animation_with_plot.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "cannot import name 'link'",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-2-972b51424294>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mpytraj\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mpt\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[1;32mfrom\u001b[0m \u001b[0mnglview\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mlink\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      6\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mnglview\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      7\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mImportError\u001b[0m: cannot import name 'link'"
     ]
    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "from pytraj import view\n",
    "import pytraj as pt\n",
    "\n",
    "from nglview import link\n",
    "import nglview\n",
    "\n",
    "fig = plt.figure(figsize=(8, 6))\n",
    "ax = fig.add_subplot(111)\n",
    "ax.set_xlabel('frame number')\n",
    "ax.set_ylabel('End to end distance (Angstrom)')\n",
    "\n",
    "traj = pt.datafiles.load_tz2()\n",
    "data = pt.radgyr(traj, '@CA')\n",
    "ax.plot(data)\n",
    "\n",
    "# convert pytraj's Trajectory to nglview.Trajectory\n",
    "\n",
    "ntraj = pt.view.to_nglview(traj)\n",
    "\n",
    "tv = nglview.TrajectoryViewer(ntraj)\n",
    "link_mpl(tv, ax, data)\n",
    "tv"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}