round-trips.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Non Round-trippable Molecule\n",
    "\n",
    "The problem with round-tripping (I like the word) this molecule seems to be a different aromaticity model for the input and the output Smiles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-03T08:39:41.555070Z",
     "start_time": "2019-09-03T08:39:41.287722Z"
    }
   },
   "outputs": [],
   "source": [
    "from rdkit.Chem import AllChem as Chem\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem import Descriptors as Desc\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "RDKit can parse the original Smiles into a valid molecule."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-03T08:39:41.604157Z",
     "start_time": "2019-09-03T08:39:41.564019Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "680.8420000000002\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fb51009fe40>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol = Chem.MolFromSmiles(\"c12c(\\C=C/c(ccc3OC)cc3Oc4ccc(cc4)\\C=C/c(cc5O1)c(CCN(C)C)cc5OC)c(CCN(C)C)c(OC)c(OC)c2OC\")\n",
    "print(Desc.MolWt(mol))\n",
    "mol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And parse it back into a Smiles."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-03T08:39:41.619655Z",
     "start_time": "2019-09-03T08:39:41.610242Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'COc1ccc2cc1-o-c1ccc(cc1)/c=c\\\\c1cc(c(OC)cc1CCN(C)C)-o-c1c(c(CCN(C)C)c(OC)c(OC)c1OC)/c=c\\\\2'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "smi = Chem.MolToSmiles(mol)\n",
    "smi"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "But the Smiles generated by RDKit can not be parsed back into a valid molecule."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-03T08:39:41.636858Z",
     "start_time": "2019-09-03T08:39:41.628453Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit ERROR: [10:39:41] Can't kekulize mol.  Unkekulized atoms: 2 3 4 5 6 7 9 10 11 12 13 14 15 16 17 18 19 20 23 24 31 32 33 39 42 45 48 49\n",
      "RDKit ERROR: \n"
     ]
    }
   ],
   "source": [
    "tmp = Chem.MolFromSmiles(smi)\n",
    "tmp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "hide_input": false,
  "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"
  },
  "toc": {
   "base_numbering": 1,
   "nav_menu": {},
   "number_sections": true,
   "sideBar": true,
   "skip_h1_title": true,
   "title_cell": "Table of Contents",
   "title_sidebar": "Contents",
   "toc_cell": false,
   "toc_position": {},
   "toc_section_display": true,
   "toc_window_display": false
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}