Sanitization.ipynb

{
 "metadata": {
  "name": "Sanitization"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from rdkit import Chem\n",
      "from rdkit.Chem.Draw import IPythonConsole\n",
      "from rdkit.Chem import Draw\n",
      "\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Building Molecules\n",
      "====\n",
      "\n",
      "Overall process\n",
      "----\n",
      "\n",
      "### From SMILES\n",
      "\n",
      "- Process SMILES\n",
      "- Remove explicit Hs from graph\n",
      "- Sanitize\n",
      "- Perceive stereochemistry: remove redundant or incorrect stereo information. Assign CIP codes.\n",
      "\n",
      "### From CTAB\n",
      "- Process CTAB\n",
      "- Remove explicit Hs from graph\n",
      "- Sanitize\n",
      "- Assign cis/trans markers to double bonds based on geometry\n",
      "- Perceive stereochemistry: remove redundant or incorrect stereo information. Assign CIP codes.\n",
      "\n",
      "\n",
      "\n",
      "Sanitization\n",
      "----\n",
      "\n",
      "\n",
      "Chem.SanitizeMol() calls the following in sequence\n",
      "         \n",
      "- `MolOps::cleanUp()` : clean up a small-set of substructures that are frequently \"incorrectly\" drawn. Example: `N(=O)=O -> [N+](=O)[O-]` \n",
      "- `mol.updatePropertyCache()` : calculate explicit and implicit valence of all atoms. **FAILS** when atoms have illegal valence.\n",
      "- `MolOps::symmetrizeSSSR()` : generates a symmetrized set of smallest rings. **FAILS** in very rare cases.\n",
      "- `MolOps::Kekulize()` : generates a Kekule structure for the molecule. **FAILS** if a Kekule form cannot be found or non-ring bonds are marked as aromatic.\n",
      "- `MolOps::assignRadicals()` : determines the number of radicals at each atom\n",
      "- `MolOps::setAromaticity()` : finds aromatic ring systems, marks their atoms as aromatic, marks their bonds as aromatic, and converts their bonds to `BondType::AROMATIC`\n",
      "- `MolOps::setConjugation()` : identifies conjugated bond systems\n",
      "- `MolOps::setHybridization()` : assigns hybridization to atoms\n",
      "- `MolOps::cleanupChirality()` : removes atom-stereochemistry markings from non-sp3 centers.\n",
      "- `MolOps::adjustHs()` : assigns explicit Hs to aromatic heteroatoms that need them. e.g. solves the `C1=CNC=C1 -> c1c[nH]cc1` problem\n",
      "\n",
      "\n",
      "How long does it all take?\n",
      "----\n",
      "\n",
      "As of this writing (21 Sept 2012), building 100K drug-like molecules from SMILES takes ~14 seconds on my linux box.\n",
      "\n",
      "Here's the percentage of total run time broken down by step:\n",
      "\n",
      "    | Step                            | Time | Percent | Notes                      |\n",
      "    | toMol()                         |  1.8 |    13.1 | SMILES parser              |\n",
      "    | MolOps::removeHs()              |  7.7 |    55.7 |                            |\n",
      "    | MolOps::sanitizeMol()           |  6.8 |    48.8 | Part of the removeHs tally |\n",
      "    | MolOps::assignStereochemistry() |  3.7 |    26.9 |                            |\n",
      "\n",
      "\n",
      "And here's a detailed view of the sanitization steps:\n",
      "\n",
      "    | Step                       | Time | Percent | Notes            |\n",
      "    | MolOps::cleanUp()          |  0.1 |     1.2 |                  |\n",
      "    | mol.updatePropertyCache()  |  0.4 |     2.8 |                  |\n",
      "    | MolOps::symmetrizeSSSR()   |  2.1 |    15.3 | 2.08 in findSSSR |\n",
      "    | MolOps::Kekulize()         |  1.0 |     6.9 |                  |\n",
      "    | MolOps::assignRadicals()   |  0.1 |     0.6 |                  |\n",
      "    | MolOps::setAromaticity()   |  1.2 |     8.7 |                  |\n",
      "    | MolOps::setConjugation()   |  0.8 |     5.5 |                  |\n",
      "    | MolOps::setHybridization() |  0.3 |     2.0 |                  |\n",
      "    | MolOps::cleanupChirality() |  0.1 |     0.5 |                  |\n",
      "    | MolOps::adjustHs()         |  0.4 |     3.1 |                  |\n",
      "\n",
      "Can it go faster?\n",
      "----\n",
      "\n",
      "### Use pickles\n",
      "Build molecules once, store pickles, build from them.\n",
      "\n",
      "This is nice because the pickle contains pretty much everything the RDKit knows about the molecule. It's also quite fast, but it's not inter-operable with other systems. It also takes up a fair amount of disk space.\n",
      "\n",
      "For the 100K drug-like molecules, creating the molecules from the pickle file takes about 1.3 seconds (compare with the 14 seconds for building the molecule from SMILES). The pickle file itself took 0.9 seconds to create and is 28.3MB (the SMILES file is 3.3MB).\n",
      "\n",
      "### Use RDKit SMILES\n",
      "Build molecules once, write canonical SMILES, build from that using limited sanitization.\n",
      "\n",
      "The idea is to trust the input SMILES to only contain correct molecules with a reasonable aromaticity assignment and no bogus stereochemistry info.\n",
      "\n",
      "For the 100K drug-like molecules, parsing the SMILES and calling `mol.updatePropertyCache()` so that atoms have valences assigned takes 2.1 seconds. \n",
      "\n",
      "These input molecules have sufficient information to allow many standard operations\n",
      "\n",
      "Calling `MolOps::fastFindRings()` to determine whether or not atoms and bonds are in rings takes 0.4 seconds. \n",
      "`MolOps::fastFindRings()` does a depth-first traversal of the molecule graph to find rings. This is a fast way to find cycles, but unfortunately it doesn't necessarily find the smallest cycles. In order to get information about about ring sizes, etc. a call to `MolOps::symmetrizeSSSR()` is required. This takes 2.1 seconds for the 100K molecules. "
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "An example of doing partial sanitization\n",
      "-----\n",
      "\n",
      "Start by building a molecule from SMILES and assigning valences:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('N#Cc1ccccc1N1C[C@H](C(=O)[O-])CC1=O',sanitize=False)\n",
      "m.UpdatePropertyCache()\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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QSqVPva6xsTHatGkDS0tLWFhYPFWU5ubmTxxv27YtzM3NYWVlBRsbGyQkJKC4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\nCBljjBk0LkLGGGMG7f8B9HfgI/l9oUIAAAAASUVORK5CYII=\n",
       "prompt_number": 2,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x42659f0>"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Notice that the depiction around the triple bond is wrong. This is because no hybridization information is present.\n",
      "\n",
      "That's easy to fix:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.SetHybridization(m)\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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JICcH+PprYONGwMGh5nhlJfD448CoUcC8eabJRER1xiIks3VrUYyhewadnJzg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\nRU5ErkJggg==\n",
       "prompt_number": 3,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x42659f0>"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tmp=m.GetSubstructMatch(Chem.MolFromSmarts('c1ccccc1'))\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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zQ3Jycv2LuHEDmD8feOMN4NFHgVatgD59gHXrgPPngU8/Nf6e6Gi1iOajjwA7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\nAElFTkSuQmCC\n",
       "prompt_number": 4,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x42659f0>"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Doing a substructure search that looks for ring information fails though:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#m.HasSubstructMatch(Chem.MolFromSmarts('[r]'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "But this can be cleared up using `FastFindRings()`:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.FastFindRings(m)\n",
      "m.HasSubstructMatch(Chem.MolFromSmarts('[r]'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 6,
       "text": [
        "True"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[list(x) for x in m.GetSubstructMatches(Chem.MolFromSmarts('[a;r]'))]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 7,
       "text": [
        "[[2], [3], [4], [5], [6], [7]]"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[list(x) for x in m.GetSubstructMatches(Chem.MolFromSmarts('[A;r]'))]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 8,
       "text": [
        "[[8], [9], [10], [14], [15]]"
       ]
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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IVqtkUoypNYNubm7w9vY2OQTq7OwMPz8/yw2P/vAD8N57gLkt3156CcjNBT75\nxDL1ENF9YRCSVStvF5nyngWWN5mm2rVrBzzzjOm2uDhg8WIgOpoH4BJZKQYhWbXydpEpLwjLm0xT\naatXAz17Aq6uQMuW6rngpUuAmUN2kZ0NTJ4M/Otf5q8hIt0xCMmqaZqGlJQUFBUVmWz73//+h4KC\nApNtGRkZuHr1avUUsny5muwSGQn8/LNaLH/6NDBsGFBcXPb64mLgqaeAvn2BF1+snhqIqEYwCMmq\nBQQEoKCgABkZGWXa/P39ISI4ePBgmTY/Pz+4uLggNTW16kXcvAn84x/AwoXA738PNGoEdO0KfP01\ncO4c8PnnZX9m3jw1iebjjwEbOTeRyF4xCMmqlTcpxtXVFb6+viaHTp2cnNCzZ8/q2Zw7ORnIywPG\njbvz/fr1gccfB7ZsufP9hATg9deBVauAFi2q/vlEVKMYhGT1ynsWWN5kmocf/j1+/rlN1QvIzQUa\nNFDrBO/WurVqv/3aCRNUD9LMQbxEZF0YhGT1ygvCXr16IS2t7NAoAHTpMg2xsU9WvYDmzYHr1wFT\nzxvPnVPtACCiQrBrV+D//q/qn0tEFsEgJKunaRrS0tJQWFhYpq1372eQnv49TG0io2nAsWPA5ctV\nLCAgQC19iIm5832DQS2PGDq09L3gYLVe0MRBvERknfi3laxejx490bfvO0hPLztztHv3+igudkZK\nStmf8/EB3NyAKh9mX68e8NprakPt6GjgyhUgIwMIDQU8PIBnn1XXOTiomaVmNtwmIuvEICSrV79+\nPeTlPY+9e+uXaXN2Vlt3mho5rVMH8Pc33XbfpkwB3n9fTYLx8ACCgoC2bdXEGB6sS2TTyh6YRmSF\nNE0FWkRE2bbAQPNhFxhYDT3CEuHh6ouIahX2CMkmBASYD7vKthERAQxCshGaBhw6BLOTYo4eVUcC\n3i0wEDhxArh4seZrJCLbxCAkm9Cjh3rmZ2ITGfj6qokxR46UbfPyUkv92CskInMYhGQTnJ0BPz91\n4tHdHB2Bw4fVtp53c3BQu6IxCInIHAYh2QxNq9zEFx+fapwwQ0S1DoOQbEZlJ754e5vuSRIRAQxC\nsiGaBqSnA9eu3fm+nx/QsOGdE2K++kpdDwB9+gC7d1uuTiKyLQxCshl+fupZoamTlerWBebPN/1z\nrq5A+/Y1WxsR2S4GIdmMunXVcojs7LJtL7wALFsGnD9v+bqIyLYxCMmm7NihZoHezccHCAlRO6AR\nEd0PBiHVGrNnA59+Cpw+rXclRGRLGIRUa3TsCDz1FPCvf+ldCRHZEm66TbXKyy+rc3E7dNC7EiKy\nFewRUq3i6QlMmgS8/bbelRCRrWAQUq3zz38CN2/qXQUR2QoHERG9iyAiItILe4RERGTXGIRERGTX\nGIRERGTXGIRERGTXGIRERGTXGIRERGTXGIRERGTXGIRERGTXGIRERGTXGIRERGTXGIRERGTXGIRE\nRGTX/h+RvsAWy24oyAAAAABJRU5ErkJggg==\n",
       "prompt_number": 9,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x42659f0>"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Here's another example of the problems that a lack of complete ring information can cause.\n",
      "\n",
      "Start with the sanitized molecule:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sm = Chem.MolFromSmiles('O=C(N[C@H]1CCCc2ccccc21)c1n[nH]c2ccccc21')\n",
      "sm"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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sCIV4k1WpVIqysjKEhITIvbmstunZsyfS0tKwb98+bNq0Ca+//jpyc3Ob7yzv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\n",
       "prompt_number": 10,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6c20>"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Now build the same thing with minimal sanitization."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('O=C(N[C@H]1CCCc2ccccc21)c1n[nH]c2ccccc21',sanitize=False)\n",
      "m.UpdatePropertyCache()\n",
      "Chem.SetHybridization(m)\n",
      "Chem.FastFindRings(m)\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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7du0a2djYCL4a86effqJmzZrRnTt3VNpSUlLqbGNPJ/5dmDWYjY0NfH199bIa\n0NfXFy1btkRmZqZG13FwAP76C5DLax93dFT+L98m1L5+/frhjTfewMSJE0GPTDg5Oztj2rRp+Pjj\nj1Hy6EOReiKXyzF9+nRMnToVbdu2rdVWWVmJmJgYtW3s6cVByAySiYkJhg4dqvHqUUdHgAh4dOGo\npSXQogUHoa588cUXyM7OxoYNG1TaoqKiYGtri1mzZglQmfJxieLiYrVvmkhKSkJFRQW/hcLIcBAy\ngxUaGort27drtHy9TRvA1FR94Dk6chDqioODAxISEjB16lQUFhbWarOwsMDy5cuxePFiZGdn67Wu\noqIiJCQkIC4uTmUV8/379zF79mzExsY2yR1xWONxEDKD5e/vDyLCvn37Gn0NU1NlGHIQ6t/kyZPh\n5OSEuLg4lTZ/f38MHz4ckydPVpk+1aXExMSax3wetXDhQrRt2xYffPCB3uphhoGDkBkssViMwMBA\nrUyPqgu8Tz8FvL01ujSrh6mpKZKSkrB69WqcOnVKpX3x4sU4c+YMvv/+e73Uc+vWLSQmJuKzzz5T\n2czh+vXrWLx4sdo29vTjxyeYQVu/fj2ioqKQl5cHkUjUqGsMHgz07g38979aLo41yIQJE3Dq1Ckc\nOXIEJo88q7JkyRLMnz8f58+f1/mD6xMmTMClS5ew59GdzAGMHTsWFy9exMGDB3VaAzNMPCJkBi0o\nKAj37t3DsWPHGn0NBwfVxTK2tsDAgf/8/d495eIZpn3z5s1Dbm4u1qxZo9L24YcfwsnJCTNnztRp\nDTk5Ofjmm28wf/58lbYzZ84gOTkZiYmJOq2BGS4OQmbQ7Ozs0L9/f42mR+uaGr1wAThwoPG1sYax\nt7fHvHnzEBMTA5lMVqvt39Onmvyy8zgzZsxAWFgYevXqpdIWExOD0NBQtW3MOHAQMoMXGhqKtLS0\nRn/e2Vn98dhYQMcDEfa3MWPGoGvXrpg2bZpKW8+ePTF69GhMnjwZCoVC633v3bsXmZmZakeDEokE\nEokECxYs0Hq/rOnge4TM4N28eRMdO3bE2bNn4e7urpVr2toC168D/v7AvHmApyfwzDPAIyv9mRad\nPXsWXl5e2Lt3L3x9fWu15efno2vXrvjss8+0umqT/t4uzdvbG0uXLq3VplAo4OXlhT59+qjdVJ4Z\nDx4RMoPn5OSEXr16ae3VTA+JRMCsWTwq1JcXXngBkydPxsSJEyF/ZKsfe3t7zJ07V+30qSbS0tJw\n4cIFtfcgf/zxR/zxxx+IjY3VWn+saeIgZE1CSEiIxhtwqxMUpHzWcMsWrV+aqZGQkID8/Hy1L3we\nO3ZsndOnjVFVVYXo6GhER0ejdevWtdoqKysxY8YMREVFoU2bNlrpjzVhwm1zyljDnT9/jxwcbtHN\nm9q5no0NUUGB8s8SCVGnTkR2dtq5Nqvfjz/+SM2aNaO8vDyVtuzsbLKwsKBDhw5p3M/evXupY8eO\nal8JlZiYSB07dqSysjKN+2FNH98jZE1Gt27A5MnKL03Z2gJ5ef88MjFgAPDrr3yPUF+GDBkCOzs7\ntXuRfvfdd/D390e7du007qe8vBxWVla1juXn5+OZZ57BwoUL1e4ww4wPByFrMmbMAI4dA7KyhK6E\naerSpUvo3r070tPTMXjwYL32HR0djR07duD06dO8iwwDwEHImpDjx5U7xNy+DdjbN+4aJ04APXpo\nty7WODNnzkRKSgrOnDkDsVislz6vXbuGrl27YuPGjRg6dKhe+mSGjxfLsCajRw/lw/Hbtzfu87m5\nQEaGVktiGpg+fTqqq6uxaNEivfUZGxuL3r17cwiyWnT/hlXGtEQkAkJCgM2bgZEjn+yz1dXKz3h6\nKt9P2MhtS5kWWVlZYcWKFQgLC8Pbb78NNze3Wu0KhQL3798HAFRXV6OoqAiA8sW6D1/qW1lZibKy\nMgDK+4EVFRUAgNLS0prXd5WUlEAul+Ovv/7C+vXrcYC3E2KP4CBkTUpoKPD660BZGWBt3fDPLVkC\n/P47kJrKIWhIAgMDMXjwYPTv3x/FxcUAgIKCggZ/3sLCAjY2NgAAS0vLmoUx1tbWNdOttra2MDc3\nB6B8dtDHx0eb3wJ7CvA9QtakyOXKTbTXrlUGYkNkZwO9egEbNgDDhum2PtY4hw4dQnl5OQCgRYsW\nEIlEEIlENW+kMDU1RfPmzQEA5ubm/OJcplUchKzJGTkSMDNThuHjVFUBr7wCvPAC8N13uq+NMdb0\n8GIZ1uSEhgJbtwIPHjz+3IQEID8f+PJLnZfFGGuiOAhZkzN4MFBeDjzuHaoHDgCffw58/z1gZ6ef\n2hhjTQ8HIWtyrK2Vb42obw/u4mLg/feVu9D07au30hhjTRAHIWuSQkOB9HTloxDqREUBNjaAmlfQ\nMcZYLRyErEkKDQXEYuDsWdW2PXuUXxs2KM9hjLH68KpRxhhjRo1HhIwxxowaByFrMmxtgYED//n7\nvXv/vEbpYfvt27XbzXjvJMbYY3AQsiblwgXlYxGMMaYtHISsSYmNBWbOFLoKxtjThIOQNSlhYUBJ\nCbB7t/r2nj0BFxfll6enPitjjDVVHISsSRGJgFmz6h4VHj+ufO9gbi7w66/6rIwx1lRxELImJygI\nMDUFtmwRuhLG2NOA19SxJmn2bGDsWKGrYIw9DXhEyJokPz/gkReaM8ZYo/DOMowxxowajwgZY4wZ\nNQ5CxhhjRo2DkDHGmFHjIGSMMWbUOAgZY4wZNQ5CxhhjRo2DkDHGmFHjIGSMMWbUOAgZY4wZNQ5C\nxhhjRo2DkDHGmFHjIGSMMWbUOAgZY4wZtf8DafeBdlUBzxUAAAAASUVORK5CYII=\n",
       "prompt_number": 11,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6b40>"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "That happened because the depiction algorithm uses ring-size information, which is not correct after calling FastFindRings()\n",
      "\n",
      "Ring membership is fine:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[list(x) for x in m.GetSubstructMatches(Chem.MolFromSmarts('[A;r]'))]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 12,
       "text": [
        "[[3], [4], [5], [6]]"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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+ehkN6O/vD0dHR6SlpWl0n3btgL/+Ampq6h93cRH+ya8Jta9v37545ZVXMHXq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\n",
       "prompt_number": 13,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6b40>"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "But the ring sizes are not:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[list(x) for x in m.GetSubstructMatches(Chem.MolFromSmarts('[r5]'))]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 14,
       "text": [
        "[]"
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "ring counts are also wrong:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[list(x) for x in m.GetSubstructMatches(Chem.MolFromSmarts('[R2]'))]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 15,
       "text": [
        "[[7], [8], [9], [10], [11], [12], [16], [17], [18], [19], [20], [21]]"
       ]
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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2/LKytDu9qGnTdKK9iE66L95cd6aJE3V+bGAg8NprtscmTdJjwcHaaiSvwSAk\ntxUbGwsRwdZKtBqqVNEwZBC6WLNmxqbLn38OrF5tHKtaFZg9Wx+npLhuXuHu3TofFtAAbtjQOJaU\nBHz8sT5+/nnPXBGHKoyDZcit9e3bF7Vq1cJbb71V4XPce6/2xg0bZvv8mjW6OtyDD1aySLIvK0sH\nzKSmAo0a6aT6ojvUx8YCmzZpMP74I1C/vnPrefhh4OuvddWbo0dtJ/w/8oje/7Z3jG56bBGSW+vR\nowdWrFiBynxeK63l16ULQ9CpgoN1qTJA779Zp09Y/eMfOuDq6lWj9egsq1ZpCAI6SKdo0H31lYYg\nAEyYwBD0QgxCcmtdu3bF+fPnK7UcWnh4ycEyoaG6gpzV+fN8/3OKnj2Bbt308cyZwKFDxrHGjY0A\n/OwzDSRnyM/XJd8A7Q4dOdI4VlBgjF5t1MgYyENehUFIbq169ero0KFDpUaPltYiPHTIaCSQE82Z\nAwQF6V6Xo0bZHps40Vh3dvRooPjeho6waJHOWQR0gEzR7tnFi3U3Fesxf3/HX5/cHoOQ3F58fDw+\n//zzCn9/gwb2n580Sd+HyckaNTJaXevXA//+t3EsKAhITNTHR48acxAdJTNTdz4BdC7sk08ax7Ky\njD+A1q2Bfv0ce23yGAxCcntxcXE4duwYfvrppwp9/7PPas9bcb166WYJRRcWIScZPx5o0kQf/+lP\nxi4VANCjh9F9OmMGcPiw467717/qKjfWcxddLm3OHOPY7Nllby1GNzUGIbm9unXrok2bNg7bo9DK\nYtEpbWwVuoC/v84tBHRN2mnTbI/Pnw+EhGj36fPPO+aaZ84Yq8N07qzLqVmdPWsM3una1diIl7wS\ng5A8QlxcHFauXOnw83btqnMNv/zS4aem4jp1MrZnSkzUPQCtGjbUjZoBbaJXoiv8V9Ona8uztKXU\nrl7VrZeKHyOvwyAkj9CrVwJ+/nnZr1vEOdJrr5VsoJCTzJ2ru5jk5+vozaLTYsaOBaKj9fH06bbH\nKsLPT4OuTx/b5dKOHNGpGwDw9NO6SDh5NQYheYQmTWqhZs0ILFvm+HN37Gi8/5KTRUToKCUA2L5d\nN3u2CgrSoHziCV3toLL37BITddPo4gNwXn1Vl3ULCeEnIALAlWXIg0yYAOzaBWzYYHYlVCn5+TpK\nc98+Xcnl0CH9pyvs2KHbh4noH9T06a65Lrk1tgjJY8TH6wIgFy9W/BxJSQ4rhyrK11d3gLBYdI8s\nV45WGj9eQzA83LgnSV6PQUgeo3Vr7Vkrun7zjUhNBVascGhJVFEPPAAMGqSPFywAvvvOede6elX3\nP/zoI+Cbb/S5CRN0jVMisGuUPMzIkcAvv9z4oMKCAl1XuWVLnT7GKWNu4MIF4M47dX27evV0srvF\noqEFAIWFwOXL+jg/XwMN0Pt71nmI16/rxHgAyM42VqbJzNQtleyJigJ++smpG0uTZ2EQkkfZuFHn\nX6en65rO5fXmmzqf+sAB4NZbnVcf3aD583W0aGCgEXrOlJioE/u7dHH+tchjMAjJo+Tl6e2dhQs1\nEMtj/36gTRvdbq5nT+fWRzeooED7rBMSjJ3sa9TQlqHFYqyEXqUKUK2aPvbz01XTAZ2oHxKijwMD\ndeQpoJ+SrC2+0FD9HkCHCNes6dyfiTwOg5A8zsCBOt5i4cLffm1uLnDffcBddwH/+pfzayMiz8PB\nMuRx4uOBlSv1ttFvmTpVR5nOn+/0sojIQzEIyeN06aLjIqwDAEvz9de6etYHH+hiJkRE9jAIyeME\nBwOxsUBZa3BfvQoMHqz7rHIXeiIqC4OQPFJ8PLBsWenLUb74oo6hsG4wQERUGgYheaT4eB0UmJxc\n8tjmzfr18cecKkZEv42jRomIyKuxRUhERF6NQUgeIzRUNxq3On/emG9tPX7mjO1xX1+XlUdEHopB\nSB7l0CGdFkFE5CgMQvIokya5dtceIrr5MQjJo/TqpRsPrF9v//jvfgdERupXy5aurIyIPBWDkDyK\nxQJMm1Z6q3D3bl27OTUV+P57V1ZGRJ6KQUgep2tX3Yzgyy/NroSIbgYcU0ce6bXXgKFDza6CiG4G\nbBGSR+rYEYiONrsKIroZcGUZIiLyamwREhGRV2MQEhGRV2MQEhGRV2MQEhGRV2MQEhGRV2MQEhGR\nV2MQEhGRV2MQEhGRV2MQEhGRV2MQEhGRV2MQEhGRV2MQEhGRV2MQEhGRV/t/CSrQ0fxg+mkAAAAA\nSUVORK5CYII=\n",
       "prompt_number": 16,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6b40>"
       ]
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Here's what the query should have generated:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[list(x) for x in sm.GetSubstructMatches(Chem.MolFromSmarts('[R2]'))]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 17,
       "text": [
        "[[7], [12], [16], [21]]"
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sm"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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BgwZhzJgxmDt3Ltzc3ODq6qrTaVW1nn8e+OADYNky4PhxYP58IClJ/6+rhrOzM5ydndVu\n1zZ1aixeekm1muWrr4Dg4Ed/Pm8eIJcD27c/2q9TJ2DLloaPnz8fuHQJ2LtXkLh6QUQoLy9XO1qS\nShHyGkJhcREagMLCQhw/fhzJycmNbm/fvj2ee+45vP7663B1dYWLi4v4t0ZauhTIyVF9+m7ZAjz9\nNPDmm+JmUkOhUODu3btix9CJdu2AmBjVrHQjPzNJXnl5OZRKpcYRYdu2bcX/99FKPCIUlgn+UzI8\nycnJGDt2LBwdHdXu8+677yI4OBhDhgwxjH/kZmbA5s2qAgSA//f/gIMHRY30uJqaGqSlpWHSpElY\ntmwZrl+/jtDQUNy50/jtmoxFUBBw8ybwxRdiJxGHthGfVEZSXITC4iIUmUKhQHJyMmbPni12lOaz\ntga++Qbo1g2orVUNU4qLRY2UlZWF8PBw2NvbY8GCBfDw8EBubi5++uknXLt2Dc7OzkhMTAQRiZqz\npezsgCVLVDPTtbVipxGetiKUykkmUrg6jjHhIhTZvn37IJPJMHXqVLGjtEyfPqozSdu2Be7eBQID\nAYGXKty+fRtxcXFwd3fHyJEjUVZWhq1bt6K0tBSxsbFwdXWFk5MTMjIysHbtWixduhTjxo3DhQsX\nBM2pK2+/rTomuHmz+n0+/1w1aH/8KyFBuIz6IpfLYW5urnaZjzGNpBQKhdptUil0Y8FFKLKkpCQE\nBwerX79nDMaMAdasUf0+Px8IDQX0POIiIuzfvx/BwcHo1asXEhMTMWvWLFy+fBkpKSkICAhA27Zt\nGzzGzMwMs2bNQm5uLp566ikMHToUcXFxGj+QDJGNjeoQ7YoVQFVV4/sEBABnzjT8MtaftR4nk8lg\nY2MDMzOzRrdPmzYNx48fFzhV89TNArm4uODYsWON7sMjQmFxEYro9u3b2LVrl3FOi/7RggVAeLjq\n9zt3Ah9+qJeXuXTpEqKiotCnTx+8+OKL6Ny5M/bv34+ioiJERkY26XZTPXr0wDfffIPPP/8c//rX\nv+Dt7Y2ff/5ZL3n1Zf581c8a6kZ5XboAQ4c2/OraVbVNLpejoqJCmKA6pm3EZ2VlZTiXJvyD2tpa\nJCYmwsnJCUuXLsWSJUvgreaCFMY0spUCLkIRbdu2Df3798fo0aPFjqIbn3wCjBun+n1MjOo2TjpQ\nXV2N1NRUTJw4Ef3790dGRgbee+89XLt2DQkJCfDx8Wl02Yk2QUFBKCwshLe3N0aOHImoqChUqRti\nGRgrK2D5cuCjj4CHD5v32OzsbJw9e1YvufSJiPDjjz+ifVWVash77ZrYkZpEoVAgMTERAwcORHR0\nNP7617+iqKgIYWFhT8xa1OGpUWFxEYooKSkJoaGhYsfQHUtL4OuvAUdH1XBl7lzVEosWys7ORnh4\nOBwcHLBgwQIMHz4c586dQ1ZWFsLCwtCpU6dWR+7cuTMSEhKQnp6O7du3Y/DgwTh06FCrn1cIc+ao\npkl37Gje4+zt7TFq1CjcuHHDaC49l56eDi8vLxzZuBGFcjnw7bfAsGE6+2FLH5RKJZKTkzFkyBBE\nRUUhPDwcFy9eREREBGxsbDQ+lkeEwuIiFMnZs2eRm5srrSIEVPNvaWmAra3qjI7AQODWrSY/XCaT\nITExEU8//TS8vLxQUlKChIQEXL16FbGxsXB3d9dL7BdeeAH5+fmYMmUKJk6ciPDwcIO4ULdCobrr\nVWMsLYHoaKCysnnP2b9/fwDA7NmzsVnTGTciIyKkpqZi8ODBCA0NxfTp03Hol19gvnSp6uSs335T\n3RZs3DigqEjsuPXqcnt6eiIiIqL+2HVkZGSTzwWQyjIQo0FMFAsXLqRJkyaJHUN/vv6ayMyMCCAa\nO5aoqkrtrkqlkjIyMigoKIisra2pb9++FBsbS1euXBEw8CPHjh2jQYMGUc+ePWnHjh2iZFAqiVJS\niNzciF56SffPn5ycTF5eXlRTU0OVlZV06dIl3b9IK6SkpNCQIUPIzs6OoqOj6c6dOw13yM4mevpp\n1fcXQGRjQxQbS1RbK07g36Wnp9OIESPU526CzMxMcnV1pd27d+shIWsMF6EIKisrqUuXLvT111+L\nHUW/oqIefVC9/fYTm2/cuEGxsbHk4uJClpaWFBQURBkZGaRQKEQI21B1dTXFxsZS27ZtKSgoiH77\n7TdBXreuAD08iDp2VH22l5fr9jWqqqrIwcGBsrKyiIho+fLl9Je//EW3L9JC+/fvp1GjRpG1tTVF\nRkbSrVu31O9cU0O0Zg2Rre2j77NRo4jy8oQL/Ltm5VbjzJkzFBAQQBYWFrRgwQI9pGTqcBGKICUl\nhezt7alKwyhJEhQKosmTH31IJSRQTU0NpaSkkJ+fH7Vp04Y8PDxozZo1dP36dbHTNurcuXPk7e1N\nnTt3poSEBL2+1rFjxyg4OJKsrYneeovo2jX9vE5ubi5FRkYSEVF2djZ169at/v//NX29qBYHDx6k\nMWPGULt27SgyMrJ5P3hcvEg0fvyj7zNLS6LISKLKSv0F/t2hQ4ca5L5582azn+PUqVPk5+dHFhYW\nFBYWRpcvX9ZDUqYJF6EI/P39KSIiQuwYwrhzh8jZmQggWceO5O7kRFZWVjRt2jTat2+fQYz+tKmp\nqaE1a9aQra0t+fv76/yD6tSpU+Tv70+WlpY0b948unJFptPnP3r0KJWUlBARUWlpKa1atYoePnxI\ntbW15O3tTZs2bSIiou+//55cXV0F/Ts5efIk+fn5kZWVFS1cuLDl0+FKJVFCApGd3aNCHDyYKDNT\nt4F/V5e7rrxakvvMmTM0efLk+uf45ZdfdB+UNQkXocCuXLlCbdq0oXPnzokdRWeUSiWtXr1a/fGQ\n3Fxa1bcvPT9iBK1du7ZFx00MQXFxMU2YMIFsbGwoNja21YWRmZnZoARKS0t1lLShupw1NTXk5ORE\nhw4dIiKijz/+mCZMmEBKpZIePHhAffv2pX379hER0a+//qqXLHV+/vnnBkWis2OUv/5K9PLLj8rQ\n3JwoLIxIppsfLrKyshrkbkl5FRYWUlBQEFlYWNDMmTMpPz9fJ9lYy3ERCuwf//gHDRs2TOwYOnXw\n4EGysrKi27dvN7pdoVBQ3759ad26dQIn0z2lUkmff/45denShUaPHt2iD7E/fpgKeaJKXcH98ssv\nZG9vT8XFxUREtGDBAgoNDSUiokuXLpG9vT3duHFD569fUFDQoAQKCgp0/hpEpDrQam//qBAdHYky\nMlr8dNnZ2fWjt5bmLioqoqCgIGrTpg0FBQVRTk5Oi/Mw3eIiFJBSqaQBAwbQJ598InYUnZo1axZN\nnTpV7faMjAyytrame/fuCZhKv3799Vd65ZVXyNLSkiIjI5t0vPfs2bMNpsLqpivFUFtbW3+yzKFD\nh8jBwaH+Bxl/f3/66KOPiIh09nd24cKFBiWQm5urk+fV6O5d1WiwrgzNzIhmziRS8wNbY3SRu7S0\nlMLCwsjS0pImT55MJ06caPZzMP3iIhTQkSNHqF27dkY7NdiY+/fvk62tLe3Zs0ftPjNmzKBXX31V\nwFTCSUlJoW7dupGHhwdlqjkedf78+QYfpnkinNWoSVFREWX8Plr68ssvydPTk6qrq6m6upo8PT3p\nwIEDLX7u4uJimjlzZv1ZwdnZ2bqK3XTffUfUp8+jQnRwIEpNbdJD//73v9O4cePoyJEjzX7ZX3/9\nlcLCwqht27Y0fvx4OnbsWLOfgwmDi1BAc+bMoWnTpokdQ6c2bNhAvXv3Vnu87O7du9SuXTv64Ycf\nBE4mnLt371JYWBiZm5tTWFgYyX4/HnXx4sUGJWAMx4U3btxIp06dIiKiDz74gPz9/YlIteRHqVQ2\n+XmuXbtWXwITJkyg48eP6yVvk5WXq84kNTd/VIiTJxNdvarxYbUtWJd448YNWrhwIdnY2NCzzz7b\nohJlwuIiFMiDBw/I1taW9u7dK3YUnRo9ejQtXbpU7fb4+Hjq06ePUZwd2lrffPMN9ejRg1xdXSk0\nNJSsra1p9OjR9OOPP4odrdmUSiW9/PLL9ccvw8PDafXq1Vofd/36dQoLCyMrKyvy9fU1vBI4epTI\n1fVRGXbqpDrbtBklr87du3cpMjKS2rdvT8OHD68fZTPDx0UokM2bN0uuEPLz88nMzIwuXLigdp8R\nI0bQ8uXLBUwlvK+++opGjhxJRKoPwzfeeIPmzZtH3333HRER7dmzh7Zt2yZmxFa5fv06ubm50f37\n90mpVFJlI+vz6krA1taWnn76acMugYoKouhoorZtHxWiry+Rhu9jTe7du0eRkZHUoUMHGjp0KKWn\npzdr9MzEx0UokLFjx9KyZcvEjqFTkZGRNHbsWLXbs7OzyczMTNSTQoQQHx9PI0aMULv9jTfeoDlz\n5giYSPfqpgh3795NM2bMqP/zx0vAy8vLsAvwj1p5mbby8nKKjY2lrl270sCBAyklJUVSP+iaEi5C\nARQUFJC5ubnaQvj+++8pKipK4FStU1NTQw4ODrR582a1+yxevJh8fX2FCyWSVatW0YQJE9Runzlz\npqQuoFB3JumePXuoR48e1K9fP9q8eTPV1NSInKwFWnCZtoqKCoqNjSV7e3tydnbmApQAvvuEALZu\n3QofHx84Ojo2ut3R0RHx8fFYv369wMla7ocffkB5eTmCg4Mb3V5TU4OtW7dK46bDWmi7ZY7U7jbe\nsWNHAMDChQsRGhqK8+fPY/bs2bCwsBA5WQtYWAAREUB2NjB+vOrPfvpJdSfjqCjgsftTVlVVYe3a\ntRg4cCDWrVuHFStWID8/H0FBQS26HyYzHPy3J4CsrCyMr/tH1ggXFxds374dixcvxsGDBwVM1nJJ\nSUkICgpSe1uZPXv2oLKyElOnThU4mfC0FaEUb7KqUChQUlKCadOmqb25rFHp3x/Yvx9ISADs7ICa\nGiAuDnj6aSiOH0diYiJcXFwQFxeH5cuXo7i4GGFhYbC0tBQ7OdMBLkIBDBw4EFu2bMHt27fV7vPC\nCy9g+fLlmDp1KoqLiwVM13y3bt3C7t27NY72kpKSEBwc3OT7rxkzbSM+Kd5kVS6Xg4ik9b7MzICw\nMODMGWDCBNWf5eZiU1AQlixZgtmzZ6OwsFDjneWZceIiFMDq1avRr18/BAYGouqxqZY/WrZsGSZO\nnIjAwECDvnP4tm3b4OTkBB8fn0a3X79+Hd99951JTIsC2kd8UpsaBVB/02KpvS8AgJMTkJEBbNyI\n0n79sOGpp1BSUoLo6GjY2dmJnY7pARehACwtLfH111/j5s2bCA8PV7ufmZkZkpKSYG1tjdDQUBCR\ngCmbbtOmTZg1a5ba7V9++SUGDBiA0aNHC5hKPKY4NSrpIgRUo8O5cxE/fTr6DhiALl26iJ2I6REX\noUC6du2KtLQ0fP3111i3bp3a/aytrfHNN9/g2LFj+PDDDwVM2DQ///wz8vPzERoaqnafjRs3atwu\nNU0pQqkVhlwuh4WFBaytrcWOoldSHM2zJ3ERCsjT0xPJyclYvHgxDhw4oHa/vn37Ii0tDf/4xz+Q\nmpoqYELtkpKS8Pzzz6Nnz56Nbs/MzERxcbFJFaFcLtc44pNiEcpkMpM4/ivFvzv2JC5Cgb3yyit4\n5513EBQUpPGkGB8fH3z88ceYM2cOcnJyBEyoXmVlJbZt26b1JJnnn38eDg4OAiYTl6YPy8rKStTW\n1kpyatQUCkKK09rsSVyEIvjggw/g4+ODV155BeXl5Wr3e+uttzB9+nQEBgbi1q1bAiZsXHp6Otq0\naYPAwMBGtz98+BDbt283mZNk6mgqBblcDkB6x9JMqQhN4X2aOi5CEZibm+OLL76AUqnEzJkzNZ4U\ns379evTp0wfTp09HbW2tgCmflJSUhBkzZqg9dXzHjh1o27YtAgICBE4mLk0fllI9qUTbdLBUmMr7\nNHVchCLp0KED0tPTceTIEaxYsULtfpaWlkhJScH58+exePFiARM2VFpain379mHu3Llq99FWlFKk\nUChQUVGh9sNSqkVoKiMlU3mfpo6LUESOjo7473//iw8//FDjSTHdu3dHeno6Nm7ciA0bNgiY8JGt\nW7di6NCh8PDwaHR7SUkJDhw4oLEopai8vFzjwnK5XI527doZ5+XHNDCVgjCV92nquAhF5ufnh7i4\nOMyZMwe5ublq9/Py8kJCQgLeeustHD58WMCEABFhy5YtGo/9JScnw8vLS21RSpW2EZ9UT7YwlWUF\npvI+TR0XoQFYtGgRXn31VQQEBGi8DFtISAjefvttBAcH4+rVq4LlO3r0KEpLSzFjxoxGtyuVSq1F\nKVXmcjmCRo2CnYapUSl+kEq14P/IVN6nqeMiNBDr1q2Dg4OD1pNiVq1aheHDhyMwMBAPHz4UJFtS\nUhJefPFFtVfXOHjwIG7evKm2KKWsx4MHSDl1Cu1sbBrdHvjwIc5KcCmJVAv+cdXV1aiqqpL8+2Rc\nhAbDysoKO3bsQGFhISIjI9XuV3fGqVwuR1hYmN5zyWQypKSkaF07qKkoJU0mAzQsLG97/z7szMwE\nDCQMUyhCqS59YU/iIjQgDg4O2LVrFz777DNs2rRJ7X6dO3dGeno6vv32W/zzn//Ua6ba2losW7YM\nfn5+jW6/d+8e0tLSTHJaFAAglwOaPihlMs3bjZQpLCuoO/4r9ffJuAgNzrBhw+pPisnMzFS7n6ur\nK5KTk/Huu+9iz549esvTuXNnLF26FG3atGl0+1dffQV7e3tMnDhRbxkMmrai01aURopHhExKuAgN\nUEhICN5880289NJLuHbtmtr9AgMD8f7772PGjBnIz88XMOEjSUlJmDlzpuneoVtbEcpkgARHFKZQ\nhDKZDG3btoWVlZXYUZiemeinl+FbtWoVhg0bhqlTp2q9h6Gvry/mzJkj+G2bcnJycPLkSZNbO9iA\ntqKT8NSoKRQhT4uaBi5CA1V3UsydO3fw+uuva90vPj4eZgKflJGcnIyxY8fC0dFR0Nc1KNqmPiU8\nNSr1kjCFsmcqXIQGrHPnzti9ezd2796NNWvWqN3Pzs4OXl5eguWqqanBuXPnTHbtYANyOaDpruVy\nueSmRhUKBR4+fCj5kjCFsmcq0rrukwS5uLhg+/btCAwMhIuLC/z9/QV77YqKChQWFqKwsBB5eXn1\nvxYXF6OmpgYzZ87ElClTBMtjkFav1rx9717g9GlhsghE22XlpMIUjoMyFS5CI/D8888jJiYGISEh\nyMzMhLOzs06fv6SkBCUlJcjLy0N+fn79r2VlZWjXrh3c3d3h5OSEwYMHY9q0aXBzc8OAAQNM6uLa\nrSKx/09SvZD4H3ERmg4uQiMRFRWFnJwcBAYG4sSJE7DTNB3XCKVSiUuXLj1RdiUlJSgrK4ONjQ0G\nDRoENzc3BAQEIDIyEu7u7ujduzcsLS319K5MhMSKsG5ZgdSnDU1hrSRT4SI0EmZmZti0aRN8fX0x\na9YspKWlNbpkQaFQoLCw8ImyKyoqwoMHD9ChQwcMGTIE7u7umDlzJtzd3eHm5oaePXuK8K4k5Px5\n4L33gAMHVMcFBwwAwsOBN9+UXBHKZDK0adMGNmouKycVPCI0HVyERsTa2ho7d+6Et7c33n//fbz8\n8ssNyi4vLw8XL15EdXU1unfvDg8PD7i5ucHPzw9OTk5cePqSlweMGQOMHQt88w3QtSvwv/8B776r\n2rZ8udgJdUomk8HW1lbws5SFxmeNmg4uQiPTs2dPfPHFF1iyZAlWrlyJjh07YtCgQXB3d8fs2bPh\n5uaGQYMGoV+/fpL/oDIYb78NODsDu3YBdaP0wYOBHj2AKVOASZOA//s/cTPqkKmMlGQyGbp16yZ2\nDCYALkIj9NxzzyEjIwPl5eX4Pwl9wBql27eBgweB5ORHJVjnlVcAJyfg22+ByZPFyacHpjJS4uUT\npoOL0Eh16tQJnTp1EjsGKy5W/TpoUOPbXV2BX34RLo8ATKUgTGXky3hBPWP6J7HrsJpKQfBZo6ZD\nWv9CGRNa//6qXwsKGt9eWKg6g1RCTGlq1BTeJ+MiZKx1nnoK8PUF1q4FlMqG29LSgJISIDhYnGx6\nIpPJJL90AuAiNCVchIy11iefAEVFwIsvAocPq5ZMfPopMHs2MH8+4OMjdkKd8vPzQ0ZGBuLj4wW/\n44mQTGXkywAzkvJ3MmNCKSgA3n8f+PFHoLz80YL6t94CJLiMZffu3ViwYAG6deuGjRs3YtiwYWJH\n0qna2lpYWlri7Nmz8PT0FDsO0zMeETKmC4MGAampwN27QFUVkJurWl8owRIEgICAAOTm5sLb2xsj\nR45EVFSUxvtmGps7d+4AkP71VJkKFyFjrEU6deqEhIQE7N+/H2lpaRg+fDhOnDghdqxWqa6uxqef\nfophw4Zh2rRp6N27t9iRmAC4CBljrfLss88iOzsbkydPxtixYxEeHl5/YW5jUVlZibi4OPTq1Qv/\n/ve/sWbNGmzbto0vOG8i+BghY0xnTpw4gXnz5qG8vBwJCQn405/+JHYkjaqqqvDZZ5/h448/hqWl\nJWJiYjB9+nQuQBPDRcgY06mamhr861//QnR0NAIDAxEfH4+uXbuKHauB2tpabN68GStXrkRtbS2i\no6Px2muv8T02TRQXIWNML3JzczFv3jxcunQJq1atwqxZs8SOBIVCgU2bNuGjjz5CZWUloqKi8Prr\nr5vEukimHhchY0xvlEolNm7ciMWLF2PcuHGIj49Hr169BM+hUCjw5ZdfIjY2Fjdv3sSSJUvw1ltv\nwdbWVvAszPDwyTKMMb0xNzdHWFgYzp07h6qqKgwePBiJiYmCLcQnIqSmpsLT0xMREREIDQ3F5cuX\nERkZySXI6vGIkDEmmNTUVCxYsADu7u7YsGEDBg4cqNfXWrFiBS5duoRFixZh4cKF6NKli95ejxkv\nHhEyxgQTFBSE3NxcdOvWDUOHDkVcXBwUCoVOX2P37t0YNWoUXnvtNfj7+6O4uBgxMTFcgkwtHhEy\nxkSh68u0HThwAO+//z6ysrIQERGBxYsXw97eXkdpmZTxiJAxJgpdXabt8OHD8PHxwZ///GcMHz4c\nRUVFiI2N5RJkTcZFyBgTTWsu03b69GlMnDgREyZMgLu7Oy5cuIC1a9eKclYqM25chIwx0TXnMm1n\nzpzBxIkTMXLkSDg5OaGoqAgJCQno06ePwKmZVHARMsYMgrW1NWJjY3HkyBEcO3YMHh4e2LdvX/32\nwsJCBAcHY8SIEejRowdycnKQkJCAfv36iReaSYKF2AEYY+xxI0eOxKlTpxAdHY3JkycjJCQEZmZm\n2Lp1K8aPH4+jR4/imWeeETsmkxA+a5QxZrCysrKwcuVKVFdXIyoqCj4+PmJHYhLERcgYY8yk8TFC\nxhhjJo2LkDHGmEnjImSMMWbSuAgZY4yZNC5CxhhjJo2LkDHGmEnjImSMMWbSuAgZY4yZNC5Cxhhj\nJo2LkDHGmEnjImSMMWbSuAgZY4yZNC5CxhhjJo2LkDHGmEnjImSMMWbSuAgZY4yZtP8PgPUTSXBG\naosAAAAASUVORK5CYII=\n",
       "prompt_number": 18,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6c20>"
       ]
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "An aside about FastFindRings\n",
      "---\n",
      "\n",
      "What rings *does* it find?"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('O=C(N[C@H]1CCCc2ccccc21)c1n[nH]c2ccccc21',sanitize=False)\n",
      "m.UpdatePropertyCache()\n",
      "Chem.FastFindRings(m)\n",
      "ri = m.GetRingInfo()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ri.AtomRings()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 20,
       "text": [
        "((12, 11, 10, 9, 8, 7, 6, 5, 4, 3),\n",
        " (12, 11, 10, 9, 8, 7),\n",
        " (21, 20, 19, 18, 17, 16, 15, 14, 13),\n",
        " (21, 20, 19, 18, 17, 16))"
       ]
      }
     ],
     "prompt_number": 20
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m,highlightAtoms=ri.AtomRings()[0])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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bJbUU7QNLRNVFioyMdFto/frrrzJ79myJiYmR2rVrS40aNSQmJkYSExNl//79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\ngg==\n",
       "prompt_number": 21,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x4416B48>"
       ]
      }
     ],
     "prompt_number": 21
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "There's an extra bond highlighted in the above drawing (the fusing bond). This is a limitation of the way atom highlighting is handled in drawings: all bonds between highlighted atoms are highlighted.\n",
      "\n",
      "We can avoid the problem by highlighting bonds instead:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m,highlightBonds=ri.BondRings()[0])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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NGzZ06f3IjsJCkX/9yzbAsk8fkfx8ycvLkxtvvFH++9//Gl2haxUUiNx1l/pe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\n",
       "prompt_number": 22,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x4419200>"
       ]
      }
     ],
     "prompt_number": 22
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m,highlightBonds=ri.BondRings()[1])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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9+vUlPDzc4cumiFhfISA4OFgGDhwoy5cv/2utJRG1YqqjV0U9fvy4ALA6EXXN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\nTkSuQmCC\n",
       "prompt_number": 23,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x4402830>"
       ]
      }
     ],
     "prompt_number": 23
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Why symmetrize the rings?\n",
      "====\n",
      "\n",
      "This is an old problem...\n",
      "\n",
      "Use a classic example: cubane only has five smallest rings."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mb=\"\"\"\n",
      "  Mrv0541 09231207052D          \n",
      "\n",
      "  8 12  0  0  0  0            999 V2000\n",
      "    0.4714    0.2946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.4420   -1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.7679    0.3241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.7973   -1.0902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.4479   -0.4184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.1432   -0.4184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.1137   -1.9800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.4479   -1.9800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0  0  0  0\n",
      "  1  3  1  0  0  0  0\n",
      "  3  4  1  0  0  0  0\n",
      "  4  2  1  0  0  0  0\n",
      "  1  5  1  0  0  0  0\n",
      "  5  6  1  0  0  0  0\n",
      "  6  3  1  0  0  0  0\n",
      "  6  7  1  0  0  0  0\n",
      "  7  4  1  0  0  0  0\n",
      "  5  8  1  0  0  0  0\n",
      "  8  7  1  0  0  0  0\n",
      "  8  2  1  0  0  0  0\n",
      "M  END\n",
      "\"\"\"\n",
      "m = Chem.MolFromMolBlock(mb)\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAMBUlEQVR4nO3df0xV9R/H8deFy+VS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\n",
       "prompt_number": 24,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6bb0>"
       ]
      }
     ],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m2 = Chem.MolFromMolBlock(mb,sanitize=False)\n",
      "m2.UpdatePropertyCache()\n",
      "Chem.GetSSSR(m2)\n",
      "m2.GetRingInfo().NumRings()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 25,
       "text": [
        "5"
       ]
      }
     ],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m2,highlightBonds=m2.GetRingInfo().BondRings()[0])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB5fY51AAAN8klEQVR4nO3df0yVZR/H8Q+IiBZi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\nAJhBsACYQbAAmEGwAJjxfyGuw8vVtwHcAAAAAElFTkSuQmCC\n",
       "prompt_number": 26,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x44190E0>"
       ]
      }
     ],
     "prompt_number": 26
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m2,highlightBonds=m2.GetRingInfo().BondRings()[1])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB5fY51AAAN5klEQVR4nO3daWxU5R7H8V+niy22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\nATDj/xbc2aGqVCJBAAAAAElFTkSuQmCC\n",
       "prompt_number": 27,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x4419C68>"
       ]
      }
     ],
     "prompt_number": 27
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m2,highlightBonds=m2.GetRingInfo().BondRings()[2])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB5fY51AAANyklEQVR4nO3df2hV9R/H8dfufvpj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\n",
       "prompt_number": 28,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x441E488>"
       ]
      }
     ],
     "prompt_number": 28
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m2,highlightBonds=m2.GetRingInfo().BondRings()[3])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB5fY51AAANpElEQVR4nO3df2hV9R/H8dd0u5tp\ny8TIhCD6ptkgqFyKzAItTS2HbWZrlUmuBi2b5B/NZvWFgqG5wgr7wcx+mCtrTpEt+wUl2fpuWCtW\nA3FlFlNT2VzOH7t33u8fn64iul93d/fe987zAcG5855zP5E8+3zOzjk3IRgMBgUABgyJ9QAAoLcI\nFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgW\nADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYA\nMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAz\nCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMI\nFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgW\nADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYA\nMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAz\nCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMIFgAzCBYAMwgWADMI\nFgAzCBYAMwgWADMIFgAzEmM9ANh29OhR1dXVSZI6OzvV1tYW1e1gMKiEhARVVVVpypQp0fhXRgwR\nLITt/fff19KlS9XR0aGkpCQNHTpUqampktSr7SFDhuiSSy6RJCUlJenqq68+7+fdbaempqqkpEQ1\nNTXaunUrwfIAgoU+O378uPLz87Vt2zaNGjVKTz/9tPLy8qI+juLiYjU0NOiWW25RUlJS1D8f0cc5\nLPRJU1OTMjIyVF9fr9raWg0bNkw+ny/q4ygrK1NpaakqKio0cuRI+f3+qI8B0Uew0GubN2/WTTfd\npAkTJqimpkbjx4+X3++P+uzm66+/VkFBgd54440zs6uOjo6ojgGxQbDQo87OThUVFSk3N1cvvvii\nysvLNWLECElSR0dHVGdYe/bs0fz587VkyRItWrRIkjv/xQzLGziHhW4dPHhQOTk52r17t7766itl\nZGSc8+fRnGG1trYqMzNTU6dO1apVq8783OfzESyPYIaFLtXU1Cg9PV2JiYmqr68/L1ZS9GZYgUBA\nOTk58vl82rBhg4YMOftXlyWhdxAsXNCaNWs0ffp0LV68WNu3b9dll112wfeFLmkYaE8++aQaGhpU\nXV19ZjkawpLQO1gS4hzt7e3Kz89XVVWVNm3apLlz53b7fr/fP+AzrLVr12rdunXasWOHxo4de96f\nsyT0DoKFMxobG5Wdna3ExETV1tZq3LhxPe4z0EvCqqoqFRYWqry8XBMnTrzge1gSegdLQkiSKioq\nNHnyZE2ZMqXXsTp9+rQ6OzsHbEnY0NCg3NxcFRcXa/78+V2+jyWhdxAsj/P7/SosLNT999+v1atX\na926dUpJSen1vpIGZIZ16NAhZWZmau7cuXruuee6fS/B8g6WhB524MAB5eTk6I8//tC3336r9PT0\nPu0fWoZFeoZ16tQpZWVlacyYMSorK1NCQkK37/f5fCwJPYIZlkd99913Sk9PV3Jysurq6vocK2ng\nZlj5+fnat2+fKisrezXbY4blHQTLg1auXKlp06YpLy9P1dXVGj16dFjHGYgZ1qpVq7RlyxZ9+umn\nuvzyy3u1D8HyDpaEHtLe3q5HHnlE27dvV0VFhe66665+HS8UrEjNsLZs2aIVK1Zo69atSktL6/V+\nBMs7CJZH/Prrr8rOzpbP51Ntba2uueaafh8zFIlIzLDq6uqUm5urkpISzZ49u0/7cg7LOwiWB2zc\nuFH5+fnKyspSaWmpUlJSdOzYsX4ft7W1VZILV3+O19zcrHnz5mnhwoVatmxZn/dnhuUdCcFgMBjr\nQWDg7N+/X9dff72OHDkS66F0KSUlRTfffLO++OILJScn93n/TZs2afny5WpqahqA0SGeMMMa5H7/\n/Xe1tbWpsbEx4sduaGjQggUL9Msvv/R46UF3CgsLNXHixLBiJbEk9BKC5RETJkyI+DFbWlqUmJio\n6667rl/HSUlJ6dd5MJaE3sFlDQhbpO4j9Pv9SkwM//+dBMs7CBbCFqlHy/T3IYAsCb2DYCFskXq0\nTH+DxQzLOwgWwhYvMyyC5R0EC2GLlxmWz+c786gbDG4EC2GL1AwrEAj0+6S7JGZZHkCwELZ4mWGF\n9uXE++BHsBC2SF7W0N8lYeg4GNwIFsIWqe8kjNQMi2ANfgQLYYuXGRZLQu8gWAhbvJx0Z0noHQQL\nYYu3k+4Ea/Dj5meEze/3a9yJE9KuXe4HF18shWZKw4dLoZilpEjDhnV7HJaE6A2ChfDs3Kk7P/9c\naT/+KPXlCyx8PhczSRo6VEpNlb+tTUkLF0pXXHH2fSNHSqFH1vQQwlDqmGENfgQLfVdXJ82Zo0lt\nbVJfZ0YdHe6fkMOH5ZeU1NwsNTeHNZwESR9ceqlSU1PD2h92ECz0TW2tNGOG1NbmZj7r10s33igF\ng9K/j0xWZ6f7c8nFqb3dbZ88KZ044baPH5dOnZIkBYqKlPTQQ9KYMW6/0C02ra3uuF0d2++X/vxT\namlRbkuLVF8v9eIbq2EXwULv7dolzZzpgjF8uFRdLU2d2q9DBgIBBYuKlLh0qXTDDX3befNmKfQV\n9rNmSdnZ/RoL4h+/JUTvNDS4KBw96s4dVVb2O1aSC5YUxjfvNDVJixe72ddVV0kffCAN4a/zYMd/\nYfSssVG67Tbp8GEpOdnFasaMiBw6rK8KO35cyspyy8TkZOmjj6RRoyIyHsQ3goXu/fabWwb+/bf7\nTd3GjW6mFSFhBeuJJ6Sff3bbq1dLkyZFbDyIbwQLXdu7V5o2TfrrL3cJwsaNbmYTQX0O1ttvS+vW\nue0HH5Qefzyi40F8I1i4sOZmt+zbt8+dGyork+65J+If06dg/fCDVFDgttPSpNdfj/h4EN8IFs53\n4ICbWe3Z4y7efPNNadGiAfmoULB6vJfw6FHp3nvdpRGpqe48WugCVHgGwcK5jhyR7rhD2r3bvX75\nZSkvb8A+rle/JQwG3fJvzx73+q23pPHjB2xMiF8EC2e1tEi33372hPbzz0uFhQP6kb1aEpaWStu2\nue2CAjfTgicRLDj//CPNmeOuFpek4mJpxYoB/9geg7Vjh7R8udvOyHAzPngWwYJ07Jg0e7b0/ffu\n9VNPSS+8EJWP9vv9SkhIuPA5rOZmacECKRCQRo+Wysv7fu8iBhWC5XUnT0p33y3t3OleFxRIJSVR\n+/guv6Y+EJByc6WDB90lFR9+KF15ZdTGhfhEsLzs1Clp3jzpyy/d6/x86dVXzz7WJQq6fNroM89I\n33zjtlescFfaw/MIllcFAtJ990mffeZeP/CAtHZtVGMldfHwvspKaeVKtz1rlvTss1EdE+IXwfKi\nUKwqK93rnBzpnXdicvPwecFqapIefpibmnFB/E3wmtOn3XVVn3ziXmdmSu+9584TxcA5wTpx4uxN\nzT4fNzXjPATLS4JB6dFHpXffda/vvFP6+OOY/ubtnGBxUzN6QLC8ZOnSszcOT5/uYhWBb73pjzPB\nWr/e3a8ouavalyyJ6bgQnwiWVyxbJr3yitu+9VZ35Xg332QTLYFAQImdndJjj7kfpKW5k//ABfCI\nZC84fVp66SW3PWmSi9VFF8V2TP/yt7Upaf9+9+z31FT32OMRI2I9LMQpgjXY/fST/hv6UoeUFHcL\nTgQebRwpc/fu1dbQt+isWSNde21sB4S4lhAMBoOxHgQGzqFDh9Q2aZL+s3dvrIfSpf/NnKnJ48ZJ\nr70W66EgzhEsL9iwwd1EHOMT7F0qKpLGjuV6K/SIYAEwg/+lATCDYAEwg2ABMINgATCDYAEwg2AB\nMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEw\ng2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCD\nYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINg\nATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2AB\nMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEw\ng2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCD\nYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINg\nATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATCDYAEwg2ABMINgATDj/1W02cr4\n0loKAAAAAElFTkSuQmCC\n",
       "prompt_number": 29,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x441ECF8>"
       ]
      }
     ],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Draw.MolToImage(m2,highlightBonds=m2.GetRingInfo().BondRings()[4])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB5fY51AAAN4klEQVR4nO3dfUyVdR/H8Q9wePKJ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\nyHKs25tmbCEAAAAASUVORK5CYII=\n",
       "prompt_number": 30,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x441F5A8>"
       ]
      }
     ],
     "prompt_number": 30
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "The front face is being missed.\n",
      "\n",
      "Isn't this all nitpicking though? Does it actually matter?\n",
      "\n",
      "It does if you want to ask questions about ring membership:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m2.GetSubstructMatches(Chem.MolFromSmarts('[R3]'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 31,
       "text": [
        "((0,), (1,), (2,), (3,))"
       ]
      }
     ],
     "prompt_number": 31
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m2"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAMG0lEQVR4nO3df0zU9QPH8dch4Gkh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\nAUolwp+NosKkAAAAAElFTkSuQmCC\n",
       "prompt_number": 32,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6360>"
       ]
      }
     ],
     "prompt_number": 32
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "The symmetrization algorithm (run by default) solves this problem:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.GetSymmSSSR(m2)\n",
      "m2.GetRingInfo().NumRings()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 33,
       "text": [
        "6"
       ]
      }
     ],
     "prompt_number": 33
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m2.GetSubstructMatches(Chem.MolFromSmarts('[R3]'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 34,
       "text": [
        "((0,), (1,), (2,), (3,), (4,), (5,), (6,), (7,))"
       ]
      }
     ],
     "prompt_number": 34
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Stereochemistry Handling\n",
      "=====\n",
      "\n",
      "### Stereochemistry information that doesn't make sense is removed:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.CanonSmiles('C[C@H](F)C') # <- two identical atoms"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 35,
       "text": [
        "'CC(C)F'"
       ]
      }
     ],
     "prompt_number": 35
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.CanonSmiles('C/C=C') # <- only substituted on one side"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 36,
       "text": [
        "'C=CC'"
       ]
      }
     ],
     "prompt_number": 36
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### CIP codes are assigned"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('C[C@](F)(Cl)Br')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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kbrjhBqtjXdaBigMKzw/XB50/0JBWQ6yOAzR4FCEgKSEhQaGhoZoyZYrVUa7I9KLp+qDk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\n",
       "prompt_number": 37,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6fa0>"
       ]
      }
     ],
     "prompt_number": 37
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetAtomWithIdx(1).GetProp('_CIPCode')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 38,
       "text": [
        "'S'"
       ]
      }
     ],
     "prompt_number": 38
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### As are Z and E labels for double bonds:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('C/C=C/C')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAJoElEQVR4nO3dX0zV9R/H8VcFqcsU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\n6gAAAABJRU5ErkJggg==\n",
       "prompt_number": 39,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6d70>"
       ]
      }
     ],
     "prompt_number": 39
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetBondWithIdx(1).GetStereo()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 40,
       "text": [
        "rdkit.Chem.rdchem.BondStereo.STEREOE"
       ]
      }
     ],
     "prompt_number": 40
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles(r'C/C=C\\C')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAHr0lEQVR4nO3dT4hVdR/H8e/kI7pw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\nApCaEAKQ2n8BfbT5OHhJF/gAAAAASUVORK5CYII=\n",
       "prompt_number": 41,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6e50>"
       ]
      }
     ],
     "prompt_number": 41
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetBondWithIdx(1).GetStereo()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 42,
       "text": [
        "rdkit.Chem.rdchem.BondStereo.STEREOZ"
       ]
      }
     ],
     "prompt_number": 42
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### Dependent stereochemistry is handled properly:\n"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('C[C@H]1CCC[C@@H](C)[C@H]1C')\n",
      "Draw.MolToImage(m,includeAtomNumbers=True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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ZDLg2guUDZWVlSk1NVXR0tMLDw/XII49o165dDbqvkSNHavXq1erSpYuPp2yY8PBwZWVl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\nSUVORK5CYII=\n",
       "prompt_number": 43,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x44256C8>"
       ]
      }
     ],
     "prompt_number": 43
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetAtomWithIdx(1).GetProp('_CIPCode'),m.GetAtomWithIdx(5).GetProp('_CIPCode'),m.GetAtomWithIdx(7).GetProp('_CIPCode')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 44,
       "text": [
        "('S', 'R', 'S')"
       ]
      }
     ],
     "prompt_number": 44
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('C[C@H]1CCC[C@H](C)[C@H]1C')\n",
      "Draw.MolToImage(m,includeAtomNumbers=True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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MiIgIx+kRzWHv3r2MiIhgcHAwc3JyLD3AXVBQwGXLlpEk9+3bx86dO7OyspJ2u51Dhgzh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\nABUEhV8Mk4IhAAAAAElFTkSuQmCC\n",
       "prompt_number": 45,
       "text": [
        "<Image.Image image mode=RGBA size=300x300 at 0x4425CF8>"
       ]
      }
     ],
     "prompt_number": 45
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles(r'C[C@H](F)/C([C@H](F)C)=C\\Cl')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAV/klEQVR4nO3dfVRUZeIH8C8MAgGh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\nkIiIFI1FSEREisYiJCIiRWMREhGRov0v1VJgc4d/3r0AAAAASUVORK5CYII=\n",
       "prompt_number": 46,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6c90>"
       ]
      }
     ],
     "prompt_number": 46
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetAtomWithIdx(1).GetProp('_CIPCode'),m.GetAtomWithIdx(4).GetProp('_CIPCode')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 47,
       "text": [
        "('S', 'R')"
       ]
      }
     ],
     "prompt_number": 47
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.MolToSmiles(m,True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 48,
       "text": [
        "'C[C@@H](F)/C(=C/Cl)[C@H](C)F'"
       ]
      }
     ],
     "prompt_number": 48
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles(r'C[C@H](F)/C([C@@H](F)C)=C\\Cl')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAUwklEQVR4nO3dfVSUVeIH8O/AAIKK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\njQAAAABJRU5ErkJggg==\n",
       "prompt_number": 49,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f6f30>"
       ]
      }
     ],
     "prompt_number": 49
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetAtomWithIdx(1).GetProp('_CIPCode'),m.GetAtomWithIdx(4).GetProp('_CIPCode')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 50,
       "text": [
        "('S', 'S')"
       ]
      }
     ],
     "prompt_number": 50
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.MolToSmiles(m,True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 51,
       "text": [
        "'C[C@H](F)C(=CCl)[C@H](C)F'"
       ]
      }
     ],
     "prompt_number": 51
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### Stereochemistry at P and S"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.CanonSmiles('F[P@@](=O)(OC(C)C)C') #<- Sarin\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 52,
       "text": [
        "'CC(C)O[P@](C)(=O)F'"
       ]
      }
     ],
     "prompt_number": 52
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('F[P@@](=O)(OC(C)C)C')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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wrFoFZfcBPHkSnE7o1AkOHYLTp6F7d3jhBZg4EZo2te+93IGtW7eSmJjIxYsXmTNnDvHx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\n3gAAAABJRU5ErkJggg==\n",
       "prompt_number": 53,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x43f68a0>"
       ]
      }
     ],
     "prompt_number": 53
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetAtomWithIdx(1).GetProp('_CIPCode')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 54,
       "text": [
        "'S'"
       ]
      }
     ],
     "prompt_number": 54
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Chem.CanonSmiles('COc1ccc2nc([nH]c2c1)[S@@](=O)Cc1ncc(C)c(OC)c1C')  # <- Esomeprazole"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 65,
       "text": [
        "'COc1ccc2nc([S@@](=O)Cc3ncc(C)c(OC)c3C)[nH]c2c1'"
       ]
      }
     ],
     "prompt_number": 65
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles('COc1ccc2nc([nH]c2c1)[S@@](=O)Cc1ncc(C)c(OC)c1C')\n",
      "m"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "png": 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LCg8Pp7t372ok0z9VVlbSnj2HaNIkopYtiaysiAYPJvrqK6IHD5RtgoKIrK2J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\n",
       "prompt_number": 70,
       "text": [
        "<rdkit.Chem.rdchem.Mol at 0x495fad0>"
       ]
      }
     ],
     "prompt_number": 70
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m.GetAtomWithIdx(11).GetProp('_CIPCode')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 67,
       "text": [
        "'S'"
       ]
      }
     ],
     "prompt_number": 67
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 60
    }
   ],
   "metadata": {}
  }
 ]
}