Combine multiple molecules in RDKit

rdkit_combine_multiple_molecules.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Combine multiple molecules in RDKit\n",
    "\n",
    "How to combine more than two molecules in RDkit?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit WARNING: [11:58:58] Enabling RDKit 2019.09.3 jupyter extensions\n"
     ]
    }
   ],
   "source": [
    "from functools import reduce  \n",
    "\n",
    "import pandas as pd\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import Draw"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Molecules\n",
    "\n",
    "Some molecules' SMILES to work with:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "smiles_list = [\n",
    "    'c1cc(CCCO)ccc1',\n",
    "    'OC=O',\n",
    "    'c1ccccc1N'\n",
    "]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get rdkit molecule objects."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7F4E056B3B00>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mols_list = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]\n",
    "Draw.MolsToGridImage(mols_list)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Combine mulitple molecules"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Combine molecules (bonds are not connected yet)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Read about `functools.reduce` here: https://docs.python.org/3/library/functools.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f4e050e88a0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combo = reduce(Chem.CombineMols, mols_list)\n",
    "combo"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Make combined molecule editable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<rdkit.Chem.rdchem.EditableMol at 0x7f4e050d4d18>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combo_editable = Chem.EditableMol(combo)\n",
    "combo_editable"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Connect manually atoms by atom IDs and bond type"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In order to know, which atom IDs to connect, let's draw the molecules with their atom IDs."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def mol_with_atom_and_molecule_index(mol):\n",
    "    \"\"\"\n",
    "    Taken from: https://iwatobipen.wordpress.com/2017/02/25/draw-molecule-with-atom-index-in-rdkit/\n",
    "    \n",
    "    Add label to each molecule's atom: \"atom_name:atom_index\"\n",
    "    \"\"\"\n",
    "    \n",
    "    for idx in range(mol.GetNumAtoms()):\n",
    "        mol.GetAtomWithIdx(idx).SetProp(\n",
    "            'molAtomMapNumber', \n",
    "            str(mol.GetAtomWithIdx(idx).GetIdx())\n",
    "        )\n",
    "        \n",
    "    return mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f4e050e88a0>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol_with_atom_and_molecule_index(combo)\n",
    "combo"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now add bonds as you wish."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "21"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combo_editable.AddBond(9, 15, order=Chem.rdchem.BondType.SINGLE)\n",
    "combo_editable.AddBond(4, 11, order=Chem.rdchem.BondType.SINGLE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f4e050e8d50>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_mol = combo_editable.GetMol()\n",
    "Chem.SanitizeMol(combined_mol)\n",
    "combined_mol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You are done!"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "kffl",
   "language": "python",
   "name": "kffl"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.8"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}

Thank you very much! saves my day :D

Thanks for this, happy this helped! :)

This script helped me in a task. Many thanks!