{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## PCA and VCD (Could delete since there were no matches)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Comput PCS and VCD features to feed into model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "half_enantiomer_data = pd.read_csv(\"half_enantiomer_data.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read in pca and vcd dataframe to use as features\n",
    "pca_vcd_values = pd.read_csv(\"../data/vcd/pca_vcd_values.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Molecule Name</th>\n",
       "      <th>0</th>\n",
       "      <th>1</th>\n",
       "      <th>2</th>\n",
       "      <th>3</th>\n",
       "      <th>4</th>\n",
       "      <th>5</th>\n",
       "      <th>6</th>\n",
       "      <th>7</th>\n",
       "      <th>8</th>\n",
       "      <th>9</th>\n",
       "      <th>10</th>\n",
       "      <th>11</th>\n",
       "      <th>12</th>\n",
       "      <th>13</th>\n",
       "      <th>14</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>(R)-(-)-Carvone</td>\n",
       "      <td>7.464317</td>\n",
       "      <td>-43.591126</td>\n",
       "      <td>-8.046428</td>\n",
       "      <td>-0.574730</td>\n",
       "      <td>-3.580254</td>\n",
       "      <td>5.872903</td>\n",
       "      <td>-2.689295</td>\n",
       "      <td>0.910235</td>\n",
       "      <td>3.263888</td>\n",
       "      <td>1.241722</td>\n",
       "      <td>-1.817992</td>\n",
       "      <td>-10.064818</td>\n",
       "      <td>-5.517172</td>\n",
       "      <td>6.956873</td>\n",
       "      <td>0.003187</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>(1R,2S,5R)-(-)-Menthol</td>\n",
       "      <td>-15.984788</td>\n",
       "      <td>-48.409755</td>\n",
       "      <td>11.599679</td>\n",
       "      <td>-6.459996</td>\n",
       "      <td>-2.895890</td>\n",
       "      <td>-21.817187</td>\n",
       "      <td>7.987366</td>\n",
       "      <td>30.168379</td>\n",
       "      <td>-4.855940</td>\n",
       "      <td>-27.966750</td>\n",
       "      <td>-15.593791</td>\n",
       "      <td>18.881794</td>\n",
       "      <td>6.680355</td>\n",
       "      <td>-3.869645</td>\n",
       "      <td>-18.299473</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>(-)-Menthyl chloride</td>\n",
       "      <td>-5.850617</td>\n",
       "      <td>-48.612997</td>\n",
       "      <td>25.383460</td>\n",
       "      <td>-1.972609</td>\n",
       "      <td>-9.623228</td>\n",
       "      <td>-12.079316</td>\n",
       "      <td>-5.014842</td>\n",
       "      <td>9.790833</td>\n",
       "      <td>-11.125811</td>\n",
       "      <td>-10.948924</td>\n",
       "      <td>12.772888</td>\n",
       "      <td>-4.068723</td>\n",
       "      <td>4.196934</td>\n",
       "      <td>0.326200</td>\n",
       "      <td>0.769741</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>(-)-Borneol</td>\n",
       "      <td>0.756580</td>\n",
       "      <td>-25.884643</td>\n",
       "      <td>-4.987043</td>\n",
       "      <td>6.148153</td>\n",
       "      <td>-18.167909</td>\n",
       "      <td>7.294051</td>\n",
       "      <td>-16.954397</td>\n",
       "      <td>9.166877</td>\n",
       "      <td>10.160046</td>\n",
       "      <td>8.512541</td>\n",
       "      <td>22.090822</td>\n",
       "      <td>-60.188603</td>\n",
       "      <td>5.246429</td>\n",
       "      <td>9.022766</td>\n",
       "      <td>-17.823573</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>(-)-Isoplegol</td>\n",
       "      <td>-12.599590</td>\n",
       "      <td>-33.717238</td>\n",
       "      <td>-12.966523</td>\n",
       "      <td>-18.479083</td>\n",
       "      <td>5.945713</td>\n",
       "      <td>-6.208222</td>\n",
       "      <td>-4.337392</td>\n",
       "      <td>10.783442</td>\n",
       "      <td>-12.640204</td>\n",
       "      <td>1.773643</td>\n",
       "      <td>1.927400</td>\n",
       "      <td>6.935122</td>\n",
       "      <td>5.856485</td>\n",
       "      <td>8.257695</td>\n",
       "      <td>-9.983220</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>156</th>\n",
       "      <td>β-Cholestanol</td>\n",
       "      <td>6.415996</td>\n",
       "      <td>-18.840982</td>\n",
       "      <td>20.303654</td>\n",
       "      <td>-29.238431</td>\n",
       "      <td>-26.058052</td>\n",
       "      <td>8.328641</td>\n",
       "      <td>-8.520251</td>\n",
       "      <td>19.753263</td>\n",
       "      <td>24.650594</td>\n",
       "      <td>37.600273</td>\n",
       "      <td>-1.058662</td>\n",
       "      <td>-16.200175</td>\n",
       "      <td>37.116864</td>\n",
       "      <td>-1.951506</td>\n",
       "      <td>-10.766619</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>157</th>\n",
       "      <td>Cholesterol Ethyl Carbonate</td>\n",
       "      <td>230.771312</td>\n",
       "      <td>139.215929</td>\n",
       "      <td>-45.562654</td>\n",
       "      <td>-28.445263</td>\n",
       "      <td>7.019739</td>\n",
       "      <td>-30.857068</td>\n",
       "      <td>18.819408</td>\n",
       "      <td>-6.542138</td>\n",
       "      <td>7.706800</td>\n",
       "      <td>-5.896378</td>\n",
       "      <td>7.642116</td>\n",
       "      <td>-5.188079</td>\n",
       "      <td>5.985704</td>\n",
       "      <td>-34.834249</td>\n",
       "      <td>-7.737224</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>158</th>\n",
       "      <td>Cholesterol n-Caprate</td>\n",
       "      <td>181.677425</td>\n",
       "      <td>33.151223</td>\n",
       "      <td>72.048835</td>\n",
       "      <td>-49.147260</td>\n",
       "      <td>19.664893</td>\n",
       "      <td>20.812246</td>\n",
       "      <td>-3.977717</td>\n",
       "      <td>5.351038</td>\n",
       "      <td>14.182154</td>\n",
       "      <td>-2.607771</td>\n",
       "      <td>6.333818</td>\n",
       "      <td>-0.251176</td>\n",
       "      <td>-7.470138</td>\n",
       "      <td>19.545668</td>\n",
       "      <td>-8.373291</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>159</th>\n",
       "      <td>Cholesterol Laurate</td>\n",
       "      <td>-130.152846</td>\n",
       "      <td>164.035229</td>\n",
       "      <td>61.091725</td>\n",
       "      <td>-37.136634</td>\n",
       "      <td>-13.847154</td>\n",
       "      <td>14.540341</td>\n",
       "      <td>-4.944992</td>\n",
       "      <td>-3.105062</td>\n",
       "      <td>2.508800</td>\n",
       "      <td>1.700032</td>\n",
       "      <td>5.700678</td>\n",
       "      <td>8.617406</td>\n",
       "      <td>-4.496284</td>\n",
       "      <td>22.150449</td>\n",
       "      <td>2.389079</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>160</th>\n",
       "      <td>Cholesterol Myristate</td>\n",
       "      <td>-132.817778</td>\n",
       "      <td>151.835799</td>\n",
       "      <td>66.528593</td>\n",
       "      <td>-50.454738</td>\n",
       "      <td>7.112731</td>\n",
       "      <td>21.576747</td>\n",
       "      <td>6.387919</td>\n",
       "      <td>-5.878909</td>\n",
       "      <td>-6.011154</td>\n",
       "      <td>7.648669</td>\n",
       "      <td>4.893929</td>\n",
       "      <td>7.866558</td>\n",
       "      <td>1.410726</td>\n",
       "      <td>11.221058</td>\n",
       "      <td>0.188386</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>161 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Molecule Name           0           1          2  \\\n",
       "0                (R)-(-)-Carvone    7.464317  -43.591126  -8.046428   \n",
       "1         (1R,2S,5R)-(-)-Menthol  -15.984788  -48.409755  11.599679   \n",
       "2           (-)-Menthyl chloride   -5.850617  -48.612997  25.383460   \n",
       "3                    (-)-Borneol    0.756580  -25.884643  -4.987043   \n",
       "4                  (-)-Isoplegol  -12.599590  -33.717238 -12.966523   \n",
       "..                           ...         ...         ...        ...   \n",
       "156               β-Cholestanol     6.415996  -18.840982  20.303654   \n",
       "157  Cholesterol Ethyl Carbonate  230.771312  139.215929 -45.562654   \n",
       "158        Cholesterol n-Caprate  181.677425   33.151223  72.048835   \n",
       "159          Cholesterol Laurate -130.152846  164.035229  61.091725   \n",
       "160        Cholesterol Myristate -132.817778  151.835799  66.528593   \n",
       "\n",
       "             3          4          5          6          7          8  \\\n",
       "0    -0.574730  -3.580254   5.872903  -2.689295   0.910235   3.263888   \n",
       "1    -6.459996  -2.895890 -21.817187   7.987366  30.168379  -4.855940   \n",
       "2    -1.972609  -9.623228 -12.079316  -5.014842   9.790833 -11.125811   \n",
       "3     6.148153 -18.167909   7.294051 -16.954397   9.166877  10.160046   \n",
       "4   -18.479083   5.945713  -6.208222  -4.337392  10.783442 -12.640204   \n",
       "..         ...        ...        ...        ...        ...        ...   \n",
       "156 -29.238431 -26.058052   8.328641  -8.520251  19.753263  24.650594   \n",
       "157 -28.445263   7.019739 -30.857068  18.819408  -6.542138   7.706800   \n",
       "158 -49.147260  19.664893  20.812246  -3.977717   5.351038  14.182154   \n",
       "159 -37.136634 -13.847154  14.540341  -4.944992  -3.105062   2.508800   \n",
       "160 -50.454738   7.112731  21.576747   6.387919  -5.878909  -6.011154   \n",
       "\n",
       "             9         10         11         12         13         14  \n",
       "0     1.241722  -1.817992 -10.064818  -5.517172   6.956873   0.003187  \n",
       "1   -27.966750 -15.593791  18.881794   6.680355  -3.869645 -18.299473  \n",
       "2   -10.948924  12.772888  -4.068723   4.196934   0.326200   0.769741  \n",
       "3     8.512541  22.090822 -60.188603   5.246429   9.022766 -17.823573  \n",
       "4     1.773643   1.927400   6.935122   5.856485   8.257695  -9.983220  \n",
       "..         ...        ...        ...        ...        ...        ...  \n",
       "156  37.600273  -1.058662 -16.200175  37.116864  -1.951506 -10.766619  \n",
       "157  -5.896378   7.642116  -5.188079   5.985704 -34.834249  -7.737224  \n",
       "158  -2.607771   6.333818  -0.251176  -7.470138  19.545668  -8.373291  \n",
       "159   1.700032   5.700678   8.617406  -4.496284  22.150449   2.389079  \n",
       "160   7.648669   4.893929   7.866558   1.410726  11.221058   0.188386  \n",
       "\n",
       "[161 rows x 16 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pca_vcd_values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set index to Molecule Name\n",
    "pca_vcd_values = pca_vcd_values.set_index('Molecule Name')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
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       "      <th>Molecule Name</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-(-)-Carvone</th>\n",
       "      <td>7.464317</td>\n",
       "      <td>-43.591126</td>\n",
       "      <td>-8.046428</td>\n",
       "      <td>-0.574730</td>\n",
       "      <td>-3.580254</td>\n",
       "      <td>5.872903</td>\n",
       "      <td>-2.689295</td>\n",
       "      <td>0.910235</td>\n",
       "      <td>3.263888</td>\n",
       "      <td>1.241722</td>\n",
       "      <td>-1.817992</td>\n",
       "      <td>-10.064818</td>\n",
       "      <td>-5.517172</td>\n",
       "      <td>6.956873</td>\n",
       "      <td>0.003187</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(1R,2S,5R)-(-)-Menthol</th>\n",
       "      <td>-15.984788</td>\n",
       "      <td>-48.409755</td>\n",
       "      <td>11.599679</td>\n",
       "      <td>-6.459996</td>\n",
       "      <td>-2.895890</td>\n",
       "      <td>-21.817187</td>\n",
       "      <td>7.987366</td>\n",
       "      <td>30.168379</td>\n",
       "      <td>-4.855940</td>\n",
       "      <td>-27.966750</td>\n",
       "      <td>-15.593791</td>\n",
       "      <td>18.881794</td>\n",
       "      <td>6.680355</td>\n",
       "      <td>-3.869645</td>\n",
       "      <td>-18.299473</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(-)-Menthyl chloride</th>\n",
       "      <td>-5.850617</td>\n",
       "      <td>-48.612997</td>\n",
       "      <td>25.383460</td>\n",
       "      <td>-1.972609</td>\n",
       "      <td>-9.623228</td>\n",
       "      <td>-12.079316</td>\n",
       "      <td>-5.014842</td>\n",
       "      <td>9.790833</td>\n",
       "      <td>-11.125811</td>\n",
       "      <td>-10.948924</td>\n",
       "      <td>12.772888</td>\n",
       "      <td>-4.068723</td>\n",
       "      <td>4.196934</td>\n",
       "      <td>0.326200</td>\n",
       "      <td>0.769741</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(-)-Borneol</th>\n",
       "      <td>0.756580</td>\n",
       "      <td>-25.884643</td>\n",
       "      <td>-4.987043</td>\n",
       "      <td>6.148153</td>\n",
       "      <td>-18.167909</td>\n",
       "      <td>7.294051</td>\n",
       "      <td>-16.954397</td>\n",
       "      <td>9.166877</td>\n",
       "      <td>10.160046</td>\n",
       "      <td>8.512541</td>\n",
       "      <td>22.090822</td>\n",
       "      <td>-60.188603</td>\n",
       "      <td>5.246429</td>\n",
       "      <td>9.022766</td>\n",
       "      <td>-17.823573</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(-)-Isoplegol</th>\n",
       "      <td>-12.599590</td>\n",
       "      <td>-33.717238</td>\n",
       "      <td>-12.966523</td>\n",
       "      <td>-18.479083</td>\n",
       "      <td>5.945713</td>\n",
       "      <td>-6.208222</td>\n",
       "      <td>-4.337392</td>\n",
       "      <td>10.783442</td>\n",
       "      <td>-12.640204</td>\n",
       "      <td>1.773643</td>\n",
       "      <td>1.927400</td>\n",
       "      <td>6.935122</td>\n",
       "      <td>5.856485</td>\n",
       "      <td>8.257695</td>\n",
       "      <td>-9.983220</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                0          1          2          3          4  \\\n",
       "Molecule Name                                                                   \n",
       "(R)-(-)-Carvone          7.464317 -43.591126  -8.046428  -0.574730  -3.580254   \n",
       "(1R,2S,5R)-(-)-Menthol -15.984788 -48.409755  11.599679  -6.459996  -2.895890   \n",
       "(-)-Menthyl chloride    -5.850617 -48.612997  25.383460  -1.972609  -9.623228   \n",
       "(-)-Borneol              0.756580 -25.884643  -4.987043   6.148153 -18.167909   \n",
       "(-)-Isoplegol          -12.599590 -33.717238 -12.966523 -18.479083   5.945713   \n",
       "\n",
       "                                5          6          7          8          9  \\\n",
       "Molecule Name                                                                   \n",
       "(R)-(-)-Carvone          5.872903  -2.689295   0.910235   3.263888   1.241722   \n",
       "(1R,2S,5R)-(-)-Menthol -21.817187   7.987366  30.168379  -4.855940 -27.966750   \n",
       "(-)-Menthyl chloride   -12.079316  -5.014842   9.790833 -11.125811 -10.948924   \n",
       "(-)-Borneol              7.294051 -16.954397   9.166877  10.160046   8.512541   \n",
       "(-)-Isoplegol           -6.208222  -4.337392  10.783442 -12.640204   1.773643   \n",
       "\n",
       "                               10         11        12        13         14  \n",
       "Molecule Name                                                                \n",
       "(R)-(-)-Carvone         -1.817992 -10.064818 -5.517172  6.956873   0.003187  \n",
       "(1R,2S,5R)-(-)-Menthol -15.593791  18.881794  6.680355 -3.869645 -18.299473  \n",
       "(-)-Menthyl chloride    12.772888  -4.068723  4.196934  0.326200   0.769741  \n",
       "(-)-Borneol             22.090822 -60.188603  5.246429  9.022766 -17.823573  \n",
       "(-)-Isoplegol            1.927400   6.935122  5.856485  8.257695  -9.983220  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pca_vcd_values.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Copy original dataframe\n",
    "half_enantiomer_data_copy = half_enantiomer_data\n",
    "half_enantiomer_data_copy;"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Keep the columns in the gme df that match the index names in original dataset\n",
    "common_index = half_enantiomer_data_copy.index.intersection(pca_vcd_values.index)\n",
    "half_enantiomer_data_copy = half_enantiomer_data_copy.loc[common_index]\n",
    "pca_vcd_features = pca_vcd_values.loc[common_index]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Combine original dataset with pca_vcd\n",
    "pca_vcd = half_enantiomer_data_copy.join(pca_vcd_features, how=\"inner\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>Unnamed: 0.1</th>\n",
       "      <th>Molecule Name</th>\n",
       "      <th>Pubchem ID #</th>\n",
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      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [Unnamed: 0, Unnamed: 0.1, Molecule Name, Pubchem ID #, Note, SMILES String, Other SMILES, Method, Contributor, Detection Threshold, Detection Units, Normalized Detection Threshold, Molecule Odour, Resources, N, log_abs, det, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]\n",
       "Index: []\n",
       "\n",
       "[0 rows x 32 columns]"
      ]
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     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pca_vcd"
   ]
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