renumbering.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "48b30764-f427-4d15-af95-402592bbc77f",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import rdmolops\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "IPythonConsole.drawOptions.addAtomIndices = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "407c3511-de71-456f-b387-a7ec275dde8f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7437ceb0e880>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol = Chem.MolFromSmiles('CC(=O)N(C)')\n",
    "Chem.MolToSmiles(mol)\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "9ffae000-45eb-413d-afee-1ee4a6089b08",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7437ceb0e810>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "newmol1 = rdmolops.RenumberAtoms(mol, [4, 1, 2, 3, 0])\n",
    "Chem.MolToSmiles(newmol1)\n",
    "newmol1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "f0be7d1a-45f4-4fc6-b239-351cd19c63df",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7437ceb0e8f0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "newmol2 = rdmolops.RenumberAtoms(mol, [4, 3, 2, 1, 0])\n",
    "Chem.MolToSmiles(newmol2)\n",
    "newmol2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "cfcbdbd4-0158-4a17-9d86-2a3a55c48455",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[4,3,1,0,2,] CNC(C)=O\n",
      "[0,3,1,4,2,] CNC(C)=O\n",
      "[0,1,3,4,2,] CNC(C)=O\n"
     ]
    }
   ],
   "source": [
    "print(mol.GetProp('_smilesAtomOutputOrder'), Chem.MolToSmiles(mol)) \n",
    "print(newmol1.GetProp('_smilesAtomOutputOrder'), Chem.MolToSmiles(newmol1))\n",
    "print(newmol2.GetProp('_smilesAtomOutputOrder'), Chem.MolToSmiles(newmol2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7e7a2970-88a4-47f7-a259-ccf2d1d0abf5",
   "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": "3.10.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}