add_formal_charges.ipynb

{
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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def add_formal_charges(m):\n",
    "    m.UpdatePropertyCache(strict=False)\n",
    "    for at in m.GetAtoms():\n",
    "        if at.GetAtomicNum() == 7 and at.GetExplicitValence()==4 and at.GetFormalCharge()==0:\n",
    "            at.SetFormalCharge(1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# bogus example:\n",
    "mb = \"\"\"\n",
    "  Mrv1642508101708072D          \n",
    "\n",
    " 23 24  0  0  0  0            999 V2000\n",
    "   -3.3185    1.1689    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -3.8377    1.8100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -3.3883    2.5019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -2.5914    2.2884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -2.5483    1.4645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.9503    2.8076    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -2.4695    3.4487    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.3092    3.3267    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.4311    2.1664    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.8338    1.0520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -3.5734    0.3842    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -4.6525    1.6809    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -3.6840    3.2721    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.1193    1.4645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.8338    0.2270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.1193   -0.1855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.4049    0.2270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.4049    1.0520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -2.5483   -0.1855    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.0762   -1.0094    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    0.2626   -0.2579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    0.3096    1.4645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.0331    2.2850    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "  1  2  1  0  0  0  0\n",
    "  2  3  2  0  0  0  0\n",
    "  4  5  2  0  0  0  0\n",
    "  1  5  1  0  0  0  0\n",
    "  3  4  1  0  0  0  0\n",
    "  4  6  1  0  0  0  0\n",
    "  6  7  1  0  0  0  0\n",
    "  6  8  1  0  0  0  0\n",
    "  6  9  1  0  0  0  0\n",
    "  5 10  1  0  0  0  0\n",
    "  1 11  1  0  0  0  0\n",
    "  2 12  1  0  0  0  0\n",
    "  3 13  1  0  0  0  0\n",
    " 15 16  1  0  0  0  0\n",
    " 16 17  2  0  0  0  0\n",
    " 17 18  1  0  0  0  0\n",
    " 14 18  2  0  0  0  0\n",
    " 14 10  1  0  0  0  0\n",
    " 10 15  2  0  0  0  0\n",
    " 15 19  1  0  0  0  0\n",
    " 16 20  1  0  0  0  0\n",
    " 17 21  1  0  0  0  0\n",
    " 18 22  1  0  0  0  0\n",
    " 14 23  1  0  0  0  0\n",
    "M  END\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "m = Chem.MolFromMolBlock(mb,sanitize=False)\n",
    "m.UpdatePropertyCache(strict=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'[NH3+]c1cc[nH]c1-c1ccc[nH+]c1'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "add_formal_charges(m)\n",
    "Chem.MolToSmiles(Chem.RemoveHs(m),isomericSmiles=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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