update_060518.ipynb

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  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import pybel\n",
    "import imolecule\n",
    "from glom import glom\n",
    "from metatlas import create_launchpad, make_xyz_from_stored_data\n",
    "\n",
    "sys.path.append('./malt')\n",
    "# from malt.algorithm.topology import Fragmentation\n",
    "\n",
    "LOCAL_DB_CONFIG = '/home/bkrull/.fireworks/local_db.ini'\n",
    "lpad = create_launchpad(LOCAL_DB_CONFIG)\n",
    "\n",
    "# frag = Fragmentation()\n",
    "# compact = frag.weights_compact\n",
    "# longrange = frag.weights_longrange\n",
    "\n",
    "tmpdir = '/home/bkrull/Desktop/tmpdir/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fw = lpad.get_fw_dict_by_id(1)\n",
    "\n",
    "def get_trajs(fw):\n",
    "    parent = glom(fw, 'launches.0.action.stored_data.parent')\n",
    "    children = glom(fw, 'launches.0.action.stored_data.protonated_children')\n",
    "\n",
    "    fbase = tmpdir + 'mol-{}-'.format(fw['fw_id'])\n",
    "    with open(fbase+'parent.xyz', 'w') as f:\n",
    "        for coords in parent['coords']:\n",
    "            f.write(\n",
    "                make_xyz_from_stored_data(parent['atom_list'], coords)\n",
    "            )\n",
    "            \n",
    "    print 'There are {} protonated children'.format(len(children))\n",
    "\n",
    "    for i, child in enumerate(children):\n",
    "        print 'This child was protonated at {}{} with hybridization {}'.format('', '', '')\n",
    "        print 'This child is predicted to fragment: {}'.format(child['likely_to_break'])\n",
    "        with open(fbase+'child-{}.xyz'.format(i), 'w') as f:\n",
    "            for coords in child['coords']:\n",
    "                f.write(\n",
    "                    make_xyz_from_stored_data(child['atom_list'], coords)\n",
    "                )\n",
    "                \n",
    "        print ''\n",
    "        \n",
    "    return parent, children"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "There are 2 protonated children\n",
      "This child was protonated at  with hybridization \n",
      "This child is predicted to fragment: True\n",
      "\n",
      "This child was protonated at  with hybridization \n",
      "This child is predicted to fragment: True\n",
      "\n"
     ]
    }
   ],
   "source": [
    "fw = lpad.get_fw_dict_by_id(5532)\n",
    "\n",
    "parent, children = get_trajs(fw)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import pickle\n",
    "    \n",
    "with open(tmpdir+'parent.pickle', 'wb') as handle:\n",
    "    pickle.dump(parent, handle, protocol=pickle.HIGHEST_PROTOCOL)  \n",
    "    \n",
    "with open(tmpdir+'children.pickle', 'wb') as handle:\n",
    "    pickle.dump(children, handle, protocol=pickle.HIGHEST_PROTOCOL)"
   ]
  },
  {
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   "execution_count": 10,
   "metadata": {
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    "imolecule.draw(pybel.readstring('xyz', make_xyz_from_stored_data(parent['atom_list'], parent['coords'][0])), \n",
    "               format=\"pybel\")"
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   "source": [
    "imolecule.draw(pybel.readstring('xyz', make_xyz_from_stored_data(children[1]['atom_list'], \n",
    "                                                                 children[1]['coords'][0])), \n",
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   "cell_type": "markdown",
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   "source": [
    "+ Picture of molecule and where it will be protonated\n",
    "+ Prediction based on simple hybridization rules. WILL IT BREAK?\n",
    "+ Animation of optimization trajectory, coords and graph\n",
    "+ Graph cut results. Did it break?"
   ]
  },
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