{
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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# %load /home/mcocdawc/startup1\n",
    "import scipy as sp\n",
    "import numpy as np\n",
    "from constants import constants, conversion # this is a custom module\n",
    "import matplotlib as mpl\n",
    "import matplotlib.pyplot as plt\n",
    "%matplotlib inline\n",
    "import pandas as pd\n",
    "import chemcoord as cc\n",
    "# unless specified else, all calculations are carried out in SI units"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "molecule = cc.read('MIL53as_stretch_Ref.xyz')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fragment = molecule.get_fragment([(12, 2), (55, 2)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "connection_array = np.array([[2, 99, 12, 18], [8, 2, 99, 12]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'row_in_buildlist' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-6-2933b0a3ee3d>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mzmolecule\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mmolecule\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mto_zmat\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfragment_list\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfragment\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mconnection_array\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32m/home/mcocdawc/.local/lib/python3.5/site-packages/chemcoord-1.2.0-py3.5.egg/chemcoord/xyz_functions.py\u001b[0m in \u001b[0;36mto_zmat\u001b[1;34m(self, buildlist, fragment_list, check_linearity)\u001b[0m\n\u001b[0;32m   1520\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1521\u001b[0m                 buildlist, big_molecule, row = create_big_molecule(\n\u001b[1;32m-> 1522\u001b[1;33m                     self, fragment_list)\n\u001b[0m\u001b[0;32m   1523\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1524\u001b[0m                 \u001b[1;32mfor\u001b[0m \u001b[0mfragment_tpl\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mfragment_list\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/mcocdawc/.local/lib/python3.5/site-packages/chemcoord-1.2.0-py3.5.egg/chemcoord/xyz_functions.py\u001b[0m in \u001b[0;36mcreate_big_molecule\u001b[1;34m(self, fragment_list)\u001b[0m\n\u001b[0;32m   1508\u001b[0m                     \u001b[0mbig_molecule\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mbig_molecule_index\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m:\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1509\u001b[0m                     \u001b[0mrow\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbig_molecule\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mn_atoms\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1510\u001b[1;33m                     \u001b[0mbuildlist\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mrow\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m:\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbig_molecule\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_get_buildlist\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1511\u001b[0m                     \u001b[1;32mreturn\u001b[0m \u001b[0mbuildlist\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mbig_molecule\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mrow\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1512\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/mcocdawc/.local/lib/python3.5/site-packages/chemcoord-1.2.0-py3.5.egg/chemcoord/xyz_functions.py\u001b[0m in \u001b[0;36m_get_buildlist\u001b[1;34m(self, fixed_buildlist)\u001b[0m\n\u001b[0;32m   1314\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mrow\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m1\u001b[0m \u001b[1;33m&\u001b[0m \u001b[1;36m1\u001b[0m \u001b[1;33m<\u001b[0m \u001b[0mbuildlist\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1315\u001b[0m                 row, already_built, to_be_built, use_index = second_atom(\n\u001b[1;32m-> 1316\u001b[1;33m                     self, already_built, to_be_built)\n\u001b[0m\u001b[0;32m   1317\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mrow\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m2\u001b[0m \u001b[1;33m&\u001b[0m \u001b[1;36m2\u001b[0m \u001b[1;33m<\u001b[0m \u001b[0mbuildlist\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1318\u001b[0m                 row, already_built, to_be_built, use_index = third_atom(\n",
      "\u001b[1;32m/home/mcocdawc/.local/lib/python3.5/site-packages/chemcoord-1.2.0-py3.5.egg/chemcoord/xyz_functions.py\u001b[0m in \u001b[0;36msecond_atom\u001b[1;34m(self, already_built, to_be_built)\u001b[0m\n\u001b[0;32m   1176\u001b[0m                 \u001b[0mnew_row_to_modify\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0malready_built\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mto_be_built\u001b[0m \u001b[1;33m=\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1177\u001b[0m                     from_topologic_center(\n\u001b[1;32m-> 1178\u001b[1;33m                         self, row_in_buildlist, already_built, to_be_built)\n\u001b[0m\u001b[0;32m   1179\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnew_atoms_set\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m>\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1180\u001b[0m                 \u001b[0muse_index\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbuildlist\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mNameError\u001b[0m: name 'row_in_buildlist' is not defined"
     ]
    }
   ],
   "source": [
    "zmolecule = molecule.to_zmat(fragment_list=[(fragment, connection_array)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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