QCArchive.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# QCArchive Demo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<h3>FractalClient</h3>\n",
       "<ul>\n",
       "  <li><b>Server:   &nbsp; </b>The MolSSI QCArchive Server</li>\n",
       "  <li><b>Address:  &nbsp; </b>https://api.qcarchive.molssi.org:443/</li>\n",
       "  <li><b>Username: &nbsp; </b>None</li>\n",
       "</ul>\n"
      ],
      "text/plain": [
       "FractalClient(server_name='The MolSSI QCArchive Server', address='https://api.qcarchive.molssi.org:443/', username='None')"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "client"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "butane = client.query_molecules(id=['61139', '70659'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Molecule(name='C4H10' formula='C4H10' hash='3bbc6db')>,\n",
       " <Molecule(name='C4H10' formula='C4H10' hash='bb665a3')>]"
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15638919483683228\"  style=\"position: relative; width: 400px; height: 400px\">\n        <p id=\"3dmolwarning_15638919483683228\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15638919483683228 = null;\nvar warn = document.getElementById(\"3dmolwarning_15638919483683228\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15638919483683228 = $3Dmol.createViewer($(\"#3dmolviewer_15638919483683228\"),{backgroundColor:\"white\"});\n\tviewer_15638919483683228.addModel(\"14\\nC4H10\\nC                     0.319142817510    -1.093637470615    -1.564414747816\\nC                    -0.290915848913     1.096758367299     1.567781812448\\nC                     0.092836854842    -0.751249438146    -0.100522397103\\nC                    -0.092794060281     0.751359940931     0.100493429943\\nH                    -0.519879641163    -0.755167725511    -2.180879601800\\nH                     1.228258374974    -0.606784705229    -1.931321629538\\nH                     0.433231534967    -2.173772344395    -1.701604611738\\nH                     0.566770197846     0.756780387768     2.156554230319\\nH                    -1.189142468703     0.614634340052     1.966519364863\\nH                    -0.390704303684     2.178094155841     1.706284173437\\nH                     0.948659303509    -1.102785828023     0.487454535126\\nH                    -0.791724567833    -1.287994152809     0.261736276668\\nH                    -0.960730259026     1.099387769483    -0.471363219252\\nH                     0.783367161017     1.289109832998    -0.280421285847\\n\",\"xyz\");\n\tviewer_15638919483683228.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n\tviewer_15638919483683228.zoomTo();\nviewer_15638919483683228.render();\n});\n</script>",
      "text/html": [
       "<div id=\"3dmolviewer_15638919483683228\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "        <p id=\"3dmolwarning_15638919483683228\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
       "    tag.async = true;\n",
       "    tag.onload = () => {\n",
       "      resolve();\n",
       "    };\n",
       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
       "});\n",
       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_15638919483683228 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_15638919483683228\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15638919483683228 = $3Dmol.createViewer($(\"#3dmolviewer_15638919483683228\"),{backgroundColor:\"white\"});\n",
       "\tviewer_15638919483683228.addModel(\"14\\nC4H10\\nC                     0.319142817510    -1.093637470615    -1.564414747816\\nC                    -0.290915848913     1.096758367299     1.567781812448\\nC                     0.092836854842    -0.751249438146    -0.100522397103\\nC                    -0.092794060281     0.751359940931     0.100493429943\\nH                    -0.519879641163    -0.755167725511    -2.180879601800\\nH                     1.228258374974    -0.606784705229    -1.931321629538\\nH                     0.433231534967    -2.173772344395    -1.701604611738\\nH                     0.566770197846     0.756780387768     2.156554230319\\nH                    -1.189142468703     0.614634340052     1.966519364863\\nH                    -0.390704303684     2.178094155841     1.706284173437\\nH                     0.948659303509    -1.102785828023     0.487454535126\\nH                    -0.791724567833    -1.287994152809     0.261736276668\\nH                    -0.960730259026     1.099387769483    -0.471363219252\\nH                     0.783367161017     1.289109832998    -0.280421285847\\n\",\"xyz\");\n",
       "\tviewer_15638919483683228.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_15638919483683228.zoomTo();\n",
       "viewer_15638919483683228.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7fbc379f43c8>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15638919975722985\"  style=\"position: relative; width: 400px; height: 400px\">\n        <p id=\"3dmolwarning_15638919975722985\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15638919975722985 = null;\nvar warn = document.getElementById(\"3dmolwarning_15638919975722985\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15638919975722985 = $3Dmol.createViewer($(\"#3dmolviewer_15638919975722985\"),{backgroundColor:\"white\"});\n\tviewer_15638919975722985.addModel(\"14\\nC4H10\\nC                    -0.367198611826    -1.239066459661    -0.895096896430\\nC                    -0.805813620019     1.122919020599     0.749193187800\\nC                     0.884999946537    -0.552975918533    -0.342565957722\\nC                     0.651313993821     0.705495331858     0.533442172609\\nH                    -1.015245486716    -1.597844274534    -0.068455110112\\nH                    -0.934555683074    -0.548936751218    -1.553770205346\\nH                    -0.065145201911    -2.119653004760    -1.500550906186\\nH                    -1.371403922022     0.320442026938     1.267036676767\\nH                    -1.290856239503     1.369335458265    -0.218296082402\\nH                    -0.835804383885     2.030484305799     1.388465658940\\nH                     1.531851627070    -0.275261564622    -1.203346997941\\nH                     1.452835145270    -1.302370505887     0.251115044454\\nH                     1.190135739619     1.564630144108     0.077322987724\\nH                     1.111261775825     0.537535321291     1.531802741680\\n\",\"xyz\");\n\tviewer_15638919975722985.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n\tviewer_15638919975722985.zoomTo();\nviewer_15638919975722985.render();\n});\n</script>",
      "text/html": [
       "<div id=\"3dmolviewer_15638919975722985\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "        <p id=\"3dmolwarning_15638919975722985\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
       "    tag.async = true;\n",
       "    tag.onload = () => {\n",
       "      resolve();\n",
       "    };\n",
       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
       "});\n",
       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_15638919975722985 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_15638919975722985\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15638919975722985 = $3Dmol.createViewer($(\"#3dmolviewer_15638919975722985\"),{backgroundColor:\"white\"});\n",
       "\tviewer_15638919975722985.addModel(\"14\\nC4H10\\nC                    -0.367198611826    -1.239066459661    -0.895096896430\\nC                    -0.805813620019     1.122919020599     0.749193187800\\nC                     0.884999946537    -0.552975918533    -0.342565957722\\nC                     0.651313993821     0.705495331858     0.533442172609\\nH                    -1.015245486716    -1.597844274534    -0.068455110112\\nH                    -0.934555683074    -0.548936751218    -1.553770205346\\nH                    -0.065145201911    -2.119653004760    -1.500550906186\\nH                    -1.371403922022     0.320442026938     1.267036676767\\nH                    -1.290856239503     1.369335458265    -0.218296082402\\nH                    -0.835804383885     2.030484305799     1.388465658940\\nH                     1.531851627070    -0.275261564622    -1.203346997941\\nH                     1.452835145270    -1.302370505887     0.251115044454\\nH                     1.190135739619     1.564630144108     0.077322987724\\nH                     1.111261775825     0.537535321291     1.531802741680\\n\",\"xyz\");\n",
       "\tviewer_15638919975722985.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_15638919975722985.zoomTo();\n",
       "viewer_15638919975722985.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7fbc379bdb38>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[1].show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].symbols"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "butane_geometries = [butane[0].geometry.copy(),butane[1].geometry.copy()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "def calculate_distance(rA, rB):\n",
    "    \"\"\"Calculate the distance between points A and B\"\"\"\n",
    "    dist_vec = (rA - rB)\n",
    "    distance = np.linalg.norm(dist_vec)\n",
    "    return distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7.314158248564329\n"
     ]
    }
   ],
   "source": [
    "atom1 = butane_geometries[0][0]\n",
    "atom2 = butane_geometries[0][1]\n",
    "measured_distance = calculate_distance(atom1,atom2)\n",
    "print(measured_distance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7.31415824856433"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].measure([0,1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6.71634950813261\n"
     ]
    }
   ],
   "source": [
    "# Use calculate_distance funtion to measure the distance between atoms 3 and 10 in the second molecule\n",
    "atom3 = butane_geometries[1][2]\n",
    "atom10 = butane_geometries[1][9]\n",
    "measured_distance = calculate_distance(atom3,atom10)\n",
    "print(measured_distance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6.71634950813261"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[1].measure([2,9])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "def build_bond_list(coordinates, max_bond=1.55, min_bond=0):\n",
    "    num_atoms = len(coordinates)\n",
    "    \n",
    "    bonds = {}\n",
    "    \n",
    "    for atom1 in range(num_atoms):\n",
    "        for atom2 in range(atom1, num_atoms):\n",
    "            distance = calculate_distance(coordinates[atom1], coordinates[atom2])\n",
    "            \n",
    "            if distance > min_bond and distance < max_bond:\n",
    "                bonds[(atom1, atom2)] = distance\n",
    "    \n",
    "    return bonds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "bond_list = build_bond_list(butane_geometries[0], max_bond=2.93)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(0, 2): 2.873020656801253,\n",
       " (0, 4): 2.068839651551603,\n",
       " (0, 5): 2.068484041315794,\n",
       " (0, 6): 2.068821759435787,\n",
       " (1, 3): 2.873059651780396,\n",
       " (1, 7): 2.068247482474781,\n",
       " (1, 8): 2.0685780442929644,\n",
       " (1, 9): 2.0687346633381822,\n",
       " (2, 3): 2.8862132661474598,\n",
       " (2, 10): 2.0715801221019885,\n",
       " (2, 11): 2.0716218178677623,\n",
       " (3, 12): 2.0713472807014583,\n",
       " (3, 13): 2.071754810836534}"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bond_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(0, 2, 1.0),\n",
       " (0, 4, 1.0),\n",
       " (0, 5, 1.0),\n",
       " (0, 6, 1.0),\n",
       " (1, 3, 1.0),\n",
       " (1, 7, 1.0),\n",
       " (1, 8, 1.0),\n",
       " (1, 9, 1.0),\n",
       " (2, 3, 1.0),\n",
       " (2, 10, 1.0),\n",
       " (2, 11, 1.0),\n",
       " (3, 12, 1.0),\n",
       " (3, 13, 1.0)]"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].connectivity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "import qcelemental\n",
    "\n",
    "angstrom_to_bohr = qcelemental.constants.conversion_factor('angstrom', 'bohr')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "max_lenght = 1.55*angstrom_to_bohr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<OptimizationRecord(id='2658710' status='COMPLETE')>"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Use qcportal to access a geometry optimization calculation\n",
    "# use query_procedures\n",
    "# id = 2658710\n",
    "\n",
    "proc = client.query_procedures(id=2658710)[0]\n",
    "proc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [],
   "source": [
    "opt = proc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15638946780825531\"  style=\"position: relative; width: 400px; height: 400px\">\n        <p id=\"3dmolwarning_15638946780825531\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15638946780825531 = null;\nvar warn = document.getElementById(\"3dmolwarning_15638946780825531\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15638946780825531 = $3Dmol.createViewer($(\"#3dmolviewer_15638946780825531\"),{backgroundColor:\"white\"});\n\tviewer_15638946780825531.addModel(\"72\\nC54H18\\nC                     1.219221001901    -4.550194001216    -2.133023000369\\nC                     1.219221001901    -4.550194001216    -0.712023002632\\nC                     1.219221001901     4.550194001216    -2.133023000369\\nC                     1.219221001901     4.550194001216    -0.712023002632\\nC                     2.355354000793    -4.079591998090    -4.266046000738\\nC                     2.355354000793    -4.079591998090    -2.845045997709\\nC                     2.355354000793    -4.079591998090     0.000000000000\\nC                     2.355354000793    -4.079591998090     1.420999997737\\nC                     2.355354000793     4.079591998090    -4.266046000738\\nC                     2.355354000793     4.079591998090    -2.845045997709\\nC                     2.355354000793     4.079591998090     0.000000000000\\nC                     2.355354000793     4.079591998090     1.420999997737\\nC                     3.330972999315    -3.330972999315    -6.399070001252\\nC                     3.330972999315    -3.330972999315    -4.978069998223\\nC                     3.330972999315    -3.330972999315    -2.133023000369\\nC                     3.330972999315    -3.330972999315    -0.712023002632\\nC                     3.330972999315    -3.330972999315     2.133023000369\\nC                     3.330972999315    -3.330972999315     3.554022998107\\nC                     3.330972999315     3.330972999315    -6.399070001252\\nC                     3.330972999315     3.330972999315    -4.978069998223\\nC                     3.330972999315     3.330972999315    -2.133023000369\\nC                     3.330972999315     3.330972999315    -0.712023002632\\nC                     3.330972999315     3.330972999315     2.133023000369\\nC                     3.330972999315     3.330972999315     3.554022998107\\nC                     4.079591998090    -2.355354000793    -7.111092998592\\nC                     4.079591998090    -2.355354000793    -4.266046000738\\nC                     4.079591998090    -2.355354000793    -2.845045997709\\nC                     4.079591998090    -2.355354000793     0.000000000000\\nC                     4.079591998090    -2.355354000793     1.420999997737\\nC                     4.079591998090    -2.355354000793     4.266046000738\\nC                     4.079591998090     2.355354000793    -7.111092998592\\nC                     4.079591998090     2.355354000793    -4.266046000738\\nC                     4.079591998090     2.355354000793    -2.845045997709\\nC                     4.079591998090     2.355354000793     0.000000000000\\nC                     4.079591998090     2.355354000793     1.420999997737\\nC                     4.079591998090     2.355354000793     4.266046000738\\nC                     4.550194001216    -1.219221001901    -6.399070001252\\nC                     4.550194001216    -1.219221001901    -4.978069998223\\nC                     4.550194001216    -1.219221001901    -2.133023000369\\nC                     4.550194001216    -1.219221001901    -0.712023002632\\nC                     4.550194001216    -1.219221001901     2.133023000369\\nC                     4.550194001216    -1.219221001901     3.554022998107\\nC                     4.550194001216     1.219221001901    -6.399070001252\\nC                     4.550194001216     1.219221001901    -4.978069998223\\nC                     4.550194001216     1.219221001901    -2.133023000369\\nC                     4.550194001216     1.219221001901    -0.712023002632\\nC                     4.550194001216     1.219221001901     2.133023000369\\nC                     4.550194001216     1.219221001901     3.554022998107\\nC                     4.710707001441     0.000000000000    -7.111092998592\\nC                     4.710707001441     0.000000000000    -4.266046000738\\nC                     4.710707001441     0.000000000000    -2.845045997709\\nC                     4.710707001441     0.000000000000     0.000000000000\\nC                     4.710707001441     0.000000000000     1.420999997737\\nC                     4.710707001441     0.000000000000     4.266046000738\\nH                     0.288683440765    -4.672701218998    -2.676455361369\\nH                     0.288683440765    -4.672701218998    -0.168590641632\\nH                     0.288683440765     4.672701218998    -2.676455361369\\nH                     0.288683440765     4.672701218998    -0.168590641632\\nH                     1.488231459635    -4.438766150819    -4.809478912082\\nH                     1.488231147420    -4.438766277821     1.964432337570\\nH                     1.488231459635     4.438766150819    -4.809478912082\\nH                     1.488231147420     4.438766277821     1.964432337570\\nH                     2.586357829400    -3.902336471225    -6.942502547464\\nH                     2.586357829400    -3.902336471225     4.097455549610\\nH                     2.586357829400     3.902336471225    -6.942502547464\\nH                     2.586357829400     3.902336471225     4.097455549610\\nH                     4.079591998090    -2.355354000793    -8.195632949853\\nH                     4.079591998090    -2.355354000793     5.350585951999\\nH                     4.079591998090     2.355354000793    -8.195632949853\\nH                     4.079591998090     2.355354000793     5.350585951999\\nH                     4.710707001441     0.000000000000    -8.195632949853\\nH                     4.710707001441     0.000000000000     5.350585951999\\n\",\"xyz\");\n\tviewer_15638946780825531.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n\tviewer_15638946780825531.zoomTo();\nviewer_15638946780825531.render();\n});\n</script>",
      "text/html": [
       "<div id=\"3dmolviewer_15638946780825531\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "        <p id=\"3dmolwarning_15638946780825531\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
       "    tag.async = true;\n",
       "    tag.onload = () => {\n",
       "      resolve();\n",
       "    };\n",
       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
       "});\n",
       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_15638946780825531 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_15638946780825531\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15638946780825531 = $3Dmol.createViewer($(\"#3dmolviewer_15638946780825531\"),{backgroundColor:\"white\"});\n",
       "\tviewer_15638946780825531.addModel(\"72\\nC54H18\\nC                     1.219221001901    -4.550194001216    -2.133023000369\\nC                     1.219221001901    -4.550194001216    -0.712023002632\\nC                     1.219221001901     4.550194001216    -2.133023000369\\nC                     1.219221001901     4.550194001216    -0.712023002632\\nC                     2.355354000793    -4.079591998090    -4.266046000738\\nC                     2.355354000793    -4.079591998090    -2.845045997709\\nC                     2.355354000793    -4.079591998090     0.000000000000\\nC                     2.355354000793    -4.079591998090     1.420999997737\\nC                     2.355354000793     4.079591998090    -4.266046000738\\nC                     2.355354000793     4.079591998090    -2.845045997709\\nC                     2.355354000793     4.079591998090     0.000000000000\\nC                     2.355354000793     4.079591998090     1.420999997737\\nC                     3.330972999315    -3.330972999315    -6.399070001252\\nC                     3.330972999315    -3.330972999315    -4.978069998223\\nC                     3.330972999315    -3.330972999315    -2.133023000369\\nC                     3.330972999315    -3.330972999315    -0.712023002632\\nC                     3.330972999315    -3.330972999315     2.133023000369\\nC                     3.330972999315    -3.330972999315     3.554022998107\\nC                     3.330972999315     3.330972999315    -6.399070001252\\nC                     3.330972999315     3.330972999315    -4.978069998223\\nC                     3.330972999315     3.330972999315    -2.133023000369\\nC                     3.330972999315     3.330972999315    -0.712023002632\\nC                     3.330972999315     3.330972999315     2.133023000369\\nC                     3.330972999315     3.330972999315     3.554022998107\\nC                     4.079591998090    -2.355354000793    -7.111092998592\\nC                     4.079591998090    -2.355354000793    -4.266046000738\\nC                     4.079591998090    -2.355354000793    -2.845045997709\\nC                     4.079591998090    -2.355354000793     0.000000000000\\nC                     4.079591998090    -2.355354000793     1.420999997737\\nC                     4.079591998090    -2.355354000793     4.266046000738\\nC                     4.079591998090     2.355354000793    -7.111092998592\\nC                     4.079591998090     2.355354000793    -4.266046000738\\nC                     4.079591998090     2.355354000793    -2.845045997709\\nC                     4.079591998090     2.355354000793     0.000000000000\\nC                     4.079591998090     2.355354000793     1.420999997737\\nC                     4.079591998090     2.355354000793     4.266046000738\\nC                     4.550194001216    -1.219221001901    -6.399070001252\\nC                     4.550194001216    -1.219221001901    -4.978069998223\\nC                     4.550194001216    -1.219221001901    -2.133023000369\\nC                     4.550194001216    -1.219221001901    -0.712023002632\\nC                     4.550194001216    -1.219221001901     2.133023000369\\nC                     4.550194001216    -1.219221001901     3.554022998107\\nC                     4.550194001216     1.219221001901    -6.399070001252\\nC                     4.550194001216     1.219221001901    -4.978069998223\\nC                     4.550194001216     1.219221001901    -2.133023000369\\nC                     4.550194001216     1.219221001901    -0.712023002632\\nC                     4.550194001216     1.219221001901     2.133023000369\\nC                     4.550194001216     1.219221001901     3.554022998107\\nC                     4.710707001441     0.000000000000    -7.111092998592\\nC                     4.710707001441     0.000000000000    -4.266046000738\\nC                     4.710707001441     0.000000000000    -2.845045997709\\nC                     4.710707001441     0.000000000000     0.000000000000\\nC                     4.710707001441     0.000000000000     1.420999997737\\nC                     4.710707001441     0.000000000000     4.266046000738\\nH                     0.288683440765    -4.672701218998    -2.676455361369\\nH                     0.288683440765    -4.672701218998    -0.168590641632\\nH                     0.288683440765     4.672701218998    -2.676455361369\\nH                     0.288683440765     4.672701218998    -0.168590641632\\nH                     1.488231459635    -4.438766150819    -4.809478912082\\nH                     1.488231147420    -4.438766277821     1.964432337570\\nH                     1.488231459635     4.438766150819    -4.809478912082\\nH                     1.488231147420     4.438766277821     1.964432337570\\nH                     2.586357829400    -3.902336471225    -6.942502547464\\nH                     2.586357829400    -3.902336471225     4.097455549610\\nH                     2.586357829400     3.902336471225    -6.942502547464\\nH                     2.586357829400     3.902336471225     4.097455549610\\nH                     4.079591998090    -2.355354000793    -8.195632949853\\nH                     4.079591998090    -2.355354000793     5.350585951999\\nH                     4.079591998090     2.355354000793    -8.195632949853\\nH                     4.079591998090     2.355354000793     5.350585951999\\nH                     4.710707001441     0.000000000000    -8.195632949853\\nH                     4.710707001441     0.000000000000     5.350585951999\\n\",\"xyz\");\n",
       "\tviewer_15638946780825531.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_15638946780825531.zoomTo();\n",
       "viewer_15638946780825531.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7fbc37929e10>"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "initial = opt.get_initial_molecule()\n",
    "initial.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15638947348324926\"  style=\"position: relative; width: 400px; height: 400px\">\n        <p id=\"3dmolwarning_15638947348324926\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15638947348324926 = null;\nvar warn = document.getElementById(\"3dmolwarning_15638947348324926\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15638947348324926 = $3Dmol.createViewer($(\"#3dmolviewer_15638947348324926\"),{backgroundColor:\"white\"});\n\tviewer_15638947348324926.addModel(\"72\\nC54H18\\nC                     2.903604033453    -6.112482329788    -2.100940515408\\nC                     2.903603382565    -6.112487304054    -0.744107403214\\nC                     2.903596069336     6.112511984879    -2.100938033567\\nC                     2.903596667306     6.112507587416    -0.744102465991\\nC                     3.136053574199    -4.883593784133    -4.251905914701\\nC                     3.094346715762    -4.901845079670    -2.857595519928\\nC                     3.094346244794    -4.901850524904     0.012547606598\\nC                     3.136053314903    -4.883599001821     1.406858858638\\nC                     3.136048917440     4.883603912585    -4.251916942755\\nC                     3.094339847042     4.901880291122    -2.857602991911\\nC                     3.094340503222     4.901874110332     0.012560248641\\nC                     3.136049510118     4.883598917152     1.406873167590\\nC                     3.394645977308    -3.657952650851    -6.402321604708\\nC                     3.305058894969    -3.696675976424    -4.965192756557\\nC                     3.244196885152    -3.681150049357    -2.134435247342\\nC                     3.244196472393    -3.681155536925    -0.710614264104\\nC                     3.305058720341    -3.696684210421     2.120150600675\\nC                     3.394647019788    -3.657948168720     3.557280274342\\nC                     3.394645098874     3.657915402067    -6.402351513804\\nC                     3.305054756803     3.696694725172    -4.965221093997\\nC                     3.244191889719     3.681190118655    -2.134434236613\\nC                     3.244192498273     3.681183837322    -0.710607638805\\nC                     3.305055450026     3.696686337713     2.120171116875\\nC                     3.394644987747     3.657920709714     3.557301145091\\nC                     3.524256092076    -2.487901551798    -7.077124981145\\nC                     3.388666317162    -2.459158958219    -4.260200068965\\nC                     3.368221169328    -2.456039649066    -2.840840076072\\nC                     3.368220878281    -2.456048248196    -0.004206440231\\nC                     3.388666089616    -2.459169414761     1.415155076692\\nC                     3.524256965218    -2.487895963687     4.232082788220\\nC                     3.524255107806     2.487850898956    -7.077141517933\\nC                     3.388663512523     2.459188676811    -4.260215658525\\nC                     3.368217973098     2.456082904011    -2.840847860268\\nC                     3.368218475816     2.456073357654    -0.004197581805\\nC                     3.388664046992     2.459177987431     1.415168443709\\nC                     3.524254938470     2.487857090329     4.232090074990\\nC                     3.542570200948    -1.219005732612    -6.395645753732\\nC                     3.475755222683    -1.228237890524    -4.970401987603\\nC                     3.430567082005    -1.228942601107    -2.131991554609\\nC                     3.430566896793    -1.228951142027    -0.713057237156\\nC                     3.475755317935    -1.228248775699     2.125359625341\\nC                     3.542570883587    -1.219000657803     3.550604449824\\nC                     3.542570624290     1.218954391839    -6.395668630062\\nC                     3.475754026742     1.228263481534    -4.970422429718\\nC                     3.430565468014     1.228989830173    -2.131990358668\\nC                     3.430565759062     1.228980892370    -0.713052998446\\nC                     3.475754375999     1.228252421730     2.125372817729\\nC                     3.542570597831     1.218959440190     3.550617933260\\nC                     3.589719842793    -0.000035147950    -7.072735233928\\nC                     3.474337885025     0.000020886625    -4.259012955145\\nC                     3.454492755355     0.000024950705    -2.840866058673\\nC                     3.454492877066     0.000012366871    -0.004179970787\\nC                     3.474338075529     0.000007260311     1.413967179690\\nC                     3.589720234384    -0.000026088436     4.227689553725\\nH                     2.754263255338    -7.040868584476    -2.642719261126\\nH                     2.754262371612    -7.040874913436    -0.202331869602\\nH                     2.754253121594     7.040900557363    -2.642711106505\\nH                     2.754253973569     7.040894381865    -0.202325625311\\nH                     3.023176751931    -5.816498889402    -4.796678967331\\nH                     3.023176122210    -5.816504429888     1.951630186150\\nH                     3.023170380637     5.816506133838    -4.796692419016\\nH                     3.023171222029     5.816500365807     1.951650501263\\nH                     3.354201333521    -4.595760440099    -6.946996256836\\nH                     3.354203053347    -4.595753105703     4.101959165179\\nH                     3.354201846823     4.595710247640    -6.947048449584\\nH                     3.354201481691     4.595718031837     4.101994244336\\nH                     3.628610462449    -2.494167650277    -8.157316857894\\nH                     3.628611483761    -2.494160733931     5.312275024810\\nH                     3.628609255925     2.494108869272    -8.157333071884\\nH                     3.628609203008     2.494116283045     5.312281745360\\nH                     3.698094795777    -0.000047170857    -8.153506247508\\nH                     3.698095055074    -0.000032935990     5.308459895251\\n\",\"xyz\");\n\tviewer_15638947348324926.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n\tviewer_15638947348324926.zoomTo();\nviewer_15638947348324926.render();\n});\n</script>",
      "text/html": [
       "<div id=\"3dmolviewer_15638947348324926\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "        <p id=\"3dmolwarning_15638947348324926\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
       "    tag.async = true;\n",
       "    tag.onload = () => {\n",
       "      resolve();\n",
       "    };\n",
       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
       "});\n",
       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_15638947348324926 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_15638947348324926\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15638947348324926 = $3Dmol.createViewer($(\"#3dmolviewer_15638947348324926\"),{backgroundColor:\"white\"});\n",
       "\tviewer_15638947348324926.addModel(\"72\\nC54H18\\nC                     2.903604033453    -6.112482329788    -2.100940515408\\nC                     2.903603382565    -6.112487304054    -0.744107403214\\nC                     2.903596069336     6.112511984879    -2.100938033567\\nC                     2.903596667306     6.112507587416    -0.744102465991\\nC                     3.136053574199    -4.883593784133    -4.251905914701\\nC                     3.094346715762    -4.901845079670    -2.857595519928\\nC                     3.094346244794    -4.901850524904     0.012547606598\\nC                     3.136053314903    -4.883599001821     1.406858858638\\nC                     3.136048917440     4.883603912585    -4.251916942755\\nC                     3.094339847042     4.901880291122    -2.857602991911\\nC                     3.094340503222     4.901874110332     0.012560248641\\nC                     3.136049510118     4.883598917152     1.406873167590\\nC                     3.394645977308    -3.657952650851    -6.402321604708\\nC                     3.305058894969    -3.696675976424    -4.965192756557\\nC                     3.244196885152    -3.681150049357    -2.134435247342\\nC                     3.244196472393    -3.681155536925    -0.710614264104\\nC                     3.305058720341    -3.696684210421     2.120150600675\\nC                     3.394647019788    -3.657948168720     3.557280274342\\nC                     3.394645098874     3.657915402067    -6.402351513804\\nC                     3.305054756803     3.696694725172    -4.965221093997\\nC                     3.244191889719     3.681190118655    -2.134434236613\\nC                     3.244192498273     3.681183837322    -0.710607638805\\nC                     3.305055450026     3.696686337713     2.120171116875\\nC                     3.394644987747     3.657920709714     3.557301145091\\nC                     3.524256092076    -2.487901551798    -7.077124981145\\nC                     3.388666317162    -2.459158958219    -4.260200068965\\nC                     3.368221169328    -2.456039649066    -2.840840076072\\nC                     3.368220878281    -2.456048248196    -0.004206440231\\nC                     3.388666089616    -2.459169414761     1.415155076692\\nC                     3.524256965218    -2.487895963687     4.232082788220\\nC                     3.524255107806     2.487850898956    -7.077141517933\\nC                     3.388663512523     2.459188676811    -4.260215658525\\nC                     3.368217973098     2.456082904011    -2.840847860268\\nC                     3.368218475816     2.456073357654    -0.004197581805\\nC                     3.388664046992     2.459177987431     1.415168443709\\nC                     3.524254938470     2.487857090329     4.232090074990\\nC                     3.542570200948    -1.219005732612    -6.395645753732\\nC                     3.475755222683    -1.228237890524    -4.970401987603\\nC                     3.430567082005    -1.228942601107    -2.131991554609\\nC                     3.430566896793    -1.228951142027    -0.713057237156\\nC                     3.475755317935    -1.228248775699     2.125359625341\\nC                     3.542570883587    -1.219000657803     3.550604449824\\nC                     3.542570624290     1.218954391839    -6.395668630062\\nC                     3.475754026742     1.228263481534    -4.970422429718\\nC                     3.430565468014     1.228989830173    -2.131990358668\\nC                     3.430565759062     1.228980892370    -0.713052998446\\nC                     3.475754375999     1.228252421730     2.125372817729\\nC                     3.542570597831     1.218959440190     3.550617933260\\nC                     3.589719842793    -0.000035147950    -7.072735233928\\nC                     3.474337885025     0.000020886625    -4.259012955145\\nC                     3.454492755355     0.000024950705    -2.840866058673\\nC                     3.454492877066     0.000012366871    -0.004179970787\\nC                     3.474338075529     0.000007260311     1.413967179690\\nC                     3.589720234384    -0.000026088436     4.227689553725\\nH                     2.754263255338    -7.040868584476    -2.642719261126\\nH                     2.754262371612    -7.040874913436    -0.202331869602\\nH                     2.754253121594     7.040900557363    -2.642711106505\\nH                     2.754253973569     7.040894381865    -0.202325625311\\nH                     3.023176751931    -5.816498889402    -4.796678967331\\nH                     3.023176122210    -5.816504429888     1.951630186150\\nH                     3.023170380637     5.816506133838    -4.796692419016\\nH                     3.023171222029     5.816500365807     1.951650501263\\nH                     3.354201333521    -4.595760440099    -6.946996256836\\nH                     3.354203053347    -4.595753105703     4.101959165179\\nH                     3.354201846823     4.595710247640    -6.947048449584\\nH                     3.354201481691     4.595718031837     4.101994244336\\nH                     3.628610462449    -2.494167650277    -8.157316857894\\nH                     3.628611483761    -2.494160733931     5.312275024810\\nH                     3.628609255925     2.494108869272    -8.157333071884\\nH                     3.628609203008     2.494116283045     5.312281745360\\nH                     3.698094795777    -0.000047170857    -8.153506247508\\nH                     3.698095055074    -0.000032935990     5.308459895251\\n\",\"xyz\");\n",
       "\tviewer_15638947348324926.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_15638947348324926.zoomTo();\n",
       "viewer_15638947348324926.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7fbc378bf080>"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final = opt.get_final_molecule()\n",
    "final.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "initial.connectivity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [],
   "source": [
    "# max bond lenght is 2.93\n",
    "initial_coordinates = initial.geometry.copy()\n",
    "final_coordinates = final.geometry.copy()\n",
    "initial_bond = build_bond_list(initial_coordinates, max_bond=2.93)\n",
    "final_bond = build_bond_list(final_coordinates, max_bond=2.93)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{(0, 1): 2.6853008199999997, (0, 5): 2.685300947458371, (0, 54): 2.0494834766860643, (1, 6): 2.6853009524690883, (1, 55): 2.0494834766860643, (2, 3): 2.6853008199999997, (2, 9): 2.685300947458371, (2, 56): 2.0494834766860643, (3, 10): 2.6853009524690883, (3, 57): 2.0494834766860643, (4, 5): 2.685300829999999, (4, 13): 2.685300829993184, (4, 58): 2.0494834770587396, (5, 14): 2.6852998829666923, (6, 7): 2.68530082, (6, 15): 2.6852998879774117, (7, 16): 2.6852998879774117, (7, 59): 2.0494834871062877, (8, 9): 2.685300829999999, (8, 19): 2.685300829993184, (8, 60): 2.0494834770587396, (9, 20): 2.6852998829666923, (10, 11): 2.68530082, (10, 21): 2.6852998879774117, (11, 22): 2.6852998879774117, (11, 61): 2.0494834871062877, (12, 13): 2.685300829999999, (12, 24): 2.6852998829666923, (12, 62): 2.049483475383679, (13, 25): 2.685300829993184, (14, 15): 2.6853008199999997, (14, 26): 2.6852998829666923, (15, 27): 2.6852998879774117, (16, 17): 2.68530082, (16, 28): 2.6852998879774117, (17, 29): 2.6852998879774117, (17, 63): 2.049483480394398, (18, 19): 2.685300829999999, (18, 30): 2.6852998829666923, (18, 64): 2.049483475383679, (19, 31): 2.685300829993184, (20, 21): 2.6853008199999997, (20, 32): 2.6852998829666923, (21, 33): 2.6852998879774117, (22, 23): 2.68530082, (22, 34): 2.6852998879774117, (23, 35): 2.6852998879774117, (23, 65): 2.049483480394398, (24, 36): 2.685300947458371, (24, 66): 2.0494834799999992, (25, 26): 2.685300829999999, (25, 37): 2.6853018944844873, (26, 38): 2.685300947458371, (27, 28): 2.68530082, (27, 39): 2.6853009524690883, (28, 40): 2.6853009524690883, (29, 41): 2.6853009524690883, (29, 67): 2.049483480000001, (30, 42): 2.685300947458371, (30, 68): 2.0494834799999992, (31, 32): 2.685300829999999, (31, 43): 2.6853018944844873, (32, 44): 2.685300947458371, (33, 34): 2.68530082, (33, 45): 2.6853009524690883, (34, 46): 2.6853009524690883, (35, 47): 2.6853009524690883, (35, 69): 2.049483480000001, (36, 37): 2.685300829999999, (36, 48): 2.6853008398744698, (37, 49): 2.685301786900624, (38, 39): 2.6853008199999997, (38, 50): 2.6853008398744698, (39, 51): 2.6853008448851874, (40, 41): 2.68530082, (40, 52): 2.6853008448851874, (41, 53): 2.6853008448851874, (42, 43): 2.685300829999999, (42, 48): 2.6853008398744698, (43, 49): 2.685301786900624, (44, 45): 2.6853008199999997, (44, 50): 2.6853008398744698, (45, 51): 2.6853008448851874, (46, 47): 2.68530082, (46, 52): 2.6853008448851874, (47, 53): 2.6853008448851874, (48, 70): 2.0494834799999992, (49, 50): 2.685300829999999, (51, 52): 2.68530082, (53, 71): 2.049483480000001}\n"
     ]
    }
   ],
   "source": [
    "print(initial_bond)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{(0, 1): 2.5640429800175255, (0, 5): 2.721830285918179, (0, 54): 2.050790758811911, (1, 6): 2.7218295881283754, (1, 55): 2.0507899790642936, (2, 3): 2.5640476200137154, (2, 9): 2.7218316161338745, (2, 56): 2.0507897182972523, (3, 10): 2.7218322358238627, (3, 57): 2.0507903323327072, (4, 5): 2.6362688969926538, (4, 13): 2.6362287673968563, (4, 58): 2.0526208230733363, (5, 14): 2.6960983036854445, (6, 7): 2.636270533714002, (6, 15): 2.6960997775436293, (7, 16): 2.6362286718268693, (7, 59): 2.052619784709002, (8, 9): 2.6362763589350253, (8, 19): 2.6362317513408633, (8, 60): 2.052618775995513, (9, 20): 2.696098946310403, (10, 11): 2.6362743770415618, (10, 21): 2.69609826814251, (11, 22): 2.636231235454784, (11, 61): 2.052619233623958, (12, 13): 2.72203531192571, (12, 24): 2.564169618543982, (12, 62): 2.0508445474196115, (13, 25): 2.696059263395006, (14, 15): 2.690631710020097, (14, 26): 2.682669276790726, (15, 27): 2.6826670389495995, (16, 17): 2.722037657492619, (16, 28): 2.6960582630681764, (17, 29): 2.5641705795606935, (17, 63): 2.050843862160726, (18, 19): 2.722041505034991, (18, 30): 2.5641788745730825, (18, 64): 2.050844447656416, (19, 31): 2.6960533339463475, (20, 21): 2.690642320026428, (20, 32): 2.6826726488841537, (21, 33): 2.682674602167853, (22, 23): 2.7220399755844102, (22, 34): 2.6960545100618356, (23, 35): 2.564176414497956, (23, 65): 2.0508448708356606, (24, 36): 2.7220230301094754, (24, 66): 2.0508044054115038, (25, 26): 2.6824863860456256, (25, 37): 2.6905465841620844, (26, 38): 2.680561957509339, (27, 28): 2.682489275183641, (27, 39): 2.6805642102547806, (28, 40): 2.6905484003099565, (29, 41): 2.722021376226541, (29, 67): 2.050805094682261, (30, 42): 2.7220185413147258, (30, 68): 2.0508036692319536, (31, 32): 2.6825010890496643, (31, 43): 2.6905580877221253, (32, 44): 2.6805640725487785, (33, 34): 2.6824977355443593, (33, 45): 2.680561091221982, (34, 46): 2.6905564118575427, (35, 47): 2.72201978044889, (35, 69): 2.0508039226853367, (36, 37): 2.696334759656457, (36, 48): 2.636532006559348, (37, 49): 2.682277014835587, (38, 39): 2.681397250048598, (38, 50): 2.6814386328151083, (39, 51): 2.6814346333317425, (40, 41): 2.696337004713522, (40, 52): 2.682275764899848, (41, 53): 2.6365345534604177, (42, 43): 2.696340442384856, (42, 48): 2.63654229620249, (43, 49): 2.682269911997115, (44, 45): 2.6814030000532503, (44, 50): 2.6814354394476605, (45, 51): 2.681438878673595, (46, 47): 2.6963381630025953, (46, 52): 2.6822704754077114, (47, 53): 2.636540300741533, (48, 70): 2.0526037064385148, (49, 50): 2.680171622154041, (51, 52): 2.6801721039324247, (53, 71): 2.0526024177470563}\n"
     ]
    }
   ],
   "source": [
    "print(final_bond)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}