{ "cells": [ { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true }, "outputs": [], "source": [ "from rdkit import Chem\n", "from rdkit.Chem import AllChem\n", "import py3Dmol" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", "" ], "text/plain": [ "" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "m = Chem.MolFromSmiles('c1cncc(c1)c1nc(ncc1)Nc1cc(ccc1C)NC(=O)c1ccc(cc1)CN1CCN(CC1)C')\n", "Chem.SanitizeMol(m)\n", "AllChem.EmbedMultipleConfs(m, 1)\n", "\n", "sdf = Chem.MolToMolBlock(m)+'$$$$\\n'\n", "\n", "for i in xrange(100):\n", " AllChem.UFFOptimizeMolecule(m,1)\n", " sdf += Chem.MolToMolBlock(m)+'$$$$\\n'\n", " \n", "view = py3Dmol.view()\n", "view.addModelsAsFrames(sdf,'sdf')\n", "view.setStyle({'stick':{}})\n", "view.zoomTo()\n", "view.animate()\n", "view.show()" ] }, { "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" }, "widgets": { "state": {}, "version": "1.1.1" } }, "nbformat": 4, "nbformat_minor": 0 }