{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "# Getting Molecules\n",
    "\n",
    "This example shows how to get a molecule from QCArchive in a number of contexts."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## From an ID\n",
    "\n",
    "Every molecule computed with QCArchive is assigned a unique ID.\n",
    "If a molecule's ID is known, it can be queried from the Molecules table. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For example, molecule 1234 is 1,2,3-trimethylbenzene."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
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       "}\n",
       "\n",
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       "if(warn) {\n",
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       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_15701205888995998 = $3Dmol.createViewer($(\"#3dmolviewer_15701205888995998\"),{backgroundColor:\"white\"});\n",
       "\tviewer_15701205888995998.addModel(\"21\\nC9H12\\nC                     0.776479871994     1.156134463385     0.121542591228\\nC                     0.438429690334     0.679567908122    -1.141595091975\\nC                     0.439577078821     0.423533055514     1.255585387764\\nC                    -0.363723536834    -0.465178778108    -1.279725991730\\nC                    -0.415502828385    -0.685937227907     1.160631416613\\nC                    -0.792912983429    -1.170236644458    -0.121804279943\\nC                    -0.744392084678    -0.917923156500    -2.666766549983\\nC                    -0.856925058179    -1.374181477949     2.427060703777\\nC                    -1.703936690413    -2.374380900784    -0.246989621254\\nH                     1.380610203168     2.049406423411     0.216714048921\\nH                     0.770290662964     1.232461941773    -2.011963177510\\nH                     0.769502950936     0.784464203584     2.222141623291\\nH                    -0.238962510978    -1.878436765084    -2.898916777516\\nH                    -0.447809351101    -0.177691478927    -3.439954373507\\nH                    -1.844638825192    -1.050455805875    -2.735084841327\\nH                    -1.962016543060    -1.480103641644     2.438815782834\\nH                    -0.562925111565    -0.802128403465     3.332572326307\\nH                    -0.383242656300    -2.377541231755     2.485353500027\\nH                    -2.761425129123    -2.038610393380    -0.229251405356\\nH                    -1.542976842368    -3.097214459361     0.578338572599\\nH                    -1.519884697209    -2.938478658464    -1.182927991461\\n\",\"xyz\");\n",
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<Molecule(name='C9H12' formula='C9H12' hash='572b510')>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol = client.query_molecules(1234)[0]\n",
    "mol "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    Geometry (in Angstrom), charge = 0.0, multiplicity = 1:\n",
      "\n",
      "       Center              X                  Y                   Z       \n",
      "    ------------   -----------------  -----------------  -----------------\n",
      "    C                 0.776479871994     1.156134463385     0.121542591228\n",
      "    C                 0.438429690334     0.679567908122    -1.141595091975\n",
      "    C                 0.439577078821     0.423533055514     1.255585387764\n",
      "    C                -0.363723536834    -0.465178778108    -1.279725991730\n",
      "    C                -0.415502828385    -0.685937227907     1.160631416613\n",
      "    C                -0.792912983429    -1.170236644458    -0.121804279943\n",
      "    C                -0.744392084678    -0.917923156500    -2.666766549983\n",
      "    C                -0.856925058179    -1.374181477949     2.427060703777\n",
      "    C                -1.703936690413    -2.374380900784    -0.246989621254\n",
      "    H                 1.380610203168     2.049406423411     0.216714048921\n",
      "    H                 0.770290662964     1.232461941773    -2.011963177510\n",
      "    H                 0.769502950936     0.784464203584     2.222141623291\n",
      "    H                -0.238962510978    -1.878436765084    -2.898916777516\n",
      "    H                -0.447809351101    -0.177691478927    -3.439954373507\n",
      "    H                -1.844638825192    -1.050455805875    -2.735084841327\n",
      "    H                -1.962016543060    -1.480103641644     2.438815782834\n",
      "    H                -0.562925111565    -0.802128403465     3.332572326307\n",
      "    H                -0.383242656300    -2.377541231755     2.485353500027\n",
      "    H                -2.761425129123    -2.038610393380    -0.229251405356\n",
      "    H                -1.542976842368    -3.097214459361     0.578338572599\n",
      "    H                -1.519884697209    -2.938478658464    -1.182927991461\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(mol)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The following sections show how to find molecule IDs from Collections."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## From a Dataset\n",
    "Load a `Dataset`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()\n",
    "\n",
    "ds = client.get_collection(\"Dataset\", \"SMIRNOFF Coverage Set 1\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`get_molecules` returns molecules corresponding to row of the `Dataset`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>molecule</th>\n",
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       "      <th>index</th>\n",
       "      <th></th>\n",
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       "      <td>C(CBr)c1n[nH]nn1-1</td>\n",
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       "<p>1109 rows × 1 columns</p>\n",
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      ],
      "text/plain": [
       "                                                             molecule\n",
       "index                                                                \n",
       "C(CBr)c1n[nH]nn1-1      Geometry (in Angstrom), charge = 0.0, mult...\n",
       "C(CBr)c1n[nH]nn1-2      Geometry (in Angstrom), charge = 0.0, mult...\n",
       "C(CBr)c1n[nH]nn1-3      Geometry (in Angstrom), charge = 0.0, mult...\n",
       "C(CBr)c1n[n-]nn1-0      Geometry (in Angstrom), charge = -1.0, mul...\n",
       "C(CBr)c1n[n-]nn1-1      Geometry (in Angstrom), charge = -1.0, mul...\n",
       "...                                                               ...\n",
       "CSSCCN=C=S-7            Geometry (in Angstrom), charge = 0.0, mult...\n",
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       "CSSCCN=C=S-11           Geometry (in Angstrom), charge = 0.0, mult...\n",
       "\n",
       "[1109 rows x 1 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "molecules = ds.get_molecules()\n",
    "molecules"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Individual `Molecule` objects may be picked out of the dataframe:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<Molecule(name='BrC3H4N4' formula='BrC3H4N4' hash='9fd48c6')>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "molecules.loc[\"C(CBr)c1n[n-]nn1-0\", \"molecule\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For large datasets, you may not want to query all molecules at once. `get_molecules` accepts a subset option for selecting specific molecules:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>C(CBr)c1n[n-]nn1-0</td>\n",
       "      <td>Geometry (in Angstrom), charge = -1.0, mul...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>CSSCCN=C=S-10</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                             molecule\n",
       "index                                                                \n",
       "C(CBr)c1n[n-]nn1-0      Geometry (in Angstrom), charge = -1.0, mul...\n",
       "CSSCCN=C=S-10           Geometry (in Angstrom), charge = 0.0, mult..."
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.get_molecules(subset=['C(CBr)c1n[n-]nn1-0','CSSCCN=C=S-10'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If a single string is provided for `subset`, the `Molecule` object is returned directly. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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       "viewer_1570120624036582 = $3Dmol.createViewer($(\"#3dmolviewer_1570120624036582\"),{backgroundColor:\"white\"});\n",
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<Molecule(name='C4H7NS3' formula='C4H7NS3' hash='fc1a1d6')>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.get_molecules(subset='CSSCCN=C=S-10')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## From a ReactionDataset\n",
    "\n",
    "Load a `ReactionDataset`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()\n",
    "\n",
    "ds = client.get_collection(\"ReactionDataset\", \"S22\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`get_molecules` returns molecules corresponding to each reaction. By default, the final molecule is returned for every reaction:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>molecule</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th>stoichiometry</th>\n",
       "      <th>idx</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>2-Pyridone-2-Aminopyridine Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Adenine-Thymine Complex Stack</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Adenine-Thymine Complex WC</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Ammonia Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Benzene Dimer PD</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Benzene Dimer T-Shape</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Benzene-Ammonia Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Benzene-HCN Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Benzene-Methane Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Benzene-Water Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Ethene Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Ethene-Ethine Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Formamide Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Formic Acid Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Indole-Benzene Complex Stack</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Indole-Benzene Complex T-Shape</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Methane Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Phenol Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Pyrazine Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Uracil Dimer HB</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Uracil Dimer Stack</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>Water Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                                                               molecule\n",
       "name                               stoichiometry idx                                                   \n",
       "2-Pyridone-2-Aminopyridine Complex default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Adenine-Thymine Complex Stack      default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Adenine-Thymine Complex WC         default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Ammonia Dimer                      default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene Dimer PD                   default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene Dimer T-Shape              default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene-Ammonia Complex            default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene-HCN Complex                default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene-Methane Complex            default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene-Water Complex              default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Ethene Dimer                       default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Ethene-Ethine Complex              default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Formamide Dimer                    default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Formic Acid Dimer                  default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Indole-Benzene Complex Stack       default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Indole-Benzene Complex T-Shape     default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Methane Dimer                      default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Phenol Dimer                       default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Pyrazine Dimer                     default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Uracil Dimer HB                    default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Uracil Dimer Stack                 default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Water Dimer                        default       0        Geometry (in Angstrom), charge = 0.0, mult..."
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dimers = ds.get_molecules()\n",
    "dimers"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Individual `Molecule` objects may be picked out of the dataframe:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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    {
     "data": {
      "text/plain": [
       "<Molecule(name='C10H11N7O2' formula='C10H11N7O2' hash='5357c2c')>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dimers.loc['Adenine-Thymine Complex WC', 'molecule'][0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Reactants and products (or monomers and complexes) may be picked out with the `stoich` keyword. For the case of an interaction energy dataset like S22, `stoich=\"default\"` corresponds to complexes and `stoich=\"default1\"` corresponds to the monomers without counterpoise corrections.  "
   ]
  },
  {
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   "execution_count": 14,
   "metadata": {
    "scrolled": false
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   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>molecule</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th>stoichiometry</th>\n",
       "      <th>idx</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">2-Pyridone-2-Aminopyridine Complex</td>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">Adenine-Thymine Complex Stack</td>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">Adenine-Thymine Complex WC</td>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">Ammonia Dimer</td>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">Benzene Dimer PD</td>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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      ],
      "text/plain": [
       "                                                                                               molecule\n",
       "name                               stoichiometry idx                                                   \n",
       "2-Pyridone-2-Aminopyridine Complex default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Adenine-Thymine Complex Stack      default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Adenine-Thymine Complex WC         default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Ammonia Dimer                      default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene Dimer PD                   default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult..."
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "monomers = ds.get_molecules(stoich=\"default1\")\n",
    "monomers.head(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As before, the individual `Molecule` objects for the monomers may be extracted from the DataFrame:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
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   "source": [
    "monomers.loc['Adenine-Thymine Complex WC', 'molecule'][0]"
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  },
  {
   "cell_type": "code",
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      "text/plain": [
       "<Molecule(name='C10H11N7O2 ((1,),[])' formula='C5H6N2O2' hash='a4f9749')>"
      ]
     },
     "execution_count": 16,
     "metadata": {},
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   ],
   "source": [
    "monomers.loc['Adenine-Thymine Complex WC', 'molecule'][1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note that it is possible to get all molecules involved in a reaction by specifying a list for `stoich`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
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       "    <tr>\n",
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       "      <th>idx</th>\n",
       "      <th></th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td rowspan=\"3\" valign=\"top\">2-Pyridone-2-Aminopyridine Complex</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
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       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "    <tr>\n",
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       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "      <td rowspan=\"3\" valign=\"top\">Benzene Dimer PD</td>\n",
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       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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      ],
      "text/plain": [
       "                                                                                               molecule\n",
       "name                               stoichiometry idx                                                   \n",
       "2-Pyridone-2-Aminopyridine Complex default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                   default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Adenine-Thymine Complex Stack      default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                   default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Adenine-Thymine Complex WC         default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                   default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Ammonia Dimer                      default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                   default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Benzene Dimer PD                   default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                   default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                                 1        Geometry (in Angstrom), charge = 0.0, mult..."
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.get_molecules(stoich=['default', 'default1']).head(15)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Counterpoise-corrected calcuations are available through `stoich=\"cp\"` and `stoich=\"cp1\"`. Counterpoise-corrected monomers contain ghost atoms:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "<Molecule(name='C10H11N7O2 ((0,),[1])' formula='C10H11N7O2' hash='d3955aa')>"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
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   ],
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    "ds.get_molecules(stoich=\"cp1\").loc['Adenine-Thymine Complex WC', 'molecule'][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<Molecule(name='C10H11N7O2 ((1,),[0])' formula='C10H11N7O2' hash='e63c41f')>"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.get_molecules(stoich=\"cp1\").loc['Adenine-Thymine Complex WC', 'molecule'][1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For large datasets, you may not want to query all molecules at once. `get_molecules` accepts a subset option for selecting specific reactions:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th></th>\n",
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       "      <th></th>\n",
       "      <th>molecule</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th>stoichiometry</th>\n",
       "      <th>idx</th>\n",
       "      <th></th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>Adenine-Thymine Complex WC</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
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       "  </tbody>\n",
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      ],
      "text/plain": [
       "                                                                                       molecule\n",
       "name                       stoichiometry idx                                                   \n",
       "Adenine-Thymine Complex WC default       0        Geometry (in Angstrom), charge = 0.0, mult..."
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.get_molecules(subset='Adenine-Thymine Complex WC')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  </thead>\n",
       "  <tbody>\n",
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       "      <td rowspan=\"3\" valign=\"top\">Adenine-Thymine Complex WC</td>\n",
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       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
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       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"3\" valign=\"top\">Ammonia Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
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       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
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       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"3\" valign=\"top\">Water Dimer</td>\n",
       "      <td>default</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td rowspan=\"2\" valign=\"top\">default1</td>\n",
       "      <td>0</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Geometry (in Angstrom), charge = 0.0, mult...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                                                       molecule\n",
       "name                       stoichiometry idx                                                   \n",
       "Adenine-Thymine Complex WC default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                           default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                         1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Ammonia Dimer              default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                           default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                         1        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "Water Dimer                default       0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                           default1      0        Geometry (in Angstrom), charge = 0.0, mult...\n",
       "                                         1        Geometry (in Angstrom), charge = 0.0, mult..."
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.get_molecules(subset=['Adenine-Thymine Complex WC', 'Ammonia Dimer', 'Water Dimer'], stoich=['default', 'default1'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## From an OptimizationDataset\n",
    "\n",
    "Load an `OptimizationDataset`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()\n",
    "\n",
    "client.list_collections()\n",
    "ds = client.get_collection(\"OptimizationDataset\", \"SMIRNOFF Coverage Set 1\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Show some available molecules:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
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       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>COC(O)OC-0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>C[S-]-0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>CS-0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>CO-0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>CCO-0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: []\n",
       "Index: [COC(O)OC-0, C[S-]-0, CS-0, CO-0, CCO-0]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Show available specifications:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Description</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>default</td>\n",
       "      <td>Standard OpenFF optimization quantum chemistry...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                               Description\n",
       "Name                                                      \n",
       "default  Standard OpenFF optimization quantum chemistry..."
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.list_specifications()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Obtain a specific record from a molecule and specification:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "r = ds.get_record(\"CCO-0\",\"default\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get the optimized molecule:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
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       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<Molecule(name='C2H6O' formula='C2H6O' hash='422ad57')>"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r.get_final_molecule()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get the optimization trajectory:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Molecule(name='C2H6O' formula='C2H6O' hash='29df3ae')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='93989e4')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='14261f7')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='3b6db86')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='b35d632')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='c900f12')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='a1e9d7a')>,\n",
       " <Molecule(name='C2H6O' formula='C2H6O' hash='422ad57')>]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r.get_molecular_trajectory()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## From a TorsionDriveDataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "import qcportal as ptl\n",
    "client = ptl.FractalClient()\n",
    "\n",
    "ds = client.get_collection(\"TorsionDriveDataset\", \"SMIRNOFF Coverage Torsion Set 1\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Show some available torsions:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>[CH3:1][O:2][CH:3]([OH:4])OC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>[CH3:1][O:2][CH:3](O)[O:4]C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>CO[CH:3]([OH:4])[O:2][CH3:1]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>C[O:4][CH:3](O)[O:2][CH3:1]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>[H:4][C:3](O)([O:2][CH3:1])OC</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: []\n",
       "Index: [[CH3:1][O:2][CH:3]([OH:4])OC, [CH3:1][O:2][CH:3](O)[O:4]C, CO[CH:3]([OH:4])[O:2][CH3:1], C[O:4][CH:3](O)[O:2][CH3:1], [H:4][C:3](O)([O:2][CH3:1])OC]"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.df.head()  "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Show available specifications:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Description</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>default</td>\n",
       "      <td>Standard OpenFF torsiondrive specification.</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                         Description\n",
       "Name                                                \n",
       "default  Standard OpenFF torsiondrive specification."
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds.list_specifications()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get a specific torsiondrive:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "td = ds.get_record(\"CO[CH:3]([OH:4])[O:2][CH3:1]\", \"default\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get molecules for each angle along the torsion scan:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(-75,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='60e16ca')>,\n",
       " (-90,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='c337c03')>,\n",
       " (-60,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='b4ff4d4')>,\n",
       " (-105,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='5b05d3a')>,\n",
       " (-30,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='8737c8f')>,\n",
       " (-45,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='240c817')>,\n",
       " (-120,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='399d214')>,\n",
       " (0,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='f1b0dd1')>,\n",
       " (-15,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='05c30a0')>,\n",
       " (15,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='f329f87')>,\n",
       " (-150,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='1c56b54')>,\n",
       " (180,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='d299528')>,\n",
       " (-165,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='c81a1fc')>,\n",
       " (-135,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='530c77d')>,\n",
       " (30,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='99156ab')>,\n",
       " (150,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='810b759')>,\n",
       " (45,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='e1f13fa')>,\n",
       " (165,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='df216e3')>,\n",
       " (60,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='e69654b')>,\n",
       " (75,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='5c12648')>,\n",
       " (135,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='35f87a2')>,\n",
       " (90,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='cdbfa17')>,\n",
       " (120,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='5271be0')>,\n",
       " (105,): <Molecule(name='C3H8O3' formula='C3H8O3' hash='c0f46d7')>}"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "td.get_final_molecules()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
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       "<Molecule(name='C3H8O3' formula='C3H8O3' hash='99156ab')>"
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   ],
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    "td.get_final_molecules()[(30,)]"
   ]
  }
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