{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import MolsToGridImage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f70160ac620>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "smiles = \"COC\"\n",
    "mol = Chem.MolFromSmiles(\"COC\")\n",
    "mol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here there are no hydrogens (as expected from the SMILES)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f70160ac5d0>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol = Chem.AddHs(mol)\n",
    "mol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here rdkit manages to add Hs to all of the carbons as expected"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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RVVUVGRmJiU+2zkFHCzyNI9fo1atXt2zZQkTbtm2Ty+UW3daUKVNKS0uFd7fs378/KCho2bJleBq0jXLE0QLP4Mg1mpyc3NDQEBsbO3HiRAk29+TEp8DAQEx8skWOOFrgGRy2Ro8dO7Znzx53d/cNGzZIud1+/frt3Lnz119/HTNmzLVr1+bNmzd58uSysjIpM4BIDjda4Nkcs0bbH8y8cuXKgQMHSh9g9OjRBQUFWVlZffr0+emnn8LCwhYuXHjnzh3pk0AXONZogb/lmDW6bdu2srKyIUOGJCcn88ogTHyqqKhQqVREtH379oCAAEx8sgmONVrgbzlgjd66dUu4RVSj0SgUCr5hevbsmZ6eXlZWNm3atHv37iUlJYWHh584cYJvKng2Bxot8DwcsEY/+uijv/76a9q0adHR0byztAkMDDx48OA333zj5+d36tSpGTNmNDQ0FBUVyWQy4eSDCYVCYZYJV9A1lr2rA2yOo9VoSUmJVqt1dXXNyMjgncWITCabM2dOTEzM+vXrBwwY4OHhwTsRPBVqFIw4VI0yxhISEgwGQ3JyckBAAO84HfDw8Fi3bh3vFPA3HGK0wPNzqBrVarVFRUW+vr7Lly/nnQVsGPZGwYjj1GhdXd2KFSuIaMuWLd7e3rzjPC+dTlddXW3yIR53yRdqFIw4To2uWrWqpqZm/PjxsbGxvLN0glar1Wq1vFOAEdQoGHGQGi0vL//000+dnJw0Go1tvUo6Kipq/vz5Jh/a1m8C+4MaBSMOUqPCg5nff//90aNH887SOUqlctasWSYfzp07l0sYENj5aIHOcoQa3bt378GDB3v27LlmzRreWcAe2PNogS6w+xrV6/WLFy8mojVr1pj9wczgmOx2tEDX2H2NpqWlXbx4MSgoaOHChbyzgJ2w29ECXWPfNXr16tW0tDSS5MHM4Djsc7RAl9l3jS5evLihoWHOnDmTJk3inQXsB34hgxE7rtH8/PzvvvvO3d1948aNvLN0xdixY592m71er5c4DDzODkcLiGGvNdra2pqQkMAYW758+aBBg3jHAbtib6MFRLLXGv3ss89Onz7t7+8vXKYHMCN7Gy0gkr3WqFKp9Pf3/+STT7g/mBnsD86NghF7rdHIyMgpU6a4urryDgJ2yN5GC4hkrzVKROhQsBA7HC0ghu3WKN6xAbzY3mgBi7LdGgXgBaMFjKBGAToLowWMoEYBOgtX6sFIcHBwZmbm4MGDeQfpIrxjA6Qnw78wsA9FRUXjxo172tLg4ODS0lIp84DjwN4o2BW8YwOkhxqFtv24xMREjUZjskihUAQGBtrQfhzesQHSw5UEAABRUKMAAKKgRgEARMG5UWiDW4UAugY1Cm20Wq1Wq+WdAsD2oEahja3fKoR3bAAvqFFog1uFALoGl5gAAERBjQIAiIIaBQAQBTUKACDK/wHf92SxSV13AwAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x7f70439c45b0>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rwmol = Chem.RWMol(mol)\n",
    "bonds = rwmol.GetBonds()\n",
    "b = rwmol.GetBondWithIdx(2)\n",
    "a1 = b.GetBeginAtomIdx()\n",
    "a2 = b.GetEndAtomIdx()\n",
    "rwmol.RemoveBond(a1,a2)\n",
    "rwmol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "After fragmentation, both fragments are unsaturated. I would like to quench them with hydrogen."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7F70439C4E10>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags = Chem.GetMolFrags(rwmol, asMols=True, sanitizeFrags=True)\n",
    "MolsToGridImage(frags)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here only the lone H has been saturated, and not the unsaturated carbon."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f70160b6210>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frag = frags[0]\n",
    "Chem.AddHs(frag)\n",
    "frag"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Explicitly adding H doesn't work either"
   ]
  },
  {
   "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": "3.7.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}