{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2016.03.2\n"
     ]
    }
   ],
   "source": [
    "from __future__ import print_function\n",
    "\n",
    "from rdkit import Chem, DataStructs\n",
    "from rdkit.Chem import Draw,PandasTools,rdMolDescriptors,AllChem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit import rdBase\n",
    "\n",
    "print(rdBase.rdkitVersion)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAFsElEQVR4nO3d3W7jNhCAUavo+7+y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\nKECIjAKEyChAyH+wbKr7EbuHuAAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6b2d9544b0>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "core = \"[a]12[a][a][a][a][a]1[a][a][a]2\"\n",
    "pattern = Chem.MolFromSmarts(core)\n",
    "smiles = \"c1(ocn2)c2cccc1\"\n",
    "mol = Chem.MolFromSmiles(smiles)\n",
    "AllChem.Compute2DCoords(pattern)\n",
    "AllChem.GenerateDepictionMatching2DStructure(mol,pattern)\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAFeklEQVR4nO3dwU4jSRBF0faI//9l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\nlsgowBIZBVgiowBL/gVqe5VGuUIucQAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6b26b5d210>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "core = \"[a]1[a][a][a][a]2[a]1[a][a][a][a]2\"\n",
    "pattern = Chem.MolFromSmarts(core)\n",
    "smiles = \"c12ccccc1cccc2\"\n",
    "mol = Chem.MolFromSmiles(smiles)\n",
    "AllChem.Compute2DCoords(pattern)\n",
    "AllChem.GenerateDepictionMatching2DStructure(mol,pattern)\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}