "115             0             0             0  4.939302  \n",
       "116             0             0             0  4.970616  \n",
       "117             0             0             0  4.102923  \n",
       "\n",
       "[118 rows x 882 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset = pd.concat([df_X,df_Y], axis=1)\n",
    "dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset.to_csv('./data/06_bioactivity_data_3class_pubchem_fp.csv', index=False)"
   ]
  }
 ],
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