{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from __future__ import print_function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import pyrogen"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import atom_types"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "m = pyrogen.MolFromFetchedCode('EFZ')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB5fY51AAAqF0lEQVR4nO3deXwcZ30/8M/32dXh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\nYII=\n",
      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "pyrogen.depict(pyrogen.prep(m))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "atom_types.set_amber_atom_types(m)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "atom CL   type CL\n",
      "atom  F1  type F\n",
      "atom  F2  type F\n",
      "atom  F3  type F\n",
      "atom  O1  type O\n",
      "atom  O2  type OS\n",
      "atom  N   type N\n",
      "atom  C1  type CA\n",
      "atom  C2  type CA\n",
      "atom  C3  type CA\n",
      "atom  C4  type CA\n",
      "atom  C5  type CA\n",
      "atom  C6  type CA\n",
      "atom  C7  type CT\n",
      "atom  C8  type C-unknown\n",
      "atom  C9  type C-unknown\n",
      "atom  C10 type CT\n",
      "atom  C11 type CT\n",
      "atom  C12 type CT\n",
      "atom  C13 type CT\n",
      "atom  C14 type C\n",
      "atom  HN  type H\n",
      "atom  H2  type HC\n",
      "atom  H3  type HC\n",
      "atom  H5  type HC\n",
      "atom H101 type HC\n",
      "atom H111 type HC\n",
      "atom H112 type HC\n",
      "atom H121 type HC\n",
      "atom H122 type HC\n"
     ]
    }
   ],
   "source": [
    "for atom in m.GetAtoms():\n",
    "    print(\"atom {} type {}\".format(atom.GetProp('name'), atom.GetProp('amber_atom_type')))"
   ]
  },
  {
   "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": "2.7.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}
