{

"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "CDD-ML-Part-1-bioactivity-data.ipynb",
"provenance": [],
"collapsed_sections": []
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "wSFbIMb87cHu",
"colab_type": "text"
},
"source": [
"# **Computational Drug Discovery [Part 1] Download Bioactivity Data**\n",
"\n",
"Chanin Nantasenamat\n",
"\n",
"[*'Data Professor' YouTube channel*](http://youtube.com/dataprofessor)\n",
"\n",
"In this Jupyter notebook, we will be building a real-life **data science
project** that you can include in your **data science portfolio**. Particularly, we
will be building a machine learning model using the ChEMBL bioactivity data.\n",
"\n",
"---"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "3iQiERxumDor",
"colab_type": "text"
},
"source": [
"## **ChEMBL Database**\n",
"\n",
"The [*ChEMBL Database*](https://www.ebi.ac.uk/chembl/) is a database that
contains curated bioactivity data of more than 2 million compounds. It is compiled
from more than 76,000 documents, 1.2 million assays and the data spans 13,000
targets and 1,800 cells and 33,000 indications.\n",
"[Data as of March 25, 2020; ChEMBL version 26]."
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "iryGAwAIQ4yf",
"colab_type": "text"
},
"source": [
"## **Installing libraries**"
 ]
},
{
"cell_type": "markdown",
"metadata": {
"id": "toGT1U_B7F2i",
"colab_type": "text"
},
"source": [
"Install the ChEMBL web service package so that we can retrieve bioactivity
data from the ChEMBL Database."
]
},
{
"cell_type": "code",
"metadata": {
"id": "cJGExHQBfLh7",
"colab_type": "code",
"outputId": "783c9cb5-c5d4-4545-a9d3-6c2a2f2b0e53",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 349
}
},
"source": [
"! pip install chembl_webresource_client"
],
"execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [
"Collecting chembl_webresource_client\n",
"\u001b[?25l Downloading
https://files.pythonhosted.org/packages/74/c4/6526156c7e2f164a0fc061aae20d383f0b6b1
e79957510a64382e676e2dc/chembl-webresource-client-0.10.1.tar.gz (53kB)\n",
"\r\u001b[K |██████▏ | 10kB 18.6MB/s eta
0:00:01\r\u001b[K |████████████▎ | 20kB 6.7MB/s eta 0:00:01\
r\u001b[K |██████████████████▍ | 30kB 7.8MB/s eta 0:00:01\r\u001b[K
|████████████████████████▌ | 40kB 8.4MB/s eta 0:00:01\r\u001b[K |
██████████████████████████████▊ | 51kB 7.2MB/s eta 0:00:01\r\u001b[K |
████████████████████████████████| 61kB 4.6MB/s \n",
"\u001b[?25hRequirement already satisfied: urllib3 in
/usr/local/lib/python3.6/dist-packages (from chembl_webresource_client) (1.24.3)\
n",
"Requirement already satisfied: requests>=2.18.4 in
/usr/local/lib/python3.6/dist-packages (from chembl_webresource_client) (2.21.0)\
n",
"Collecting requests-cache>=0.4.7\n",
" Downloading
https://files.pythonhosted.org/packages/7f/55/9b1c40eb83c16d8fc79c5f6c2ffade04208b0
80670fbfc35e0a5effb5a92/requests_cache-0.5.2-py2.py3-none-any.whl\n",
"Requirement already satisfied: easydict in
/usr/local/lib/python3.6/dist-packages (from chembl_webresource_client) (1.9)\n",
"Requirement already satisfied: chardet<3.1.0,>=3.0.2 in
/usr/local/lib/python3.6/dist-packages (from requests>=2.18.4-
>chembl_webresource_client) (3.0.4)\n",
"Requirement already satisfied: certifi>=2017.4.17 in
/usr/local/lib/python3.6/dist-packages (from requests>=2.18.4-
>chembl_webresource_client) (2020.4.5.1)\n",
"Requirement already satisfied: idna<2.9,>=2.5 in
/usr/local/lib/python3.6/dist-packages (from requests>=2.18.4-
>chembl_webresource_client) (2.8)\n",
"Building wheels for collected packages: chembl-webresource-client\n",
" Building wheel for chembl-webresource-client (setup.py) ... \u001b[?
25l\u001b[?25hdone\n",
" Created wheel for chembl-webresource-client:
filename=chembl_webresource_client-0.10.1-cp36-none-any.whl size=57153
sha256=c1e2f3e1514ff0b430f04c4dfe2d1bf8fc00e424b9883d7caae9ac0f6d94c36a\n",
" Stored in directory:
/root/.cache/pip/wheels/81/8e/3b/4ec9940a01673307821600bfac28b17971caf84ff2b64653cb
\n",
"Successfully built chembl-webresource-client\n",
"Installing collected packages: requests-cache, chembl-webresource-
client\n",
"Successfully installed chembl-webresource-client-0.10.1 requests-
cache-0.5.2\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "J0kJjL8gb5nX",
"colab_type": "text"
},
"source": [
"## **Importing libraries**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "RXoCvMPPfNrv",
"colab_type": "code",
"colab": {}
},
"source": [
"# Import necessary libraries\n",
"import pandas as pd\n",
"from chembl_webresource_client.new_client import new_client"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "1FgUai1bfigC",
"colab_type": "text"
},
"source": [
"## **Search for Target protein**"
]
},
{
 "cell_type": "markdown",
"metadata": {
"id": "7lBsDrD0gAqH",
"colab_type": "text"
},
"source": [
"### **Target search for coronavirus**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "Vxtp79so4ZjF",
"colab_type": "code",
"outputId": "e90dde45-1c0d-4fd9-f693-cb6e6032e2cd",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 145
}
},
"source": [
"# Target search for coronavirus\n",
"target = new_client.target\n",
"target_query = target.search('aromatase')\n",
"targets = pd.DataFrame.from_dict(target_query)\n",
"targets"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"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>cross_references</th>\n",
" <th>organism</th>\n",
" <th>pref_name</th>\n",
" <th>score</th>\n",
" <th>species_group_flag</th>\n",
" <th>target_chembl_id</th>\n",
" <th>target_components</th>\n",
" <th>target_type</th>\n",
 " <th>tax_id</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>[{'xref_id': 'P11511', 'xref_name': None, 'xre...</td>\n",
" <td>Homo sapiens</td>\n",
" <td>Cytochrome P450 19A1</td>\n",
" <td>19.0</td>\n",
" <td>False</td>\n",
" <td>CHEMBL1978</td>\n",
" <td>[{'accession': 'P11511', 'component_descriptio...</td>\n",
" <td>SINGLE PROTEIN</td>\n",
" <td>9606</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>[{'xref_id': 'P22443', 'xref_name': None, 'xre...</td>\n",
" <td>Rattus norvegicus</td>\n",
" <td>Cytochrome P450 19A1</td>\n",
" <td>19.0</td>\n",
" <td>False</td>\n",
" <td>CHEMBL3859</td>\n",
" <td>[{'accession': 'P22443', 'component_descriptio...</td>\n",
" <td>SINGLE PROTEIN</td>\n",
" <td>10116</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" cross_references ... tax_id\n",
"0 [{'xref_id': 'P11511', 'xref_name': None, 'xre... ... 9606\n",
"1 [{'xref_id': 'P22443', 'xref_name': None, 'xre... ... 10116\n",
"\n",
"[2 rows x 9 columns]"
]
},
"metadata": {
"tags": []
},
"execution_count": 42
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "Y5OPfEALjAfZ",
"colab_type": "text"
},
"source": [
"### **Select and retrieve bioactivity data for *SARS coronavirus 3C-like
proteinase* (fifth entry)**"
]
},
{
 "cell_type": "markdown",
"metadata": {
"id": "gSQ3aroOgML7",
"colab_type": "text"
},
"source": [
"We will assign the fifth entry (which corresponds to the target protein,
*coronavirus 3C-like proteinase*) to the ***selected_target*** variable "
]
},
{
"cell_type": "code",
"metadata": {
"id": "StrcHMVLha7u",
"colab_type": "code",
"outputId": "a558535b-c66a-42ce-8604-3cf34dbff90b",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 35
}
},
"source": [
"selected_target = targets.target_chembl_id[4]\n",
"selected_target"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"'CHEMBL3927'"
]
},
"metadata": {
"tags": []
},
"execution_count": 4
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "GWd2DRalgjzB",
"colab_type": "text"
},
"source": [
"Here, we will retrieve only bioactivity data for *coronavirus 3C-like
proteinase* (CHEMBL3927) that are reported as IC$_{50}$ values in nM (nanomolar)
unit."
]
},
{
"cell_type": "code",
"metadata": {
"id": "LeFbV_CsSP8D",
"colab_type": "code",
"colab": {}
 },
"source": [
"activity = new_client.activity\n",
"res =
activity.filter(target_chembl_id=selected_target).filter(standard_type=\"IC50\")"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "RC4T-NEmSWV-",
"colab_type": "code",
"colab": {}
},
"source": [
"df = pd.DataFrame.from_dict(res)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "s9iUAXFdSkoM",
"colab_type": "code",
"outputId": "c9b681cc-97ab-40fb-a735-5e2b39612f8c",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 265
}
},
"source": [
"df.head(3)"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"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>activity_comment</th>\n",
" <th>activity_id</th>\n",
" <th>activity_properties</th>\n",
" <th>assay_chembl_id</th>\n",
" <th>assay_description</th>\n",
" <th>assay_type</th>\n",
" <th>bao_endpoint</th>\n",
" <th>bao_format</th>\n",
" <th>bao_label</th>\n",
" <th>canonical_smiles</th>\n",
" <th>data_validity_comment</th>\n",
" <th>data_validity_description</th>\n",
" <th>document_chembl_id</th>\n",
" <th>document_journal</th>\n",
" <th>document_year</th>\n",
" <th>ligand_efficiency</th>\n",
" <th>molecule_chembl_id</th>\n",
" <th>molecule_pref_name</th>\n",
" <th>parent_molecule_chembl_id</th>\n",
" <th>pchembl_value</th>\n",
" <th>potential_duplicate</th>\n",
" <th>qudt_units</th>\n",
" <th>record_id</th>\n",
" <th>relation</th>\n",
" <th>src_id</th>\n",
" <th>standard_flag</th>\n",
" <th>standard_relation</th>\n",
" <th>standard_text_value</th>\n",
" <th>standard_type</th>\n",
" <th>standard_units</th>\n",
" <th>standard_upper_value</th>\n",
" <th>standard_value</th>\n",
" <th>target_chembl_id</th>\n",
" <th>target_organism</th>\n",
" <th>target_pref_name</th>\n",
" <th>target_tax_id</th>\n",
" <th>text_value</th>\n",
" <th>toid</th>\n",
" <th>type</th>\n",
" <th>units</th>\n",
" <th>uo_units</th>\n",
" <th>upper_value</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>None</td>\n",
" <td>1480935</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL829584</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '18.28', 'le': '0.33', 'lle': '3.25', ...</td>\n",
" <td>CHEMBL187579</td>\n",
" <td>None</td>\n",
" <td>CHEMBL187579</td>\n",
" <td>5.14</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>384103</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>7200.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>7.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>None</td>\n",
" <td>1480936</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL829584</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '12.10', 'le': '0.33', 'lle': '1.22', ...</td>\n",
" <td>CHEMBL188487</td>\n",
" <td>None</td>\n",
" <td>CHEMBL188487</td>\n",
" <td>5.03</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>383984</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>9400.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>9.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>None</td>\n",
" <td>1481061</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL830868</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '11.56', 'le': '0.29', 'lle': '2.21', ...</td>\n",
" <td>CHEMBL185698</td>\n",
" <td>None</td>\n",
" <td>CHEMBL185698</td>\n",
" <td>4.87</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>384106</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>13500.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
 " <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>13.5</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" activity_comment activity_id ... upper_value value\n",
"0 None 1480935 ... None 7.2\n",
"1 None 1480936 ... None 9.4\n",
"2 None 1481061 ... None 13.5\n",
"\n",
"[3 rows x 43 columns]"
]
},
"metadata": {
"tags": []
},
"execution_count": 8
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "oNtBv36dYhxy",
"colab_type": "code",
"outputId": "db6a7832-55eb-484c-b56c-98cdcd5944dd",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 35
}
},
"source": [
"df.standard_type.unique()"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"array(['IC50'], dtype=object)"
]
},
"metadata": {
"tags": []
},
"execution_count": 11
}
]
},
{
 "cell_type": "markdown",
"metadata": {
"id": "fQ78N26Fg15T",
"colab_type": "text"
},
"source": [
"Finally we will save the resulting bioactivity data to a CSV file
**bioactivity_data.csv**."
]
},
{
"cell_type": "code",
"metadata": {
"id": "ZvUUEIVxTOH1",
"colab_type": "code",
"colab": {}
},
"source": [
"df.to_csv('bioactivity_data.csv', index=False)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "BOrSrTGjOWU7",
"colab_type": "text"
},
"source": [
"## **Copying files to Google Drive**"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "PRputWaI7ZW7",
"colab_type": "text"
},
"source": [
"Firstly, we need to mount the Google Drive into Colab so that we can have
access to our Google adrive from within Colab."
]
},
{
"cell_type": "code",
"metadata": {
"id": "6RBX658q65A5",
"colab_type": "code",
"outputId": "04a014cd-9f34-4a8f-e45f-50b380d9d41b",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 124
}
},
"source": [
"from google.colab import drive\n",
"drive.mount('/content/gdrive/', force_remount=True)\n"
],
 "execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [
"Go to this URL in a browser:
https://accounts.google.com/o/oauth2/auth?client_id=947318989803-
6bn6qk8qdgf4n4g3pfee6491hc0brc4i.apps.googleusercontent.com&redirect_uri=urn%3aietf
%3awg%3aoauth%3a2.0%3aoob&response_type=code&scope=email%20https%3a%2f
%2fwww.googleapis.com%2fauth%2fdocs.test%20https%3a%2f%2fptop.only.wip.la%3a443%2fhttps%2fwww.googleapis.com%2fauth
%2fdrive%20https%3a%2f%2fptop.only.wip.la%3a443%2fhttps%2fwww.googleapis.com%2fauth%2fdrive.photos.readonly%20https
%3a%2f%2fwww.googleapis.com%2fauth%2fpeopleapi.readonly\n",
"\n",
"Enter your authorization code:\n",
"··········\n",
"Mounted at /content/gdrive/\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "CMlY0xudN1mL",
"colab_type": "text"
},
"source": [
"Next, we create a **data** folder in our **Colab Notebooks** folder on
Google Drive."
]
},
{
"cell_type": "code",
"metadata": {
"id": "tew-UtUWIS__",
"colab_type": "code",
"colab": {}
},
"source": [
"! mkdir \"/content/gdrive/My Drive/Colab Notebooks/data2\""
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "YDMBpK2XJ_rJ",
"colab_type": "code",
"colab": {}
},
"source": [
"! cp bioactivity_data.csv \"/content/gdrive/My Drive/Colab
Notebooks/data\""
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "iRIr1QiEJtuw",
"colab_type": "code",
"outputId": "e400f4d9-3ce7-4822-8837-33eb2499c1c1",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 52
}
},
"source": [
"! ls -l \"/content/gdrive/My Drive/Colab Notebooks/data\""
],
"execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [
"total 69\n",
"-rw------- 1 root root 70010 Apr 29 17:10 bioactivity_data.csv\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "z9NwrYJni8CH",
"colab_type": "text"
},
"source": [
"Let's see the CSV files that we have so far."
]
},
{
"cell_type": "code",
"metadata": {
"id": "FO3cZC5vnCht",
"colab_type": "code",
"outputId": "f5e07f1f-7a24-4d8e-ca52-e5e36e4daea1",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 35
}
},
"source": [
"! ls"
],
"execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [
"bioactivity_data.csv gdrive sample_data\n"
],
"name": "stdout"
}
 ]
},
{
"cell_type": "markdown",
"metadata": {
"id": "7UAasSu5jAeB",
"colab_type": "text"
},
"source": [
"Taking a glimpse of the **bioactivity_data.csv** file that we've just
created."
]
},
{
"cell_type": "code",
"metadata": {
"id": "jwEJjx5b5gAn",
"colab_type": "code",
"outputId": "69dce8c6-565d-4537-952e-b01da9f2fd83",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 211
}
},
"source": [
"! head bioactivity_data.csv"
],
"execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [

"activity_comment,activity_id,activity_properties,assay_chembl_id,assay_description
,assay_type,bao_endpoint,bao_format,bao_label,canonical_smiles,data_validity_commen
t,data_validity_description,document_chembl_id,document_journal,document_year,ligan
d_efficiency,molecule_chembl_id,molecule_pref_name,parent_molecule_chembl_id,pchemb
l_value,potential_duplicate,qudt_units,record_id,relation,src_id,standard_flag,stan
dard_relation,standard_text_value,standard_type,standard_units,standard_upper_value
,standard_value,target_chembl_id,target_organism,target_pref_name,target_tax_id,tex
t_value,toid,type,units,uo_units,upper_value,value\n",
",1480935,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '18.28', 'le': '0.33', 'lle': '3.25', 'sei':
'5.90'}\",CHEMBL187579,,CHEMBL187579,5.14,False,http://www.openphacts.org/units/
Nanomolar,384103,=,1,True,=,,IC50,nM,,7200.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,7.2\n",
",1480936,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '12.10', 'le': '0.33', 'lle': '1.22', 'sei':
'13.45'}\",CHEMBL188487,,CHEMBL188487,5.03,False,http://www.openphacts.org/units/
Nanomolar,383984,=,1,True,=,,IC50,nM,,9400.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,9.4\n",
",1481061,[],CHEMBL830868,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like protease) at 20
uM,B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '11.56', 'le': '0.29', 'lle': '2.21', 'sei':
'8.72'}\",CHEMBL185698,,CHEMBL185698,4.87,False,http://www.openphacts.org/units/
Nanomolar,384106,=,1,True,=,,IC50,nM,,13500.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,13.5\n",
",1481065,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '16.64', 'le': '0.32', 'lle': '1.25', 'sei':
'13.06'}\",CHEMBL426082,,CHEMBL426082,4.88,False,http://www.openphacts.org/units/
Nanomolar,384075,=,1,True,=,,IC50,nM,,13110.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,13.11\n",
",1481066,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-],,,CHEMBL1139624,Bioorg. Med.
Chem. Lett.,2005,\"{'bei': '16.84', 'le': '0.32', 'lle': '2.16', 'sei':
'7.08'}\",CHEMBL187717,,CHEMBL187717,5.70,False,http://www.openphacts.org/units/
Nanomolar,384234,=,1,True,=,,IC50,nM,,2000.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,2.0\n",
",1481068,[],CHEMBL828143,In vitro inhibitory concentration SARS
coronavirus main protease (SARS CoV 3C-like
protease) ,B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2cc3ccccc3s2)c2c(Br)cccc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '16.14', 'le': '0.37', 'lle': '1.62', 'sei':
'16.07'}\",CHEMBL365134,,CHEMBL365134,6.01,False,http://www.openphacts.org/units/
Nanomolar,384081,=,1,True,=,,IC50,nM,,980.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,0.98\n",
",1481088,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccc(F)cc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '17.08', 'le': '0.33', 'lle': '1.55', 'sei':
'14.22'}\",CHEMBL187598,,CHEMBL187598,5.32,False,http://www.openphacts.org/units/
Nanomolar,384303,=,1,True,=,,IC50,nM,,4820.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,4.82\n",
",1481089,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccc(I)cc21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '14.36', 'le': '0.37', 'lle': '1.78', 'sei':
'16.11'}\",CHEMBL190743,,CHEMBL190743,6.02,False,http://www.openphacts.org/units/
Nanomolar,384329,=,1,True,=,,IC50,nM,,950.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,0.95\n",
",1481093,[],CHEMBL829584,In vitro inhibitory concentration against
SARS coronavirus main protease (SARS CoV 3C-like
protease),B,BAO_0000190,BAO_0000357,single protein
format,O=C1C(=O)N(Cc2cc3ccccc3s2)c2cccc(Cl)c21,,,CHEMBL1139624,Bioorg. Med. Chem.
Lett.,2005,\"{'bei': '15.10', 'le': '0.31', 'lle': '0.67', 'sei':
'13.24'}\",CHEMBL365469,,CHEMBL365469,4.95,False,http://www.openphacts.org/units/
Nanomolar,384283,=,1,True,=,,IC50,nM,,11200.0,CHEMBL3927,SARS coronavirus,SARS
coronavirus 3C-like proteinase,227859,,,IC50,uM,UO_0000065,,11.2\n"
],
"name": "stdout"
}
]
},
 {
"cell_type": "markdown",
"metadata": {
"id": "_GXMpFNUOn_8",
"colab_type": "text"
},
"source": [
"## **Handling missing data**\n",
"If any compounds has missing value for the **standard_value** column then
drop it"
]
},
{
"cell_type": "code",
"metadata": {
"id": "hkVOdk6ZR396",
"colab_type": "code",
"outputId": "fc08d57e-f832-4cb0-90f2-dc7394b0209d",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 782
}
},
"source": [
"df2 = df[df.standard_value.notna()]\n",
"df2"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"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>activity_comment</th>\n",
" <th>activity_id</th>\n",
" <th>activity_properties</th>\n",
" <th>assay_chembl_id</th>\n",
" <th>assay_description</th>\n",
" <th>assay_type</th>\n",
" <th>bao_endpoint</th>\n",
" <th>bao_format</th>\n",
" <th>bao_label</th>\n",
" <th>canonical_smiles</th>\n",
" <th>data_validity_comment</th>\n",
" <th>data_validity_description</th>\n",
" <th>document_chembl_id</th>\n",
" <th>document_journal</th>\n",
" <th>document_year</th>\n",
" <th>ligand_efficiency</th>\n",
" <th>molecule_chembl_id</th>\n",
" <th>molecule_pref_name</th>\n",
" <th>parent_molecule_chembl_id</th>\n",
" <th>pchembl_value</th>\n",
" <th>potential_duplicate</th>\n",
" <th>qudt_units</th>\n",
" <th>record_id</th>\n",
" <th>relation</th>\n",
" <th>src_id</th>\n",
" <th>standard_flag</th>\n",
" <th>standard_relation</th>\n",
" <th>standard_text_value</th>\n",
" <th>standard_type</th>\n",
" <th>standard_units</th>\n",
" <th>standard_upper_value</th>\n",
" <th>standard_value</th>\n",
" <th>target_chembl_id</th>\n",
" <th>target_organism</th>\n",
" <th>target_pref_name</th>\n",
" <th>target_tax_id</th>\n",
" <th>text_value</th>\n",
" <th>toid</th>\n",
" <th>type</th>\n",
" <th>units</th>\n",
" <th>uo_units</th>\n",
" <th>upper_value</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>None</td>\n",
" <td>1480935</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL829584</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '18.28', 'le': '0.33', 'lle': '3.25', ...</td>\n",
" <td>CHEMBL187579</td>\n",
" <td>None</td>\n",
" <td>CHEMBL187579</td>\n",
" <td>5.14</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>384103</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>7200.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>7.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>None</td>\n",
" <td>1480936</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL829584</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '12.10', 'le': '0.33', 'lle': '1.22', ...</td>\n",
" <td>CHEMBL188487</td>\n",
" <td>None</td>\n",
" <td>CHEMBL188487</td>\n",
" <td>5.03</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>383984</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>9400.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>9.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>None</td>\n",
" <td>1481061</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL830868</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '11.56', 'le': '0.29', 'lle': '2.21', ...</td>\n",
" <td>CHEMBL185698</td>\n",
" <td>None</td>\n",
" <td>CHEMBL185698</td>\n",
" <td>4.87</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>384106</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>13500.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>13.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>None</td>\n",
" <td>1481065</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL829584</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '16.64', 'le': '0.32', 'lle': '1.25', ...</td>\n",
" <td>CHEMBL426082</td>\n",
" <td>None</td>\n",
" <td>CHEMBL426082</td>\n",
" <td>4.88</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>384075</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>13110.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>13.11</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>None</td>\n",
" <td>1481066</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL829584</td>\n",
" <td>In vitro inhibitory concentration against SARS...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000357</td>\n",
" <td>single protein format</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL1139624</td>\n",
" <td>Bioorg. Med. Chem. Lett.</td>\n",
" <td>2005</td>\n",
" <td>{'bei': '16.84', 'le': '0.32', 'lle': '2.16', ...</td>\n",
" <td>CHEMBL187717</td>\n",
" <td>None</td>\n",
" <td>CHEMBL187717</td>\n",
" <td>5.70</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>384234</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>2000.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>2.0</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",
" <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",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>128</th>\n",
" <td>None</td>\n",
" <td>12041507</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL2150313</td>\n",
" <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000019</td>\n",
" <td>assay format</td>\n",
" <td>COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL2146458</td>\n",
" <td>Bioorg. Med. Chem.</td>\n",
" <td>2012</td>\n",
" <td>{'bei': '14.70', 'le': '0.27', 'lle': '1.57', ...</td>\n",
" <td>CHEMBL2146517</td>\n",
" <td>METHYL TANSHINONATE</td>\n",
" <td>CHEMBL2146517</td>\n",
" <td>4.97</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>1727226</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>10600.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>10.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>129</th>\n",
" <td>None</td>\n",
" <td>12041508</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL2150313</td>\n",
" <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000019</td>\n",
" <td>assay format</td>\n",
" <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL2146458</td>\n",
" <td>Bioorg. Med. Chem.</td>\n",
" <td>2012</td>\n",
" <td>{'bei': '16.86', 'le': '0.31', 'lle': '1.56', ...</td>\n",
" <td>CHEMBL187460</td>\n",
" <td>CRYPTOTANSHINONE</td>\n",
" <td>CHEMBL187460</td>\n",
" <td>5.00</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>1727227</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>10100.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>10.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>130</th>\n",
" <td>None</td>\n",
" <td>12041509</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL2150313</td>\n",
" <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000019</td>\n",
" <td>assay format</td>\n",
" <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL2146458</td>\n",
" <td>Bioorg. Med. Chem.</td>\n",
" <td>2012</td>\n",
" <td>{'bei': '17.88', 'le': '0.32', 'lle': '0.84', ...</td>\n",
" <td>CHEMBL363535</td>\n",
" <td>TANSHINONE I</td>\n",
" <td>CHEMBL363535</td>\n",
" <td>4.94</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>1727228</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>11500.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>11.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>131</th>\n",
" <td>None</td>\n",
" <td>12041510</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL2150313</td>\n",
" <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000019</td>\n",
" <td>assay format</td>\n",
" <td>Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL2146458</td>\n",
" <td>Bioorg. Med. Chem.</td>\n",
" <td>2012</td>\n",
" <td>{'bei': '17.86', 'le': '0.32', 'lle': '1.68', ...</td>\n",
" <td>CHEMBL227075</td>\n",
" <td>DIHYDROTANSHINONE I</td>\n",
" <td>CHEMBL227075</td>\n",
" <td>4.97</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>1727229</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
" <td>10700.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>10.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>132</th>\n",
" <td>None</td>\n",
" <td>12041511</td>\n",
" <td>[]</td>\n",
" <td>CHEMBL2150313</td>\n",
" <td>Inhibition of SARS-CoV PLpro expressed in Esch...</td>\n",
" <td>B</td>\n",
" <td>BAO_0000190</td>\n",
" <td>BAO_0000019</td>\n",
" <td>assay format</td>\n",
" <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CHEMBL2146458</td>\n",
" <td>Bioorg. Med. Chem.</td>\n",
" <td>2012</td>\n",
" <td>{'bei': '14.53', 'le': '0.27', 'lle': '-0.01',...</td>\n",
" <td>CHEMBL45830</td>\n",
" <td>MILTIRONE</td>\n",
" <td>CHEMBL45830</td>\n",
" <td>4.10</td>\n",
" <td>False</td>\n",
" <td>http://www.openphacts.org/units/Nanomolar</td>\n",
" <td>1727230</td>\n",
" <td>=</td>\n",
" <td>1</td>\n",
" <td>True</td>\n",
" <td>=</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>nM</td>\n",
" <td>None</td>\n",
 " <td>78900.0</td>\n",
" <td>CHEMBL3927</td>\n",
" <td>SARS coronavirus</td>\n",
" <td>SARS coronavirus 3C-like proteinase</td>\n",
" <td>227859</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IC50</td>\n",
" <td>uM</td>\n",
" <td>UO_0000065</td>\n",
" <td>None</td>\n",
" <td>78.9</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>133 rows × 43 columns</p>\n",
"</div>"
],
"text/plain": [
" activity_comment activity_id ... upper_value value\n",
"0 None 1480935 ... None 7.2\n",
"1 None 1480936 ... None 9.4\n",
"2 None 1481061 ... None 13.5\n",
"3 None 1481065 ... None 13.11\n",
"4 None 1481066 ... None 2.0\n",
".. ... ... ... ... ...\n",
"128 None 12041507 ... None 10.6\n",
"129 None 12041508 ... None 10.1\n",
"130 None 12041509 ... None 11.5\n",
"131 None 12041510 ... None 10.7\n",
"132 None 12041511 ... None 78.9\n",
"\n",
"[133 rows x 43 columns]"
]
},
"metadata": {
"tags": []
},
"execution_count": 23
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "Y-qNsUlmjS25",
"colab_type": "text"
},
"source": [
"Apparently, for this dataset there is no missing data. But we can use the
above code cell for bioactivity data of other target protein."
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "5H4sSFAWhV9B",
"colab_type": "text"
},
 "source": [
"## **Data pre-processing of the bioactivity data**"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "tO22XVlzhkXR",
"colab_type": "text"
},
"source": [
"### **Labeling compounds as either being active, inactive or
intermediate**\n",
"The bioactivity data is in the IC50 unit. Compounds having values of less
than 1000 nM will be considered to be **active** while those greater than 10,000 nM
will be considered to be **inactive**. As for those values in between 1,000 and
10,000 nM will be referred to as **intermediate**. "
]
},
{
"cell_type": "code",
"metadata": {
"id": "1E8rz7oMOd-5",
"colab_type": "code",
"colab": {}
},
"source": [
"bioactivity_class = []\n",
"for i in df2.standard_value:\n",
" if float(i) >= 10000:\n",
" bioactivity_class.append(\"inactive\")\n",
" elif float(i) <= 1000:\n",
" bioactivity_class.append(\"active\")\n",
" else:\n",
" bioactivity_class.append(\"intermediate\")"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "PFsmb2N9hnTB",
"colab_type": "text"
},
"source": [
"### **Iterate the *molecule_chembl_id* to a list**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "DMJng9xnVnMM",
"colab_type": "code",
"colab": {}
},
"source": [
"mol_cid = []\n",
"for i in df2.molecule_chembl_id:\n",
 " mol_cid.append(i)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "YRieJc9dhuVZ",
"colab_type": "text"
},
"source": [
"### **Iterate *canonical_smiles* to a list**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "AT8qUBk1eVmj",
"colab_type": "code",
"colab": {}
},
"source": [
"canonical_smiles = []\n",
"for i in df2.canonical_smiles:\n",
" canonical_smiles.append(i)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "DZFugUXxhwjE",
"colab_type": "text"
},
"source": [
"### **Iterate *standard_value* to a list**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "ZaPt-FjEZNBe",
"colab_type": "code",
"colab": {}
},
"source": [
"standard_value = []\n",
"for i in df2.standard_value:\n",
" standard_value.append(i)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "Nv2dzid_hzKd",
 "colab_type": "text"
},
"source": [
"### **Combine the 4 lists into a dataframe**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "TWlYO4I3Wrh-",
"colab_type": "code",
"colab": {}
},
"source": [
"data_tuples = list(zip(mol_cid, canonical_smiles, bioactivity_class,
standard_value))\n",
"df3 = pd.DataFrame( data_tuples, columns=['molecule_chembl_id',
'canonical_smiles', 'bioactivity_class', 'standard_value'])"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "Li64nUiZQ-y2",
"colab_type": "code",
"outputId": "a1d4cdb5-922d-4573-9f8b-abcb7ef72a58",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 415
}
},
"source": [
"df3"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"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>molecule_chembl_id</th>\n",
" <th>canonical_smiles</th>\n",
" <th>bioactivity_class</th>\n",
" <th>standard_value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CHEMBL187579</td>\n",
" <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
" <td>intermediate</td>\n",
" <td>7200.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CHEMBL188487</td>\n",
" <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
" <td>intermediate</td>\n",
" <td>9400.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>CHEMBL185698</td>\n",
" <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
" <td>inactive</td>\n",
" <td>13500.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>CHEMBL426082</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
" <td>inactive</td>\n",
" <td>13110.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>CHEMBL187717</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]</td>\n",
" <td>intermediate</td>\n",
" <td>2000.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>128</th>\n",
" <td>CHEMBL2146517</td>\n",
" <td>COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...</td>\n",
" <td>inactive</td>\n",
" <td>10600.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>129</th>\n",
 " <td>CHEMBL187460</td>\n",
" <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
" <td>inactive</td>\n",
" <td>10100.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>130</th>\n",
" <td>CHEMBL363535</td>\n",
" <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
" <td>inactive</td>\n",
" <td>11500.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>131</th>\n",
" <td>CHEMBL227075</td>\n",
" <td>Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1</td>\n",
" <td>inactive</td>\n",
" <td>10700.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>132</th>\n",
" <td>CHEMBL45830</td>\n",
" <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
" <td>inactive</td>\n",
" <td>78900.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>133 rows × 4 columns</p>\n",
"</div>"
],
"text/plain": [
" molecule_chembl_id ... standard_value\n",
"0 CHEMBL187579 ... 7200.0\n",
"1 CHEMBL188487 ... 9400.0\n",
"2 CHEMBL185698 ... 13500.0\n",
"3 CHEMBL426082 ... 13110.0\n",
"4 CHEMBL187717 ... 2000.0\n",
".. ... ... ...\n",
"128 CHEMBL2146517 ... 10600.0\n",
"129 CHEMBL187460 ... 10100.0\n",
"130 CHEMBL363535 ... 11500.0\n",
"131 CHEMBL227075 ... 10700.0\n",
"132 CHEMBL45830 ... 78900.0\n",
"\n",
"[133 rows x 4 columns]"
]
},
"metadata": {
"tags": []
},
"execution_count": 34
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "vE0Vvo6ic3MI",
 "colab_type": "text"
},
"source": [
"### **Alternative method**"
]
},
{
"cell_type": "code",
"metadata": {
"id": "VICiiCtqc2ne",
"colab_type": "code",
"outputId": "0b39e703-b724-4f02-d86c-ea07791cdeed",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 415
}
},
"source": [
"selection = ['molecule_chembl_id', 'canonical_smiles', 'standard_value']\
n",
"df3 = df2[selection]\n",
"df3"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"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>molecule_chembl_id</th>\n",
" <th>canonical_smiles</th>\n",
" <th>standard_value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CHEMBL187579</td>\n",
" <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
" <td>7200.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CHEMBL188487</td>\n",
" <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
" <td>9400.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>CHEMBL185698</td>\n",
" <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
" <td>13500.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>CHEMBL426082</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
" <td>13110.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>CHEMBL187717</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]</td>\n",
" <td>2000.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>128</th>\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",
" </tr>\n",
" <tr>\n",
" <th>129</th>\n",
" <td>CHEMBL187460</td>\n",
" <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
" <td>10100.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>130</th>\n",
" <td>CHEMBL363535</td>\n",
" <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
" <td>11500.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>131</th>\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",
" </tr>\n",
" <tr>\n",
" <th>132</th>\n",
" <td>CHEMBL45830</td>\n",
" <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
" <td>78900.0</td>\n",
 " </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>133 rows × 3 columns</p>\n",
"</div>"
],
"text/plain": [
" molecule_chembl_id ... standard_value\n",
"0 CHEMBL187579 ... 7200.0\n",
"1 CHEMBL188487 ... 9400.0\n",
"2 CHEMBL185698 ... 13500.0\n",
"3 CHEMBL426082 ... 13110.0\n",
"4 CHEMBL187717 ... 2000.0\n",
".. ... ... ...\n",
"128 CHEMBL2146517 ... 10600.0\n",
"129 CHEMBL187460 ... 10100.0\n",
"130 CHEMBL363535 ... 11500.0\n",
"131 CHEMBL227075 ... 10700.0\n",
"132 CHEMBL45830 ... 78900.0\n",
"\n",
"[133 rows x 3 columns]"
]
},
"metadata": {
"tags": []
},
"execution_count": 37
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "d8nV77oWdbq1",
"colab_type": "code",
"outputId": "2df59721-3567-48bc-a732-a0b09fa8aa12",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 415
}
},
"source": [
"pd.concat([df3,pd.Series(bioactivity_class)], axis=1)"
],
"execution_count": 0,
"outputs": [
{
"output_type": "execute_result",
"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>molecule_chembl_id</th>\n",
" <th>canonical_smiles</th>\n",
" <th>bioactivity_class</th>\n",
" <th>standard_value</th>\n",
" <th>0</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CHEMBL187579</td>\n",
" <td>Cc1noc(C)c1CN1C(=O)C(=O)c2cc(C#N)ccc21</td>\n",
" <td>intermediate</td>\n",
" <td>7200.0</td>\n",
" <td>intermediate</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CHEMBL188487</td>\n",
" <td>O=C1C(=O)N(Cc2ccc(F)cc2Cl)c2ccc(I)cc21</td>\n",
" <td>intermediate</td>\n",
" <td>9400.0</td>\n",
" <td>intermediate</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>CHEMBL185698</td>\n",
" <td>O=C1C(=O)N(CC2COc3ccccc3O2)c2ccc(I)cc21</td>\n",
" <td>inactive</td>\n",
" <td>13500.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>CHEMBL426082</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2ccccc21</td>\n",
" <td>inactive</td>\n",
" <td>13110.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>CHEMBL187717</td>\n",
" <td>O=C1C(=O)N(Cc2cc3ccccc3s2)c2c1cccc2[N+](=O)[O-]</td>\n",
" <td>intermediate</td>\n",
" <td>2000.0</td>\n",
" <td>intermediate</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
 " <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>128</th>\n",
" <td>CHEMBL2146517</td>\n",
" <td>COC(=O)[C@@]1(C)CCCc2c1ccc1c2C(=O)C(=O)c2c(C)c...</td>\n",
" <td>inactive</td>\n",
" <td>10600.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" <tr>\n",
" <th>129</th>\n",
" <td>CHEMBL187460</td>\n",
" <td>C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C</td>\n",
" <td>inactive</td>\n",
" <td>10100.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" <tr>\n",
" <th>130</th>\n",
" <td>CHEMBL363535</td>\n",
" <td>Cc1coc2c1C(=O)C(=O)c1c-2ccc2c(C)cccc12</td>\n",
" <td>inactive</td>\n",
" <td>11500.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" <tr>\n",
" <th>131</th>\n",
" <td>CHEMBL227075</td>\n",
" <td>Cc1cccc2c3c(ccc12)C1=C(C(=O)C3=O)[C@@H](C)CO1</td>\n",
" <td>inactive</td>\n",
" <td>10700.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" <tr>\n",
" <th>132</th>\n",
" <td>CHEMBL45830</td>\n",
" <td>CC(C)C1=Cc2ccc3c(c2C(=O)C1=O)CCCC3(C)C</td>\n",
" <td>inactive</td>\n",
" <td>78900.0</td>\n",
" <td>inactive</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>133 rows × 5 columns</p>\n",
"</div>"
],
"text/plain": [
" molecule_chembl_id ... 0\n",
"0 CHEMBL187579 ... intermediate\n",
"1 CHEMBL188487 ... intermediate\n",
"2 CHEMBL185698 ... inactive\n",
"3 CHEMBL426082 ... inactive\n",
"4 CHEMBL187717 ... intermediate\n",
".. ... ... ...\n",
 "128 CHEMBL2146517 ... inactive\n",
"129 CHEMBL187460 ... inactive\n",
"130 CHEMBL363535 ... inactive\n",
"131 CHEMBL227075 ... inactive\n",
"132 CHEMBL45830 ... inactive\n",
"\n",
"[133 rows x 5 columns]"
]
},
"metadata": {
"tags": []
},
"execution_count": 36
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "9tlgyexWh7YJ",
"colab_type": "text"
},
"source": [
"Saves dataframe to CSV file"
]
},
{
"cell_type": "code",
"metadata": {
"id": "nSNia7suXstR",
"colab_type": "code",
"colab": {}
},
"source": [
"df3.to_csv('bioactivity_preprocessed_data.csv', index=False)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "UuZf5-MEd-H5",
"colab_type": "code",
"outputId": "19e008f4-267b-490b-9b2c-e5f88a47a48a",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 104
}
},
"source": [
"! ls -l"
],
"execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [
"total 92\n",
 "-rw-r--r-- 1 root root 70010 Apr 29 17:07 bioactivity_data.csv\n",
"-rw-r--r-- 1 root root 9326 Apr 29 17:24
bioactivity_preprocessed_data.csv\n",
"drwx------ 4 root root 4096 Apr 29 17:08 gdrive\n",
"drwxr-xr-x 1 root root 4096 Apr 3 16:24 sample_data\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "_C7rqJKTePhV",
"colab_type": "text"
},
"source": [
"Let's copy to the Google Drive"
]
},
{
"cell_type": "code",
"metadata": {
"id": "ZfyvJcENeHDB",
"colab_type": "code",
"colab": {}
},
"source": [
"! cp bioactivity_preprocessed_data.csv \"/content/gdrive/My Drive/Colab
Notebooks/data\""
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "7PU7yU9leLV5",
"colab_type": "code",
"outputId": "c07ddf6b-e372-4807-bc0f-7f0b2944a0cf",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 35
}
},
"source": [
"! ls \"/content/gdrive/My Drive/Colab Notebooks/data\""
],
"execution_count": 0,
"outputs": [
{
"output_type": "stream",
"text": [
"bioactivity_data.csv bioactivity_preprocessed_data.csv\n"
],
"name": "stdout"
}
]
},
 {
"cell_type": "markdown",
"metadata": {
"id": "ZywB5K_Dlawb",
"colab_type": "text"
},
"source": [
"---"
]
}
]
}