greglandrum/sample.ipynb

## sample.ipynb
{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import Draw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rxn = AllChem.ReactionFromSmarts('([*:1]-[O:2][CH3:3].[*:4]-[O:5][CH3:6])>>([*:1]-[O:2][C:3]C.[*:4]-[O:5][C:6]C)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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ixXqF4ZZaFcScw3AB7xVceYz6fL6PP/5YPVETExMPHz6ME9UoPp/vyJEjWVlZ6vRn3759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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7ff652783bc0>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m=Chem.MolFromSmiles('COCCCOC')\n",
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2\n"
     ]
    },
    {
     "data": {
      "image/png": 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bWWy4e/fu3r17mbmqqko8mAsGQxuT9vPPP5eWlqoPRBgBqRiFt0hMpIEBCgTIYon8hkCA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\nQmCC\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7ff6802301e8>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ps = rxn.RunReactants((m,))\n",
    "print(len(ps))\n",
    "ps[0][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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2nPHzo8XFYZwfPXdOamslNVUAsdnEbhdL9nYYozS5AwcOzJs3z/jsKDs7e/ytc80ujaYm\nrPOj3d2iaZKWNhagZmw2jhI2EQHRZIaHh19++WWXy5WTk5OcnPzSSy+NTsdTbPD7sWkTtm7FyAgW\nLMDf/obL93i9eT090HW8+ip6ewGgqgq//z2WL1cvNnYxRuk6Ll265PP5cnJyjNkkij1NTdi4EceO\nwWbDM89g61ZcbnDfmB9+wLZteOUVdHcDwCOPYPNmrFgR2mJjEWOUyAKGhrBtG/7wBwwOIj8fbjcu\nz7BNid+PV17B1q34/nsAWLUKmzdj5cowFRtzGKNEltHcjI0b0d4Omw2//S10HRkZ1/mWvj789a94\n+WWcPw8ApaX405/A3s6VeJpGZBnLlqGtDW430tLw739jaCj4uMeDsjKkpyM9HWVleP314ON79mDh\nQrzwAs6fx/3348030dTEDL0aj0aJrKezE19/jUcfBYBnn0VTE3QdK1fCZsPBg9A0lJVh+3a0tKC0\nFMXF+OMfUVUFm83suqMUY5TIwt5+Gy++iCNHkJ4+9mBvL5Ytw5YtePxx7NqFNWuQlGReiTGAMUpk\nYb/8JX7zGzz55MTH33gDf/87du0yo6bYwxglsrAZM3DsGGbOnPh4VxcWLQp+rETXwxglsrCkJPT3\nT3LOPjSE1NSxz6DomvhJPZGFZWUFr6WfoLsbWVkRryZWMUaJLKykBI2Nkzze2IiSkohXE6sYo0QW\nVlODTZvg813xoM+HzZtRU2NSTbGHMUpkYevXo7wclZXYswc+H/x+NDSgshIVFVi3zuziYgY/YiKy\nvB07UFeHjg4AWLgQNTV4+mmza4oljFEiIiU8qSciUsIYJSJSwhglIlLCGCUiUsIYJSJSwhglIlLC\nGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJSwhgl\nIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJS\nwhglIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJSwhglIlLCGCUiUsIYJSJS8v85B/Zq5IwbAAAA\nAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7ff652783c60>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m=Chem.MolFromSmiles('COCCOC')\n",
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2\n"
     ]
    },
    {
     "data": {
      "image/png": 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d1514oMuXL7/55pthYWGOjAx88QUCA6HT4dQp7N+PpKS+0qEAwsLw73/DYEB7O958E4mJ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\nc4GJiGRhjRIRycIaJSKShTVKRCTL/wMkATHz06SxugAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7ff653152df0>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ps = rxn.RunReactants((m,))\n",
    "print(len(ps))\n",
    "ps[0][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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Z4pf58ksGfXf4MJvNA7jDR2RbvvvhB0yDtPvxCVaMTk9P22w23h3wwbfoDsDn4sWLu3fv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\nRK5CYII=\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7ff65279b760>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m=Chem.MolFromSmiles('COCOC')\n",
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n"
     ]
    }
   ],
   "source": [
    "ps = rxn.RunReactants((m,))\n",
    "print(len(ps))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now do a ring-opening reaction:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1\n"
     ]
    },
    {
     "data": {
      "image/png": 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oH/9YRaP3PBiNqp/8RO3ZY9NMwAMRo3Ceb3xDbdqktmxRf/6zikbV+Lg6fFht2aIaGtTX\nv273cMBsWh8xAUn01lvql79U//ynUkrV1Kg9e9R3vmP3TMAciFEA0MKLegDQQowCgBZiFAC0EKMA\noIUYBQAtxCgAaCFGAUALMQoAWohRANBCjAKAFmIUALQQowCghRgFAC3EKABoIUYBQAsxCgBaiFEA\n0EKMAoAWYhQAtBCjAKCFGAUALcQoAGghRgFACzEKAFqIUQDQQowCgBZiFAC0EKMAoIUYBQAtxCgA\naCFGAUALMQoAWohRANBCjAKAFmIUALQQowCghRgFAC3EKABo+R8OCneYC+mGFQAAAABJRU5ErkJg\ngg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7ff65279f5b0>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rxn2 = AllChem.ReactionFromSmarts('[O:1]@[N:2]>>[O:2][C:3]C')\n",
    "m = Chem.MolFromSmiles('CNOC.Cl')\n",
    "ps = rxn2.RunReactants((m,))\n",
    "print(len(ps))\n",
    "ps[0][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "hide_input": false,
  "kernelspec": {
   "display_name": "Python [default]",
   "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": "3.5.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}