Draw Murcko Scaffolds Extraction as Reaction with Kekulized Molecules

draw_murcko_scaffolds.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Representing Kekulized Molecules in a Reaction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "import rdkit\n",
    "from rdkit.Chem import AllChem as Chem\n",
    "from rdkit.Chem import PandasTools\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem import rdChemReactions\n",
    "from rdkit.Chem.Draw import rdMolDraw2D\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem.Scaffolds import MurckoScaffold\n",
    "from IPython.display import SVG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "RDKIT:              2019.03.4\n"
     ]
    }
   ],
   "source": [
    "print('RDKIT:'.ljust(20) + f\"{rdkit.__version__}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I would like to represent the Murcko Scaffold extraction with an image (preferientially SVG).  \n",
    "To get started, I define an example molecule."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f7e2b396d50>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "smi1 = 'OC1=CC=CC=C1'\n",
    "mol1 = Chem.MolFromSmiles(smi1)\n",
    "mol1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I extract the Murcko Scaffold from the molecule above (see below).  \n",
    "I kekulize the SMILES because I want the rendered image to show kekulized Molecules instead of the aromatic representation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f7e29c26c10>"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol2 = MurckoScaffold.GetScaffoldForMol(mol1)\n",
    "Chem.Kekulize(mol2)\n",
    "smi2 = Chem.MolToSmiles(mol2, kekuleSmiles=True)\n",
    "mol2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I compute the reaction from smarts (could not find any function for smiles). The useSmiles argument looks promising."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "rxn_str=OC1=CC=CC=C1>>C1=CC=CC=C1\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdChemReactions.ChemicalReaction at 0x7f7e29c269e0>"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rxn_str = f\"{smi1}>>{smi2}\"\n",
    "print(f\"rxn_str={rxn_str}\")\n",
    "rxn = rdChemReactions.ReactionFromSmarts(rxn_str, useSmiles=True)\n",
    "rxn"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The molecules are shown with anaromatic representation instead of a kekulized representation.  \n",
    "Am I missing something?"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}