Day_2-Part_1.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# QCArchive Demo\n",
    "## MolSSI Software Summer School"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "#qcarchive contains a bunch of quantum mechanical information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "client "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "butane = client.query_molecules(id=['61139', '70659']) #id numbers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Molecule(name='C4H10' formula='C4H10' hash='3bbc6db')>,\n",
       " <Molecule(name='C4H10' formula='C4H10' hash='bb665a3')>]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
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       "$3Dmolpromise = null;\n",
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       "\n",
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       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_1563891421188414 = $3Dmol.createViewer($(\"#3dmolviewer_1563891421188414\"),{backgroundColor:\"white\"});\n",
       "\tviewer_1563891421188414.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_1563891421188414.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
       "\tviewer_1563891421188414.zoomTo();\n",
       "viewer_1563891421188414.render();\n",
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       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7f7f5cb1f358>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].show() #visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15638915179883578\"  style=\"position: relative; width: 400px; height: 400px\">\n        <p id=\"3dmolwarning_15638915179883578\" 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_15638915179883578 = null;\nvar warn = document.getElementById(\"3dmolwarning_15638915179883578\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15638915179883578 = $3Dmol.createViewer($(\"#3dmolviewer_15638915179883578\"),{backgroundColor:\"white\"});\n\tviewer_15638915179883578.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_15638915179883578.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n\tviewer_15638915179883578.zoomTo();\nviewer_15638915179883578.render();\n});\n</script>",
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       "<div id=\"3dmolviewer_15638915179883578\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "        <p id=\"3dmolwarning_15638915179883578\" 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",
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       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_15638915179883578 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_15638915179883578\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15638915179883578 = $3Dmol.createViewer($(\"#3dmolviewer_15638915179883578\"),{backgroundColor:\"white\"});\n",
       "\tviewer_15638915179883578.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_15638915179883578.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
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     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7f7f34d43860>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[1].show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Config',\n",
       " '__abstractmethods__',\n",
       " '__annotations__',\n",
       " '__class__',\n",
       " '__config__',\n",
       " '__delattr__',\n",
       " '__dict__',\n",
       " '__dir__',\n",
       " '__doc__',\n",
       " '__eq__',\n",
       " '__fields__',\n",
       " '__fields_set__',\n",
       " '__format__',\n",
       " '__ge__',\n",
       " '__get_validators__',\n",
       " '__getattr__',\n",
       " '__getattribute__',\n",
       " '__getstate__',\n",
       " '__gt__',\n",
       " '__hash__',\n",
       " '__init__',\n",
       " '__init_subclass__',\n",
       " '__iter__',\n",
       " '__le__',\n",
       " '__lt__',\n",
       " '__module__',\n",
       " '__ne__',\n",
       " '__new__',\n",
       " '__reduce__',\n",
       " '__reduce_ex__',\n",
       " '__repr__',\n",
       " '__setattr__',\n",
       " '__setstate__',\n",
       " '__sizeof__',\n",
       " '__slots__',\n",
       " '__str__',\n",
       " '__subclasshook__',\n",
       " '__validators__',\n",
       " '__values__',\n",
       " '__weakref__',\n",
       " '_abc_impl',\n",
       " '_calculate_keys',\n",
       " '_custom_root_type',\n",
       " '_decompose_class',\n",
       " '_get_key_factory',\n",
       " '_get_value',\n",
       " '_inertial_tensor',\n",
       " '_iter',\n",
       " '_json_encoder',\n",
       " '_orient_molecule_internal',\n",
       " '_repr_html_',\n",
       " '_schema_cache',\n",
       " 'align',\n",
       " 'atom_labels',\n",
       " 'atomic_numbers',\n",
       " 'comment',\n",
       " 'compare',\n",
       " 'connectivity',\n",
       " 'construct',\n",
       " 'copy',\n",
       " 'dict',\n",
       " 'extras',\n",
       " 'fields',\n",
       " 'fix_com',\n",
       " 'fix_orientation',\n",
       " 'fix_symmetry',\n",
       " 'fragment_charges',\n",
       " 'fragment_multiplicities',\n",
       " 'fragments',\n",
       " 'from_data',\n",
       " 'from_file',\n",
       " 'from_orm',\n",
       " 'geometry',\n",
       " 'get_fragment',\n",
       " 'get_hash',\n",
       " 'get_molecular_formula',\n",
       " 'hash_fields',\n",
       " 'id',\n",
       " 'identifiers',\n",
       " 'json',\n",
       " 'json_dict',\n",
       " 'mass_numbers',\n",
       " 'masses',\n",
       " 'measure',\n",
       " 'min_zero',\n",
       " 'molecular_charge',\n",
       " 'molecular_multiplicity',\n",
       " 'must_be_3n',\n",
       " 'must_be_n',\n",
       " 'must_be_n_frag',\n",
       " 'name',\n",
       " 'nelectrons',\n",
       " 'nuclear_repulsion_energy',\n",
       " 'orient_molecule',\n",
       " 'parse_file',\n",
       " 'parse_obj',\n",
       " 'parse_raw',\n",
       " 'populate_real',\n",
       " 'pretty_print',\n",
       " 'provenance',\n",
       " 'real',\n",
       " 'schema',\n",
       " 'schema_json',\n",
       " 'schema_name',\n",
       " 'schema_version',\n",
       " 'scramble',\n",
       " 'show',\n",
       " 'symbols',\n",
       " 'to_file',\n",
       " 'to_string',\n",
       " 'update_forward_refs',\n",
       " 'validate']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dir(butane[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0.60309252, -2.0666753 , -2.95631542],\n",
       "       [-0.54975128,  2.07257294,  2.96267825],\n",
       "       [ 0.17543623, -1.41965569, -0.1899598 ],\n",
       "       [-0.17535536,  1.41986451,  0.18990506],\n",
       "       [-0.98243014, -1.42706018, -4.12126516],\n",
       "       [ 2.32107194, -1.14665691, -3.64966894],\n",
       "       [ 0.81868895, -4.10783439, -3.21556669],\n",
       "       [ 1.07104045,  1.43010767,  4.07529687],\n",
       "       [-2.24715359,  1.16149057,  3.71618302],\n",
       "       [-0.73832413,  4.11600143,  3.22440978],\n",
       "       [ 1.79270627, -2.08396319,  0.92115557],\n",
       "       [-1.4961426 , -2.4339562 ,  0.49460988],\n",
       "       [-1.81551707,  2.07754179, -0.89074739],\n",
       "       [ 1.48034939,  2.43606453, -0.52991943]])"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].geometry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "butane_geometries = [butane[0].geometry.copy(), butane[1].geometry.copy()] \n",
    "#copy because it's a numpy array and don't want to overwrite\n",
    "#index into list via brackets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "def calculate_distance(rA, rB):\n",
    "    '''Calculate the distance between points A and B'''\n",
    "    dist_vect = (rA - rB)\n",
    "    distance = np.linalg.norm(dist_vect)\n",
    "    return distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[ 0.60309252 -2.0666753  -2.95631542]\n"
     ]
    }
   ],
   "source": [
    "atom1 = butane_geometries[0][0]\n",
    "print(atom1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[-0.54975128  2.07257294  2.96267825]\n"
     ]
    }
   ],
   "source": [
    "atom2= butane_geometries[0][1]\n",
    "print(atom2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7.314158248564329\n"
     ]
    }
   ],
   "source": [
    "measured_distance = calculate_distance(atom1, atom2)\n",
    "print(measured_distance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7.31415824856433"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].measure([0, 1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[ 1.67240752 -1.04497304 -0.64735584]\n"
     ]
    }
   ],
   "source": [
    "atom2 = butane_geometries[1][2]\n",
    "print(atom3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[-1.57944138  3.83705924  2.62381983]\n"
     ]
    }
   ],
   "source": [
    "atom9 = butane_geometries[1][9]\n",
    "print(atom10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6.71634950813261\n"
     ]
    }
   ],
   "source": [
    "#Use calculate_density function to measure the distance between atoms 3 and 10\n",
    "#in the second butane molecule\n",
    "atom2 = butane_geometries[1][2]\n",
    "print(atom3)\n",
    "\n",
    "atom9 = butane_geometries[1][9]\n",
    "print(atom10)\n",
    "\n",
    "measured_distance_exercise = calculate_distance(atom2, atom9)\n",
    "print(measured_distance_exercise)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6.71634950813261\n"
     ]
    }
   ],
   "source": [
    "qarchive_distance = butane[1].measure([2, 9])\n",
    "print(qarchive_distance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "#this function will determine whether something is a bond or not\n",
    "def build_bond_list(coordinates, max_bond=2.93, 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": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "bond_list = build_bond_list(butane_geometries[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "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": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bond_list #didn't print because our max bond is too low, we were thinking angstroms and it's actually Bohrs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "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": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "butane[0].connectivity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.8897261254578281\n"
     ]
    }
   ],
   "source": [
    "import qcelemental\n",
    "\n",
    "angstrom_to_bohr = qcelemental.constants.conversion_factor(\"angstrom\", \"bohr\")\n",
    "print(angstrom_to_bohr)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [],
   "source": [
    "max_length = 1.55*angstrom_to_bohr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[<OptimizationRecord(id='2658710' status='COMPLETE')>]\n"
     ]
    }
   ],
   "source": [
    "#Use qcportal to access a geomtry optimization calculation\n",
    "#use query_procedures\n",
    "#id = 2658710\n",
    "\n",
    "geometry_opt = client.query_procedures(id=['2658710'])\n",
    "print(geometry_opt)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [],
   "source": [
    "opt = geometry_opt[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
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     "data": {
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       "<py3Dmol.view at 0x7f7f34d2fba8>"
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     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "initial = opt.get_initial_molecule()\n",
    "initial.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
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       "        <p id=\"3dmolwarning_15638946891492398\" 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",
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       "\n",
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       "\tviewer_15638946891492398.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                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       "\tviewer_15638946891492398.setStyle({\"stick\": {\"radius\": 0.2}, \"sphere\": {\"scale\": 0.3}});\n",
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<py3Dmol.view at 0x7f7f33f4b940>"
      ]
     },
     "execution_count": 58,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final = opt.get_final_molecule()\n",
    "final.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [],
   "source": [
    "initial.connectivity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [],
   "source": [
    "# max bond length is 2.93\n",
    "initial_coordinates = initial.geometry.copy()\n",
    "final_coordinates = final.geometry.copy()\n",
    "\n",
    "initial_bonds = build_bond_list(initial_coordinates)\n",
    "final_bonds = build_bond_list(final_coordinates)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(0, 1): 2.6853008199999997,\n",
       " (0, 5): 2.685300947458371,\n",
       " (0, 54): 2.0494834766860643,\n",
       " (1, 6): 2.6853009524690883,\n",
       " (1, 55): 2.0494834766860643,\n",
       " (2, 3): 2.6853008199999997,\n",
       " (2, 9): 2.685300947458371,\n",
       " (2, 56): 2.0494834766860643,\n",
       " (3, 10): 2.6853009524690883,\n",
       " (3, 57): 2.0494834766860643,\n",
       " (4, 5): 2.685300829999999,\n",
       " (4, 13): 2.685300829993184,\n",
       " (4, 58): 2.0494834770587396,\n",
       " (5, 14): 2.6852998829666923,\n",
       " (6, 7): 2.68530082,\n",
       " (6, 15): 2.6852998879774117,\n",
       " (7, 16): 2.6852998879774117,\n",
       " (7, 59): 2.0494834871062877,\n",
       " (8, 9): 2.685300829999999,\n",
       " (8, 19): 2.685300829993184,\n",
       " (8, 60): 2.0494834770587396,\n",
       " (9, 20): 2.6852998829666923,\n",
       " (10, 11): 2.68530082,\n",
       " (10, 21): 2.6852998879774117,\n",
       " (11, 22): 2.6852998879774117,\n",
       " (11, 61): 2.0494834871062877,\n",
       " (12, 13): 2.685300829999999,\n",
       " (12, 24): 2.6852998829666923,\n",
       " (12, 62): 2.049483475383679,\n",
       " (13, 25): 2.685300829993184,\n",
       " (14, 15): 2.6853008199999997,\n",
       " (14, 26): 2.6852998829666923,\n",
       " (15, 27): 2.6852998879774117,\n",
       " (16, 17): 2.68530082,\n",
       " (16, 28): 2.6852998879774117,\n",
       " (17, 29): 2.6852998879774117,\n",
       " (17, 63): 2.049483480394398,\n",
       " (18, 19): 2.685300829999999,\n",
       " (18, 30): 2.6852998829666923,\n",
       " (18, 64): 2.049483475383679,\n",
       " (19, 31): 2.685300829993184,\n",
       " (20, 21): 2.6853008199999997,\n",
       " (20, 32): 2.6852998829666923,\n",
       " (21, 33): 2.6852998879774117,\n",
       " (22, 23): 2.68530082,\n",
       " (22, 34): 2.6852998879774117,\n",
       " (23, 35): 2.6852998879774117,\n",
       " (23, 65): 2.049483480394398,\n",
       " (24, 36): 2.685300947458371,\n",
       " (24, 66): 2.0494834799999992,\n",
       " (25, 26): 2.685300829999999,\n",
       " (25, 37): 2.6853018944844873,\n",
       " (26, 38): 2.685300947458371,\n",
       " (27, 28): 2.68530082,\n",
       " (27, 39): 2.6853009524690883,\n",
       " (28, 40): 2.6853009524690883,\n",
       " (29, 41): 2.6853009524690883,\n",
       " (29, 67): 2.049483480000001,\n",
       " (30, 42): 2.685300947458371,\n",
       " (30, 68): 2.0494834799999992,\n",
       " (31, 32): 2.685300829999999,\n",
       " (31, 43): 2.6853018944844873,\n",
       " (32, 44): 2.685300947458371,\n",
       " (33, 34): 2.68530082,\n",
       " (33, 45): 2.6853009524690883,\n",
       " (34, 46): 2.6853009524690883,\n",
       " (35, 47): 2.6853009524690883,\n",
       " (35, 69): 2.049483480000001,\n",
       " (36, 37): 2.685300829999999,\n",
       " (36, 48): 2.6853008398744698,\n",
       " (37, 49): 2.685301786900624,\n",
       " (38, 39): 2.6853008199999997,\n",
       " (38, 50): 2.6853008398744698,\n",
       " (39, 51): 2.6853008448851874,\n",
       " (40, 41): 2.68530082,\n",
       " (40, 52): 2.6853008448851874,\n",
       " (41, 53): 2.6853008448851874,\n",
       " (42, 43): 2.685300829999999,\n",
       " (42, 48): 2.6853008398744698,\n",
       " (43, 49): 2.685301786900624,\n",
       " (44, 45): 2.6853008199999997,\n",
       " (44, 50): 2.6853008398744698,\n",
       " (45, 51): 2.6853008448851874,\n",
       " (46, 47): 2.68530082,\n",
       " (46, 52): 2.6853008448851874,\n",
       " (47, 53): 2.6853008448851874,\n",
       " (48, 70): 2.0494834799999992,\n",
       " (49, 50): 2.685300829999999,\n",
       " (51, 52): 2.68530082,\n",
       " (53, 71): 2.049483480000001}"
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "initial_bonds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(0, 1): 2.5640429800175255,\n",
       " (0, 5): 2.721830285918179,\n",
       " (0, 54): 2.050790758811911,\n",
       " (1, 6): 2.7218295881283754,\n",
       " (1, 55): 2.0507899790642936,\n",
       " (2, 3): 2.5640476200137154,\n",
       " (2, 9): 2.7218316161338745,\n",
       " (2, 56): 2.0507897182972523,\n",
       " (3, 10): 2.7218322358238627,\n",
       " (3, 57): 2.0507903323327072,\n",
       " (4, 5): 2.6362688969926538,\n",
       " (4, 13): 2.6362287673968563,\n",
       " (4, 58): 2.0526208230733363,\n",
       " (5, 14): 2.6960983036854445,\n",
       " (6, 7): 2.636270533714002,\n",
       " (6, 15): 2.6960997775436293,\n",
       " (7, 16): 2.6362286718268693,\n",
       " (7, 59): 2.052619784709002,\n",
       " (8, 9): 2.6362763589350253,\n",
       " (8, 19): 2.6362317513408633,\n",
       " (8, 60): 2.052618775995513,\n",
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       " (10, 11): 2.6362743770415618,\n",
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       " (32, 44): 2.6805640725487785,\n",
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       " (40, 41): 2.696337004713522,\n",
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       " (42, 43): 2.696340442384856,\n",
       " (42, 48): 2.63654229620249,\n",
       " (43, 49): 2.682269911997115,\n",
       " (44, 45): 2.6814030000532503,\n",
       " (44, 50): 2.6814354394476605,\n",
       " (45, 51): 2.681438878673595,\n",
       " (46, 47): 2.6963381630025953,\n",
       " (46, 52): 2.6822704754077114,\n",
       " (47, 53): 2.636540300741533,\n",
       " (48, 70): 2.0526037064385148,\n",
       " (49, 50): 2.680171622154041,\n",
       " (51, 52): 2.6801721039324247,\n",
       " (53, 71): 2.0526024177470563}"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final_bonds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Compare the two dictionaries initial_bonds and final_bonds to find the change in bond length for each bond.\n",
    "#did not complete\n",
    "\n",
    "def bond_difference(coordinates):\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": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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