descriptor_calculation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/opt/homebrew/bin:/Users/wendiyang/miniconda3/bin:/Users/wendiyang/miniconda3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "\n",
    "# Set the PATH to include the directory where wget is installed\n",
    "os.environ['PATH'] = '/opt/homebrew/bin:' + os.environ['PATH']\n",
    "\n",
    "# Verify the PATH\n",
    "print(os.environ['PATH'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2024-06-29 17:30:57--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
      "Resolving github.com (github.com)... 198.18.0.45\n",
      "Connecting to github.com (github.com)|198.18.0.45|:443... connected.\n",
      "HTTP request sent, awaiting response... 302 Found\n",
      "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip [following]\n",
      "--2024-06-29 17:30:58--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.zip\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 198.18.0.56\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|198.18.0.56|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 25768637 (25M) [application/zip]\n",
      "Saving to: ‘padel.zip’\n",
      "\n",
      "padel.zip           100%[===================>]  24.57M  9.60MB/s    in 2.6s    \n",
      "\n",
      "2024-06-29 17:31:02 (9.60 MB/s) - ‘padel.zip’ saved [25768637/25768637]\n",
      "\n",
      "--2024-06-29 17:31:03--  https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh\n",
      "Resolving github.com (github.com)... 198.18.0.45\n",
      "Connecting to github.com (github.com)|198.18.0.45|:443... connected.\n",
      "HTTP request sent, awaiting response... 302 Found\n",
      "Location: https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh [following]\n",
      "--2024-06-29 17:31:03--  https://raw.githubusercontent.com/dataprofessor/bioinformatics/master/padel.sh\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 198.18.0.56\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|198.18.0.56|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 231 [text/plain]\n",
      "Saving to: ‘padel.sh.1’\n",
      "\n",
      "padel.sh.1          100%[===================>]     231  --.-KB/s    in 0s      \n",
      "\n",
      "2024-06-29 17:31:04 (5.80 MB/s) - ‘padel.sh.1’ saved [231/231]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.zip\n",
    "! wget https://github.com/dataprofessor/bioinformatics/raw/master/padel.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Archive:  padel.zip\n",
      "   creating: PaDEL-Descriptor/\n",
      "  inflating: __MACOSX/._PaDEL-Descriptor  \n",
      "  inflating: PaDEL-Descriptor/MACCSFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._MACCSFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/AtomPairs2DFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._AtomPairs2DFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/EStateFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._EStateFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/Fingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._Fingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/.DS_Store  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._.DS_Store  \n",
      "   creating: PaDEL-Descriptor/license/\n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._license  \n",
      "  inflating: PaDEL-Descriptor/KlekotaRothFingerprintCount.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._KlekotaRothFingerprintCount.xml  \n",
      "  inflating: PaDEL-Descriptor/config  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._config  \n",
      "  inflating: PaDEL-Descriptor/PubchemFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._PubchemFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/ExtendedFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._ExtendedFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/KlekotaRothFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._KlekotaRothFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/GraphOnlyFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._GraphOnlyFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/SubstructureFingerprinter.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._SubstructureFingerprinter.xml  \n",
      "  inflating: PaDEL-Descriptor/Descriptors.xls  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._Descriptors.xls  \n",
      "   creating: PaDEL-Descriptor/lib/\n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._lib  \n",
      "  inflating: PaDEL-Descriptor/PaDEL-Descriptor.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._PaDEL-Descriptor.jar  \n",
      "  inflating: PaDEL-Descriptor/SubstructureFingerprintCount.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._SubstructureFingerprintCount.xml  \n",
      "  inflating: PaDEL-Descriptor/AtomPairs2DFingerprintCount.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._AtomPairs2DFingerprintCount.xml  \n",
      "  inflating: PaDEL-Descriptor/descriptors.xml  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/._descriptors.xml  \n",
      "  inflating: PaDEL-Descriptor/license/lgpl-2.1.txt  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/license/._lgpl-2.1.txt  \n",
      "  inflating: PaDEL-Descriptor/license/LICENSE.txt  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/license/._LICENSE.txt  \n",
      "  inflating: PaDEL-Descriptor/license/README - CDK  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/license/._README - CDK  \n",
      "  inflating: PaDEL-Descriptor/license/lgpl.license  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/license/._lgpl.license  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(6).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(6).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(4).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(4).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/xom-1.1(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._xom-1.1(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/swing-worker-1.1.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._swing-worker-1.1.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(5).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(5).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/appframework-1.0.3.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._appframework-1.0.3.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(7).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(7).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/vecmath1.2-1.14.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._vecmath1.2-1.14.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(6).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(6).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(6).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(6).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(4).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(4).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-base-2.4.7-SNAPSHOT.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(8).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(8).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(4).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(4).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/xom-1.1.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._xom-1.1.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(5).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(5).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(7).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(7).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(6).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(6).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(4).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(4).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/l2fprod-common-all(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._l2fprod-common-all(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/l2fprod-common-all.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._l2fprod-common-all.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(5).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(5).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(7).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(7).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Descriptor.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Descriptor.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(4).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(4).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/cdk-1.4.15.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._cdk-1.4.15.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(5).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(5).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-core-2.4.7-SNAPSHOT(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(8).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(8).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jgrapht-0.6.0(6).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jgrapht-0.6.0(6).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(2).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(2).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/jama(3).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._jama(3).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/commons-cli-1.2(1).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._commons-cli-1.2(1).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/guava-17.0.jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._guava-17.0.jar  \n",
      "  inflating: PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(4).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._ambit2-smarts-2.4.7-SNAPSHOT(4).jar  \n",
      "  inflating: PaDEL-Descriptor/lib/libPaDEL-Jobs(5).jar  \n",
      "  inflating: __MACOSX/PaDEL-Descriptor/lib/._libPaDEL-Jobs(5).jar  \n"
     ]
    }
   ],
   "source": [
    "! unzip padel.zip"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mol_cid</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>bioactivity_class</th>\n",
       "      <th>MW</th>\n",
       "      <th>LogP</th>\n",
       "      <th>NumHDonors</th>\n",
       "      <th>NumHAcceptors</th>\n",
       "      <th>pAC50</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL110094</td>\n",
       "      <td>CN(C)CCC=C1c2ccccc2C(C)(C)c2ccccc21</td>\n",
       "      <td>inactive</td>\n",
       "      <td>291.438</td>\n",
       "      <td>4.70930</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL1435</td>\n",
       "      <td>Cc1nnc(SCC2=C(C(=O)O)N3C(=O)[C@@H](NC(=O)Cn4cn...</td>\n",
       "      <td>inactive</td>\n",
       "      <td>454.519</td>\n",
       "      <td>-0.63608</td>\n",
       "      <td>2.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>3.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL428</td>\n",
       "      <td>N[C@@H]1[C@H]2CN(c3nc4c(cc3F)c(=O)c(C(=O)O)cn4...</td>\n",
       "      <td>inactive</td>\n",
       "      <td>416.359</td>\n",
       "      <td>1.89450</td>\n",
       "      <td>2.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL671</td>\n",
       "      <td>S=P(N1CC1)(N1CC1)N1CC1</td>\n",
       "      <td>inactive</td>\n",
       "      <td>189.224</td>\n",
       "      <td>0.15770</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL526</td>\n",
       "      <td>CC(C)c1cccc(C(C)C)c1O</td>\n",
       "      <td>inactive</td>\n",
       "      <td>178.275</td>\n",
       "      <td>3.63900</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>4.522879</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>74</th>\n",
       "      <td>CHEMBL1407943</td>\n",
       "      <td>Clc1ccc(Cn2c(CN3CCCC3)nc3ccccc32)cc1</td>\n",
       "      <td>inactive</td>\n",
       "      <td>325.843</td>\n",
       "      <td>4.33380</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75</th>\n",
       "      <td>CHEMBL1371770</td>\n",
       "      <td>c1cnc(N2CCN(Cc3ccc4c(c3)OCO4)CC2)nc1</td>\n",
       "      <td>inactive</td>\n",
       "      <td>298.346</td>\n",
       "      <td>1.52750</td>\n",
       "      <td>0.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>CHEMBL75880</td>\n",
       "      <td>C1CCC(C(CC2CCCCN2)C2CCCCC2)CC1</td>\n",
       "      <td>inactive</td>\n",
       "      <td>277.496</td>\n",
       "      <td>5.29540</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>CHEMBL810</td>\n",
       "      <td>Cn1nnc2c(C(N)=O)ncn2c1=O</td>\n",
       "      <td>inactive</td>\n",
       "      <td>194.154</td>\n",
       "      <td>-2.07810</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>78</th>\n",
       "      <td>CHEMBL1393</td>\n",
       "      <td>CC(=O)S[C@@H]1CC2=CC(=O)CC[C@]2(C)[C@H]2CC[C@@...</td>\n",
       "      <td>inactive</td>\n",
       "      <td>416.583</td>\n",
       "      <td>4.85230</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>4.522879</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>79 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          mol_cid                                   canonical_smiles  \\\n",
       "0    CHEMBL110094                CN(C)CCC=C1c2ccccc2C(C)(C)c2ccccc21   \n",
       "1      CHEMBL1435  Cc1nnc(SCC2=C(C(=O)O)N3C(=O)[C@@H](NC(=O)Cn4cn...   \n",
       "2       CHEMBL428  N[C@@H]1[C@H]2CN(c3nc4c(cc3F)c(=O)c(C(=O)O)cn4...   \n",
       "3       CHEMBL671                             S=P(N1CC1)(N1CC1)N1CC1   \n",
       "4       CHEMBL526                              CC(C)c1cccc(C(C)C)c1O   \n",
       "..            ...                                                ...   \n",
       "74  CHEMBL1407943               Clc1ccc(Cn2c(CN3CCCC3)nc3ccccc32)cc1   \n",
       "75  CHEMBL1371770               c1cnc(N2CCN(Cc3ccc4c(c3)OCO4)CC2)nc1   \n",
       "76    CHEMBL75880                     C1CCC(C(CC2CCCCN2)C2CCCCC2)CC1   \n",
       "77      CHEMBL810                           Cn1nnc2c(C(N)=O)ncn2c1=O   \n",
       "78     CHEMBL1393  CC(=O)S[C@@H]1CC2=CC(=O)CC[C@]2(C)[C@H]2CC[C@@...   \n",
       "\n",
       "   bioactivity_class       MW     LogP  NumHDonors  NumHAcceptors     pAC50  \n",
       "0           inactive  291.438  4.70930         0.0            1.0  4.522879  \n",
       "1           inactive  454.519 -0.63608         2.0           12.0  3.522879  \n",
       "2           inactive  416.359  1.89450         2.0            6.0  4.522879  \n",
       "3           inactive  189.224  0.15770         0.0            1.0  4.522879  \n",
       "4           inactive  178.275  3.63900         1.0            1.0  4.522879  \n",
       "..               ...      ...      ...         ...            ...       ...  \n",
       "74          inactive  325.843  4.33380         0.0            3.0  4.522879  \n",
       "75          inactive  298.346  1.52750         0.0            6.0  4.522879  \n",
       "76          inactive  277.496  5.29540         1.0            1.0  4.522879  \n",
       "77          inactive  194.154 -2.07810         1.0            7.0  4.522879  \n",
       "78          inactive  416.583  4.85230         0.0            5.0  4.522879  \n",
       "\n",
       "[79 rows x 8 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3 = pd.read_csv('bioactivity_data_pAC50.csv')\n",
    "     \n",
    "df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "selection = ['canonical_smiles','mol_cid']\n",
    "df3_selection = df3[selection]\n",
    "df3_selection.to_csv('molecule.smi', sep='\\t', index=False, header=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CN(C)CCC=C1c2ccccc2C(C)(C)c2ccccc21\tCHEMBL110094\n",
      "Cc1nnc(SCC2=C(C(=O)O)N3C(=O)[C@@H](NC(=O)Cn4cnnn4)[C@H]3SC2)s1\tCHEMBL1435\n",
      "N[C@@H]1[C@H]2CN(c3nc4c(cc3F)c(=O)c(C(=O)O)cn4-c3ccc(F)cc3F)C[C@@H]12\tCHEMBL428\n",
      "S=P(N1CC1)(N1CC1)N1CC1\tCHEMBL671\n",
      "CC(C)c1cccc(C(C)C)c1O\tCHEMBL526\n"
     ]
    }
   ],
   "source": [
    "! cat molecule.smi | head -5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      79\n"
     ]
    }
   ],
   "source": [
    "! cat molecule.smi | wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "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": "markdown",
   "metadata": {},
   "source": [
    "This right here runs the script, and saves the output into a file descriptors_output.csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processing CHEMBL110094 in molecule.smi (1/79). \n",
      "Processing CHEMBL1435 in molecule.smi (2/79). \n",
      "Processing CHEMBL428 in molecule.smi (3/79). \n",
      "Processing CHEMBL671 in molecule.smi (4/79). \n",
      "Processing CHEMBL526 in molecule.smi (5/79). \n",
      "Processing CHEMBL3353410 in molecule.smi (6/79). \n",
      "Processing CHEMBL2110816 in molecule.smi (7/79). \n",
      "Processing CHEMBL146095 in molecule.smi (8/79). \n",
      "Processing CHEMBL474579 in molecule.smi (10/79). Average speed: 1.36 s/mol.\n",
      "Processing CHEMBL1303 in molecule.smi (9/79). Average speed: 2.70 s/mol.\n",
      "Processing CHEMBL16 in molecule.smi (11/79). Average speed: 0.93 s/mol.\n",
      "Processing CHEMBL1112 in molecule.smi (12/79). Average speed: 0.74 s/mol.\n",
      "Processing CHEMBL3039502 in molecule.smi (13/79). Average speed: 0.60 s/mol.\n",
      "Processing CHEMBL41632 in molecule.smi (16/79). Average speed: 0.51 s/mol.\n",
      "Processing CHEMBL92401 in molecule.smi (14/79). Average speed: 0.51 s/mol.\n",
      "Processing CHEMBL85 in molecule.smi (15/79). Average speed: 0.51 s/mol.\n",
      "Processing CHEMBL2147777 in molecule.smi (19/79). Average speed: 0.33 s/mol.\n",
      "Processing CHEMBL3545185 in molecule.smi (18/79). Average speed: 0.36 s/mol.\n",
      "Processing CHEMBL1101 in molecule.smi (17/79). Average speed: 0.36 s/mol.\n",
      "Processing CHEMBL2107333 in molecule.smi (20/79). Average speed: 0.30 s/mol.\n",
      "Processing CHEMBL1171837 in molecule.smi (21/79). Average speed: 0.28 s/mol.\n",
      "Processing CHEMBL360328 in molecule.smi (23/79). Average speed: 0.28 s/mol.\n",
      "Processing CHEMBL51934 in molecule.smi (22/79). Average speed: 0.28 s/mol.\n",
      "Processing CHEMBL158 in molecule.smi (24/79). Average speed: 0.23 s/mol.\n",
      "Processing CHEMBL1214185 in molecule.smi (25/79). Average speed: 0.22 s/mol.\n",
      "Processing CHEMBL532 in molecule.smi (26/79). Average speed: 0.22 s/mol.\n",
      "Processing CHEMBL190461 in molecule.smi (27/79). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL341812 in molecule.smi (28/79). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL2106919 in molecule.smi (30/79). Average speed: 0.20 s/mol.\n",
      "Processing CHEMBL222559 in molecule.smi (29/79). Average speed: 0.21 s/mol.\n",
      "Processing CHEMBL36506 in molecule.smi (31/79). Average speed: 0.19 s/mol.\n",
      "Processing CHEMBL601719 in molecule.smi (32/79). Average speed: 0.18 s/mol.\n",
      "Processing CHEMBL148 in molecule.smi (33/79). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL339323 in molecule.smi (34/79). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL127 in molecule.smi (35/79). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL940 in molecule.smi (37/79). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL491571 in molecule.smi (36/79). Average speed: 0.17 s/mol.\n",
      "Processing CHEMBL605846 in molecule.smi (38/79). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL2110602 in molecule.smi (39/79). Average speed: 0.16 s/mol.\n",
      "Processing CHEMBL1201203 in molecule.smi (40/79). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL269732 in molecule.smi (41/79). Average speed: 0.15 s/mol.\n",
      "Processing CHEMBL111 in molecule.smi (42/79). Average speed: 0.14 s/mol.\n",
      "Processing CHEMBL503160 in molecule.smi (43/79). Average speed: 0.14 s/mol.\n",
      "Processing CHEMBL1237021 in molecule.smi (44/79). Average speed: 0.14 s/mol.\n",
      "Processing CHEMBL589 in molecule.smi (45/79). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL701 in molecule.smi (46/79). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL1396 in molecule.smi (47/79). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL186 in molecule.smi (48/79). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL1095097 in molecule.smi (49/79). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL3414621 in molecule.smi (50/79). Average speed: 0.13 s/mol.\n",
      "Processing CHEMBL1289926 in molecule.smi (51/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL1336 in molecule.smi (52/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL285802 in molecule.smi (53/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL416956 in molecule.smi (54/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL3187365 in molecule.smi (55/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL654 in molecule.smi (56/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL531 in molecule.smi (57/79). Average speed: 0.12 s/mol.\n",
      "Processing CHEMBL107 in molecule.smi (58/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL117785 in molecule.smi (59/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL24828 in molecule.smi (60/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL939 in molecule.smi (61/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL3187723 in molecule.smi (62/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL1614658 in molecule.smi (63/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL514800 in molecule.smi (64/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL404108 in molecule.smi (65/79). Average speed: 0.11 s/mol.\n",
      "Processing CHEMBL1241951 in molecule.smi (66/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL493 in molecule.smi (67/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1059 in molecule.smi (68/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL222645 in molecule.smi (69/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL54 in molecule.smi (70/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1454 in molecule.smi (71/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1551 in molecule.smi (72/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL240597 in molecule.smi (73/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1421 in molecule.smi (74/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1407943 in molecule.smi (75/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1371770 in molecule.smi (76/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL75880 in molecule.smi (77/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL810 in molecule.smi (78/79). Average speed: 0.10 s/mol.\n",
      "Processing CHEMBL1393 in molecule.smi (79/79). Average speed: 0.09 s/mol.\n",
      "Descriptor calculation completed in 6.982 secs . Average speed: 0.09 s/mol.\n"
     ]
    }
   ],
   "source": [
    "! bash padel.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>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>CHEMBL671</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",
       "      <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>CHEMBL1435</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",
       "      <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>2</th>\n",
       "      <td>CHEMBL526</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>3</th>\n",
       "      <td>CHEMBL428</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",
       "      <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>4</th>\n",
       "      <td>CHEMBL146095</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>...</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>74</th>\n",
       "      <td>CHEMBL810</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>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>75</th>\n",
       "      <td>CHEMBL1551</td>\n",
       "      <td>1</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>...</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>76</th>\n",
       "      <td>CHEMBL75880</td>\n",
       "      <td>1</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>...</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>77</th>\n",
       "      <td>CHEMBL240597</td>\n",
       "      <td>1</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>...</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>78</th>\n",
       "      <td>CHEMBL1393</td>\n",
       "      <td>1</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>...</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>79 rows × 882 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Name  PubchemFP0  PubchemFP1  PubchemFP2  PubchemFP3  PubchemFP4  \\\n",
       "0      CHEMBL671           1           1           0           0           0   \n",
       "1     CHEMBL1435           1           1           0           0           0   \n",
       "2      CHEMBL526           1           1           1           0           0   \n",
       "3      CHEMBL428           1           1           0           0           0   \n",
       "4   CHEMBL146095           1           1           1           0           0   \n",
       "..           ...         ...         ...         ...         ...         ...   \n",
       "74     CHEMBL810           1           0           0           0           0   \n",
       "75    CHEMBL1551           1           1           1           1           0   \n",
       "76   CHEMBL75880           1           1           1           1           0   \n",
       "77  CHEMBL240597           1           1           1           1           0   \n",
       "78    CHEMBL1393           1           1           1           1           0   \n",
       "\n",
       "    PubchemFP5  PubchemFP6  PubchemFP7  PubchemFP8  ...  PubchemFP871  \\\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",
       "74           0           0           0           0  ...             0   \n",
       "75           0           0           0           0  ...             0   \n",
       "76           0           0           0           0  ...             0   \n",
       "77           0           0           0           0  ...             0   \n",
       "78           0           0           0           0  ...             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",
       "74             0             0             0             0             0   \n",
       "75             0             0             0             0             0   \n",
       "76             0             0             0             0             0   \n",
       "77             0             0             0             0             0   \n",
       "78             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",
       "74             0             0             0             0  \n",
       "75             0             0             0             0  \n",
       "76             0             0             0             0  \n",
       "77             0             0             0             0  \n",
       "78             0             0             0             0  \n",
       "\n",
       "[79 rows x 882 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3_X = pd.read_csv(\"descriptors_output.csv\")\n",
    "\n",
    "df3_X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>PubchemFP0</th>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>79 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           1           0           0           0   \n",
       "3            1           1           0           0           0           0   \n",
       "4            1           1           1           0           0           0   \n",
       "..         ...         ...         ...         ...         ...         ...   \n",
       "74           1           0           0           0           0           0   \n",
       "75           1           1           1           1           0           0   \n",
       "76           1           1           1           1           0           0   \n",
       "77           1           1           1           1           0           0   \n",
       "78           1           1           1           1           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",
       "74           0           0           0           1  ...             0   \n",
       "75           0           0           0           1  ...             0   \n",
       "76           0           0           0           1  ...             0   \n",
       "77           0           0           0           1  ...             0   \n",
       "78           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",
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       "75             0             0             0             0             0   \n",
       "76             0             0             0             0             0   \n",
       "77             0             0             0             0             0   \n",
       "78             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",
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       "..           ...           ...           ...           ...  \n",
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       "\n",
       "[79 rows x 881 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3_X = df3_X.drop(columns=[\"Name\"])\n",
    "\n",
    "df3_X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     4.522879\n",
       "1     3.522879\n",
       "2     4.522879\n",
       "3     4.522879\n",
       "4     4.522879\n",
       "        ...   \n",
       "74    4.522879\n",
       "75    4.522879\n",
       "76    4.522879\n",
       "77    4.522879\n",
       "78    4.522879\n",
       "Name: pAC50, Length: 79, dtype: float64"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df3_Y = df3['pAC50']\n",
    "df3_Y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>PubchemFP0</th>\n",
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       "    <tr>\n",
       "      <th>76</th>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>78</th>\n",
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       "      <td>1</td>\n",
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       "      <td>4.522879</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>79 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           1           0           0           0   \n",
       "3            1           1           0           0           0           0   \n",
       "4            1           1           1           0           0           0   \n",
       "..         ...         ...         ...         ...         ...         ...   \n",
       "74           1           0           0           0           0           0   \n",
       "75           1           1           1           1           0           0   \n",
       "76           1           1           1           1           0           0   \n",
       "77           1           1           1           1           0           0   \n",
       "78           1           1           1           1           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",
       "74           0           0           0           1  ...             0   \n",
       "75           0           0           0           1  ...             0   \n",
       "76           0           0           0           1  ...             0   \n",
       "77           0           0           0           1  ...             0   \n",
       "78           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",
       "74             0             0             0             0             0   \n",
       "75             0             0             0             0             0   \n",
       "76             0             0             0             0             0   \n",
       "77             0             0             0             0             0   \n",
       "78             0             0             0             0             0   \n",
       "\n",
       "    PubchemFP878  PubchemFP879  PubchemFP880     pAC50  \n",
       "0              0             0             0  4.522879  \n",
       "1              0             0             0  3.522879  \n",
       "2              0             0             0  4.522879  \n",
       "3              0             0             0  4.522879  \n",
       "4              0             0             0  4.522879  \n",
       "..           ...           ...           ...       ...  \n",
       "74             0             0             0  4.522879  \n",
       "75             0             0             0  4.522879  \n",
       "76             0             0             0  4.522879  \n",
       "77             0             0             0  4.522879  \n",
       "78             0             0             0  4.522879  \n",
       "\n",
       "[79 rows x 882 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset3 = pd.concat([df3_X,df3_Y], axis=1)\n",
    "dataset3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset3.to_csv('ERBB_bioactivity_data_pubchem.csv', index=False)"
   ]
  }
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