Depiction2D.ipynb

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   "cells": [
    {
     "cell_type": "code",
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     "input": [
      "from rdkit import Chem\n",
      "from rdkit.Chem import rdDepictor\n",
      "from rdkit.Chem.Draw import rdMolDraw2D\n",
      "from rdkit.Chem.Draw import IPythonConsole\n",
      "from IPython.display import SVG"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m = Chem.MolFromSmiles(\"CCCCC[C@@H](CC[C@H]1[C@@H](C[C@@H]([C@@H]1CCCCCCC(=O)O)O)O)O\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "q = Chem.MolFromSmarts('C(=O)O')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "rdDepictor.Compute2DCoords(m)\n",
      "drawer = rdMolDraw2D.MolDraw2DSVG(400, 200)\n",
      "drawer.DrawMolecule(m, highlightAtoms = m.GetSubstructMatch(q))\n",
      "drawer.FinishDrawing()\n",
      "svg = drawer.GetDrawingText().replace('svg:','')\n",
      "SVG(svg)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
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