{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 128,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Xe can be handled as we want if imported from smiles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 129,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'[Xe]c1ccccc1'"
      ]
     },
     "execution_count": 129,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x = Chem.MolFromSmiles(\"[Xe]c1ccccc1\")\n",
    "Chem.MolToSmiles(x)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Add Xe atom to benzene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 130,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6"
      ]
     },
     "execution_count": 130,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles(\"c1ccccc1\")\n",
    "mw = Chem.RWMol(m)\n",
    "mw.GetNumAtoms()\n",
    "xe = Chem.Atom(54)\n",
    "idx = mw.AddAtom(xe)\n",
    "idx"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create the bond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 131,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1"
      ]
     },
     "execution_count": 131,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mw.AddBond(0,6,Chem.BondType.SINGLE)\n",
    "Chem.SanitizeMol(mw)\n",
    "atom = mw.GetAtomWithIdx(idx)\n",
    "atom.GetExplicitValence()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Why the extra H when we write to smiles?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 132,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'[XeH]c1ccccc1'"
      ]
     },
     "execution_count": 132,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.MolToSmiles(mw)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "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,
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}