{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2016.09.2\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit import rdBase\n",
    "from __future__ import print_function\n",
    "print(rdBase.rdkitVersion)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "our test molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "m = Chem.MolFromSmiles('COC(C=C1)=CC=C1C2=CC=CC=C2OC3=CC=CO3')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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Ghrfeeuv5558vKyuzxECtra2bNm2aN2/e2bNnJ02apFKpSkpK4uPjDc85ceJEaGjoRx99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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fed254fcd00>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "our substructure; of note substitution pattern is important"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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drVu3GA/Y3Nwsl8vpAaOjo8vKyuiv379/X6vVzpo1ixASGBio1WotFgtzfPBSqFHX1dzc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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fed08f1ead0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "core = Chem.MolFromSmiles('*c1ccccc1*')\n",
    "corea = Chem.AdjustQueryProperties(core)\n",
    "corea"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "get atom mappings; this includes the matched atoms of the wildcard atoms "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "maps = m.GetSubstructMatch(corea)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(7, 8, 9, 10, 11, 12, 13, 14)"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "maps"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "get the indices of all ring atoms by ring"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rings = m.GetRingInfo().AtomRings()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "((2, 5, 6, 7, 4, 3), (9, 10, 11, 12, 13, 8), (16, 15, 19, 18, 17))"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rings"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "rather clumpsy way to remove the substituents in maps\n",
    "a) we sort the atom indices in the rings\n",
    "b) we check if any of the rings is a subset of the larger pattern map ring index set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "sortedRings = ()\n",
    "for ring in rings:\n",
    "    mytuple = ()\n",
    "    ring = tuple(sorted(ring))\n",
    "    mytuple = (ring,)\n",
    "    sortedRings = sortedRings + mytuple"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "for sortedRing in sortedRings:\n",
    "    if set(sortedRing).issubset(maps):\n",
    "        updatedMapping = sortedRing"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "now that we have the correct ring atom indices we assign atom maps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "i = 0\n",
    "\n",
    "for index in updatedMapping:\n",
    "    at = m.GetAtomWithIdx(index)\n",
    "   \n",
    "    if Chem.Atom.IsInRing(at):\n",
    "        at.SetProp('molAtomMapNumber', str(i))\n",
    "        i = i + 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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PPgMfH1BVlWANXC4cOwZffQV1daCqCnPngoMD0GjdfURJCVxdYfZsCVbVL3fu\n3GEymXfu3AEAJyenkJCQmTNn9vKzLBbr4MGD+/bt43A46urqW7Zs2bZtm7KysugxCQkJ/v7+f/31\nFwC4u7sfPnzY2tq6xzOz2exDhw7t37+fxWLp6eo+//RTlc8/B5G+LZJbOKgfChwcYNw4+PprEAiA\nywUmE/75T9DXBycnMDCA7GxYtw4mToSvv5bUhGl8PEydCps2QV0dLFkCOTkt94p2M+nJYIClJcya\nJZF6BsbFxSUlJUU4YZqenu7m5ubt7V1UVNTjB5OSkszMzHbt2sXlcv/9738XFBTs3LlTNENLSkpW\nr149b968v/76y9TU9OzZs/Hx8b3JUABQU1PbsWNHXl6ej4/PlilTVHbvhokT4fBhwAlT+Sfr7jDq\nycWLhMUi5eXknXeIoSExNCS+vqShoWUvh0POniXOzgSAABAlJeLjQ7KzB631vDyyeHHLyS0sSHR0\n267mZnLxIvnmG7J7d9soXjiQ37uXZGQMWg0S09DQEBQUpKKiAgBqamr/93//V19f383xxcXFI0aM\ncHBwSE1N7bCLzWbv27dPXV1deKqgoKDGxsb+V3b3Lpk1q+WP3c6OJCT0/1RI8jBG5dtvvxEqlcyc\nSbjcHo68dYusXEno9JafPVdXcvYs4fH63XJNTU3A559XGBgQADJqFAkLE19DdTW5cYP897/k0CES\nEkIiIkh6Omlq6ne70ic6YWpsbNz9hOnff//deW+Hmc2ioqLBqSwqikyY0PIXumQJwQlTeYUxKscS\nEoiyMgEghw719iNPnhA/P6KhIfzZ4zo4HD16tKG169o7fD7/xx9/FN43vnb2bLJuHXn1qs/FDzV3\n7tyZMWOGMAodHR2Tk5N786lHjx55enoKP2VnZ3fr1q1BLovNJvv2EU3NlqGGnx/p9lIVkgmMUXn1\n4AEZNYoAkM8+6/Nn6+rIiRPEwuL23LkAoKmp6efn9+zZs958NCMjozVNnJyc0tLS+tz6kCUQCM6e\nPTt27FgAoFAoK1eu7OYPrbq62s/Pj06nA4C2tnZoaChvAH3/Hrx4QdauJTQaASA6OiQ0dCDjDDTo\nMEblUkkJGTOGABBvb8Ln9/MkPN61P/5wc3MTZiKdTvf29u48qdeqtLR07dq1wufQexzbDmPCCVNV\nVdWuJkz5fH54eLhwjTs6nb527dpX0umtp6cTV9eWMf727aSignh7ExMTYg8Yll0AAAgISURBVGJC\n1q4lLJY0akDiYIzKn5oaYmtLAMicOYMyyZiVlbV27VrhhRQAsLe3Dw8Pb25ubj2gubk5NDRUuCam\nkpKSn59fXV3dwNsd0oqLi0UnTE+cOMHn8wkhCQkJU6dOFf5JCq/IS7uyqChiY0NevCDu7mT3biIQ\nEC6XfPIJ8fWVdiXoDYxROdPY2HKJ1tqaVFcP4onLy8uDgoJ03zymaWBgEBQUVFlZGRcXZ2Vl1Xp5\nBG/8FnXr1i0HB4fWf34WLFgg/PWECRMuXLggs7IEAnL3LjE1bRup1NcTLS3y8qXMSlJsGKPyhM8n\n77xDAIixMXn+XBItsNnskydPtt7J2HrPo5WVVVxcnCRaHOpEJ0w1NTUH4WamQdH5wTYHB5KYKKNq\nFB0+xSRPNm2Cw4dh5EhISgJbW4k2lZycvHfv3lu3btHp9ICAACaTqSSjV30MCQ0NDVFRUTo6OtbW\n1iYmJrIuByAiAi5dgsjIti0ODhAcLIfPjCkCjFF5sW/fvtFXrnx0/z5cvSqdh3+uX7/u4eExZ86c\nhIQEKTSHBlNXzwfr68u6MkWED4PKhTNnzgQGBvqmpt45c0ZqD1CWlZUBgJGRkXSaQ4Opq+eDkSxg\njMrezZs3fX19CSHBwcEuS5dKqBU2m80SfbcHQGlpKWCMDl2//go5OWBiAuPGAYUCYWGyLkhxYYzK\n2N9//71ixQoOhxMQEOAvyTXtz549q66u7uvr27pF2Bs1NDSUXKNIgkaPhshI+OADsLaGzz5rW+MV\nSR3GqCwVFhYuXLiwpqZm1apVe/fulWhbwr6nrsi69NgbHQ7u3YP4eKiqknUdCg1jVGaqqqoWL15c\nXl4+b968U6dOib52QhI69z2xNzocCL9t8EKxTGGMykZjY+PSpUtzc3NtbGwuXLjQYd1fSejc98Te\n6HCAMSoHMEZlgM/nf/DBBykpKSYmJlevXtXS0pJCo51Ds7y8HLA3OtQJb3gSfeU1kjqMURk4c+bM\nhQsXdHR04uLipHYvd4chfE1NDYvFUldX18DXVAxp2BuVAxijMkCj0VRUVN59993JkyeLbi8qKnr8\n+LEkWiSEdOh74k2jwwTGqBzAGJUBQ0PDpqam06dPCwfaQjExMZaWlmvXrpVEi1VVVRwOZ9SoUapv\nXnuHE6PDBA7q5QDGqAy4u7svW7asvr4+MDCwdaOLi4u6unpCQkKk6IPSg6RzaOJl+mECe6NyAGNU\nNg4dOqSiohIREZGcnCzcoqWl9c033wDAli1bOjxuNHCdQxN7o8MExqgcwBiVjYkTJ27ZsoUQsmnT\nJsGbEZmvr6+jo2NxcfHBgwcHtznsjQ5bOKiXAxijMhMYGDhu3LjMzMzw8HDhFiqVGhoaSqFQDhw4\n8OzZs0FsC3ujwxb2RuUAxqjMqKmpffvttwAQEBBQW1sr3Dhz5sxVq1Y1NjZ+8cUXg9gWPsI0XP1q\nYhIyY8Y9Ol3WhSg0jFFZWrVq1Zw5cyoqKnbv3t268cCBA+rq6pGRkXFxcYPVED7CNFxdKCvbfPt2\nAYcj60IUGsaojIWGhtJotLCwsNzcXOEWY2Pjbdu2AQCTyeTxeIPSCj7CNFwJl2LAxddlC2NUxqZN\nm+br68vlcjdu3Ni6cevWrWZmZjk5OSdOnBiUVvARpuEKY1QeYIzK3t69e3V0dOLj4y9duiTcoqSk\nJLxYv2PHjsrKygGeHx9hGsaoVCoACPBKvUxhjMqetrb2V199BQBMJpPzZpJr6dKlXl5er1+/Fu4a\nCHyEaRjD3qg8wBiVC+vXr7exsSkoKAgJCWndGBwczGAwTp48mZ2dPZCT402jwxjGqDzAGJULNBot\nNDQUAPbs2dP6oL2lpeWGDRv4fP769esH8nOCN40OYziolwcYo/Ji/vz5K1asaGhoCAgIaN24c+dO\nAwODlJSUs2fPDuTMJSUlJ0+ebN2CvdFhA3uj8gBjVI6EhISoqamdOXPm1q1bwi2amprCW0q3bt3a\n7wftGQyGsbHxhAkTWrdgb3TYwBiVBxijcmTs2LGdH7T/+OOPnZycSkpKDhw4MFgNYW902MBBvTzA\nGJUv27ZtGzduXFZW1qlTp4RbRB+0LywsHJRWsDc6bGBvVB5Q8C9A3vz+++//+te/9PX18/LyWl/T\n5Ovrq6uru337dnV19f6dls1mZ2Vl3blz586dO3/++SePx6utrdXU1By8wpEMJCYm5uXlzZkzx8LC\nQta1KC6MUXk0b968hIQEJpMZHBw8kPOUlpampKQkJydnZmbevXuXI/Lk9YMHD6ytrQdcKUIIY1Qu\n5eTkTJs2DQDu3bs3ZcqU3n+wvr4+OztbGJ1paWmvXr1q3UWj0SwsLOzt7d3c3FxdXS0tLYXTagih\nAcIYlVOfffbZ8ePH3d3d4+PjuzmMz+fn5uZmZmZmZmampKTcu3dP9GqDoaGh/RuzZs2SzpucEVI0\nGKNyqrq62tzcvKqq6uLFi0uXLhXdVV5enpGRIYzO5OTkmpqa1l0MBsPW1tbV1VUYnThsR0gKMEbl\n15EjRzZu3Dhx4sT79+/n5+cLpzgzMzMfPnwoepihoaFwnG5vb+/o6KisrCyrghFSTBij8ovH402f\nPv3vv/+m0Wh8Pr91+8iRI52cnFxcXJydnZ2dnXV1dWVYJEIIY1SupaSk3L59OyAgQHh1SHiByM7O\nDq8OISQ/MEblHZ/Pb2xs7PftogghScMYRQihAcGxIUIIDQjGKEIIDQjGKEIIDQjGKEIIDcj/A4Zf\nB+h4ed/BAAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fed254fcd00>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "use case to show my problem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "i = 0\n",
    "\n",
    "for index in maps:\n",
    "    at = m.GetAtomWithIdx(index)\n",
    "   \n",
    "    if Chem.Atom.IsInRing(at):\n",
    "        at.SetProp('molAtomMapNumber', str(i))\n",
    "        i = i + 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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F8vf3P3r0aHNzs4qKyq5du/bs2SMvLy98TVRUlJeX16NHjwBg8eLFp06dMjc3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\nAElFTkSuQmCC\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fed254fcd00>"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "kernelspec": {
   "display_name": "Python [conda env:092016]",
   "language": "python",
   "name": "conda-env-092016-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}