jp-um/jabel

## jabel
{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/lib/python2.7/dist-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated since IPython 4.0. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`.\n",
      "  \"`IPython.html.widgets` has moved to `ipywidgets`.\", ShimWarning)\n"
     ]
    }
   ],
   "source": [
    "import rdkit\n",
    "from rdkit import Chem\n",
    "from rdkit import DataStructs\n",
    "from rdkit.Chem import AllChem\n",
    "\n",
    "from rdkit.Chem.Draw import IPythonConsole #Needed to show molecules\n",
    "from rdkit.Chem import Draw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# John wants some alkenes (or alkanes?) ... let us show him some\n",
    "\n",
    "# alkene\n",
    "ethene = Chem.MolFromSmiles(\"C=C\")\n",
    "propene = Chem.MolFromSmiles(\"CC=C\")\n",
    "\n",
    "# alkane\n",
    "methane = Chem.MolFromSmiles(\"C\")\n",
    "ethane = Chem.MolFromSmiles(\"CC\")\n",
    "\n",
    "# note in cheminformatics we typically ignore Hs, as these are everywhere and double the size of the graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAKAklEQVR4nO3dYUjUhx/H8c+VlXYZ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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6a180b16e0>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.AddHs(ethene) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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3KysrtWbNmlDHhMM4NQpnxcfH6/bbb7cdI6gqKytVX1+vkSNH2o6i3r17KzU1lVe0IexQ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\nIgQAOI0iBAA4jSIEADiNIgQAOO0/CLSx3rjDrOMAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6a1800f130>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.AddHs(propene)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAD7klEQVR4nO3dIW4qaxjH4bc3FYhB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\nhABEE0IAogkhANGEEIBovwBiLZZNp3I9KgAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6a05e1a670>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.AddHs(methane) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAEnklEQVR4nO3dMWpbWQCF4ZuJCxUS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\nNCEEIJoQAhBNCAGIJoQARBNCAKL9DVcE6YqqoaqKAAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6a05e1a910>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.AddHs(ethane)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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U5f5ALy8vfPzxx5g+fTp+/vlnAEBJSTqys1cjN/d7lJSk6zqyZJmYmCAmJgaxsbFITEwU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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6a05e1ac20>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# ok ok, you are not blown off your feet.  Let me show you something a little bit more complicated\n",
    "m1 = Chem.MolFromSmiles('COc1ccc2c(c1)[nH]c(n2)[S@@](=O)Cc1ncc(c(c1C)OC)C')\n",
    "m1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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t2lSrR/dk0fT396f09PQ6vX9dqVREO3cSTZxI1KwZkYUF0ahRj9vt7Ii++47I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\nZo0LIWOMMbP2f90UnnsNSC8EAAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f6a05e1a830>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# now we remove a methyl group on the left to show you similar\n",
    "m2 = Chem.MolFromSmiles('Oc1ccc2c(c1)[nH]c(n2)[S@@](=O)Cc1ncc(c(c1C)OC)C')\n",
    "m2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Let us generate fingerprints and calculate the similarity (Jaccard) between the two\n",
    "fp1 = AllChem.GetMorganFingerprint(m1, 2)\n",
    "fp2 = AllChem.GetMorganFingerprint(m2, 2)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.0\n",
      "0.885496183206\n",
      "0.0547945205479\n"
     ]
    }
   ],
   "source": [
    "print DataStructs.DiceSimilarity(fp1, fp1) # identical\n",
    "print DataStructs.DiceSimilarity(fp1, fp2) # very similar\n",
    "print DataStructs.DiceSimilarity(fp1, AllChem.GetMorganFingerprint(Chem.MolFromSmiles('CC=O'), 2)) # dissimilar"
   ]
  },
  {
   "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": "2.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}