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PatWalters/circle_grid_demo.ipynb

Last active December 7, 2023 08:11
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A quick demo of the circle_grid facility in datamol
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circle_grid_demo.ipynb
{
"cells": [
{
"cell_type": "markdown",
"id": "1c4606a5",
"metadata": {},
"source": [
"### Demo the Circle Grid in DataMol\n",
"\n",
"In this notebook, we'll do the following. \n",
"1. Read a dataset consisting of carbonic anhydrase inhibitors.\n",
"2. Use the [fuzzy_scaffolding](https://docs.datamol.io/stable/tutorials/Fuzzy_Scaffolds.html) feature in [datamol](https://datamol.io) to divide the dataset into scaffolds.\n",
"3. Use the [circle_grid](https://docs.datamol.io/stable/tutorials/Visualization.html#circlegrid) facility in datamol to plot the dataset. "
]
},
{
"cell_type": "markdown",
"id": "19a36e2e",
"metadata": {},
"source": [
"Install the required libraries\n",
"```\n",
"pip install pandas datamol rdkit\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "7b8cf647",
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"import datamol as dm\n",
"from rdkit import Chem"
]
},
{
"cell_type": "markdown",
"id": "33809925",
"metadata": {},
"source": [
"### 1. Read a dataset consisting of carbonic anhydrase inhibitors."
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "e55083e3",
"metadata": {},
"outputs": [],
"source": [
"url = \"https://raw.githubusercontent.com/PatWalters/yamc/main/data/Carbonic.smi\"\n",
"df = pd.read_csv(url,sep=\" \",names=[\"SMILES\",\"Name\",\"pIC50\"])"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "b5b3c4f1",
"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>SMILES</th>\n",
" <th>Name</th>\n",
" <th>pIC50</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CC(C)CN(C)Cc1cc(ccc1O)C(=O)c2cc(sc2)S(=O)(=O)N</td>\n",
" <td>CHEMBL544127</td>\n",
" <td>8.05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>COc1ccc(cc1)C(=O)c2cc(oc2)S(=O)(=O)N</td>\n",
" <td>CHEMBL340519</td>\n",
" <td>8.70</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>CN(C)Cc1cc(ccc1O)C(=O)c2cc(sc2)S(=O)(=O)N</td>\n",
" <td>CHEMBL541089</td>\n",
" <td>8.19</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>c1cc(ccc1CN2CCOCC2)S(=O)(=O)c3cc(sc3)S(=O)(=O)N</td>\n",
" <td>CHEMBL555153</td>\n",
" <td>8.12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>CC(C)CN(C)Cc1cc(ccc1O)S(=O)(=O)c2cc(sc2)S(=O)(...</td>\n",
" <td>CHEMBL539817</td>\n",
" <td>8.30</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>551</th>\n",
" <td>CN(C)C(=O)NC1CCc2c(cccc2OC)C1</td>\n",
" <td>CHEMBL3786651</td>\n",
" <td>7.76</td>\n",
" </tr>\n",
" <tr>\n",
" <th>552</th>\n",
" <td>CN(C)C(=O)NC1CCc2ccc(cc2C1)O</td>\n",
" <td>CHEMBL3785207</td>\n",
" <td>7.22</td>\n",
" </tr>\n",
" <tr>\n",
" <th>553</th>\n",
" <td>CN(C)S(=O)(=O)NC1CCc2c(cccc2O)C1</td>\n",
" <td>CHEMBL3786873</td>\n",
" <td>7.81</td>\n",
" </tr>\n",
" <tr>\n",
" <th>554</th>\n",
" <td>CN(C)S(=O)(=O)NC1CCc2cc(ccc2C1)O</td>\n",
" <td>CHEMBL3786442</td>\n",
" <td>7.89</td>\n",
" </tr>\n",
" <tr>\n",
" <th>555</th>\n",
" <td>CN(C)S(=O)(=O)NC1CCc2ccc(cc2C1)O</td>\n",
" <td>CHEMBL3786719</td>\n",
" <td>7.97</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>556 rows × 3 columns</p>\n",
"</div>"
],
"text/plain": [
" SMILES Name pIC50\n",
"0 CC(C)CN(C)Cc1cc(ccc1O)C(=O)c2cc(sc2)S(=O)(=O)N CHEMBL544127 8.05\n",
"1 COc1ccc(cc1)C(=O)c2cc(oc2)S(=O)(=O)N CHEMBL340519 8.70\n",
"2 CN(C)Cc1cc(ccc1O)C(=O)c2cc(sc2)S(=O)(=O)N CHEMBL541089 8.19\n",
"3 c1cc(ccc1CN2CCOCC2)S(=O)(=O)c3cc(sc3)S(=O)(=O)N CHEMBL555153 8.12\n",
"4 CC(C)CN(C)Cc1cc(ccc1O)S(=O)(=O)c2cc(sc2)S(=O)(... CHEMBL539817 8.30\n",
".. ... ... ...\n",
"551 CN(C)C(=O)NC1CCc2c(cccc2OC)C1 CHEMBL3786651 7.76\n",
"552 CN(C)C(=O)NC1CCc2ccc(cc2C1)O CHEMBL3785207 7.22\n",
"553 CN(C)S(=O)(=O)NC1CCc2c(cccc2O)C1 CHEMBL3786873 7.81\n",
"554 CN(C)S(=O)(=O)NC1CCc2cc(ccc2C1)O CHEMBL3786442 7.89\n",
"555 CN(C)S(=O)(=O)NC1CCc2ccc(cc2C1)O CHEMBL3786719 7.97\n",
"\n",
"[556 rows x 3 columns]"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df"
]
},
{
"cell_type": "markdown",
"id": "3d9ac4f1",
"metadata": {},
"source": [
"Add an an RDKit molecule to the dataframe. We're going to add an InChI key so that we can match molecules back to scaffolds. "
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "14e4665a",
"metadata": {},
"outputs": [],
"source": [
"df[\"mol\"] = df.SMILES.apply(dm.to_mol)\n",
"df[\"inchi_key\"] = df.mol.apply(Chem.MolToInchiKey)"
]
},
{
"cell_type": "markdown",
"id": "de2d8b42",
"metadata": {},
"source": [
"Create a dictionary with activity values. This will be used in the plot. "
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "b6c735c4",
"metadata": {},
"outputs": [],
"source": [
"activity_dict = {}\n",
"for mol, pIC50 in df[[\"mol\",\"pIC50\"]].values:\n",
" activity_dict[mol] = {\"pIC50\" : pIC50}"
]
},
{
"cell_type": "markdown",
"id": "f792399a",
"metadata": {},
"source": [
"### 2. Use the fuzzy_scaffolding feature in datamol to divide the dataset into scaffolds."
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "00c45b06",
"metadata": {},
"outputs": [],
"source": [
"with dm.without_rdkit_log():\n",
" scaffolds, scf2infos, scf2groups = dm.scaffold.fuzzy_scaffolding(df.mol.tolist())"
]
},
{
"cell_type": "markdown",
"id": "91c49067",
"metadata": {},
"source": [
"Determine the number of molecules in each scaffold group."
]
},
{
"cell_type": "code",
"execution_count": 19,
"id": "75687d4a",
"metadata": {},
"outputs": [],
"source": [
"scf2infos['num_mols'] = [len(x) for x in scf2infos.mols]"
]
},
{
"cell_type": "markdown",
"id": "531b2e37",
"metadata": {},
"source": [
"Create a dataframe with molecules from one scaffold"
]
},
{
"cell_type": "code",
"execution_count": 20,
"id": "71b37d84",
"metadata": {},
"outputs": [],
"source": [
"scaffold_idx = 8\n",
"mols = scf2infos.sort_values(\"num_mols\",ascending=False).mols.values[scaffold_idx]\n",
"inchi_keys = [Chem.MolToInchiKey(x) for x in mols]\n",
"scaffold_df = df.query(\"inchi_key in @inchi_keys\").copy()"
]
},
{
"cell_type": "markdown",
"id": "bd8d220a",
"metadata": {},
"source": [
"### 3. Use the circle_grid facility in datamol to plot the dataset."
]
},
{
"cell_type": "markdown",
"id": "75f16660",
"metadata": {},
"source": [
"The circle_grid gets kind of crowded with more than 9 molecules. Also, we want the grid to be sorted clockwise."
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "64238115",
"metadata": {},
"outputs": [],
"source": [
"scaffold_df = scaffold_df.sample(9)\n",
"scaffold_df.sort_values(\"pIC50\",inplace=True)"
]
},
{
"cell_type": "markdown",
"id": "28f2db4a",
"metadata": {},
"source": [
"Put the most active molecule in the center and the rest arround it"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "4a8df273",
"metadata": {},
"outputs": [],
"source": [
"center_mol = scaffold_df.mol.values[-1]\n",
"ring_mols = scaffold_df.mol.values[0:-1][:8]"
]
},
{
"cell_type": "markdown",
"id": "415e1cb7",
"metadata": {},
"source": [
"Plot the circle grid"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "35457b55",
"metadata": {},
"outputs": [
{
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"out = dm.viz.circle_grid(center_mol, \n",
" ring_mols,\n",
" act_mapper=activity_dict, \n",
" legend=\"Carbonic Anhydrase Inhibitors\", \n",
" ring_color=None,\n",
" margin=70, \n",
" ring_scaler=0.6, \n",
" align=None, \n",
" legendFontSize=16)\n",
"out"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8e45723b",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.3"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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