3.create_cellpainting_index.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_all = pd.read_csv(\"csv/processed_data_concat.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_all['Metadata_Plate'] = df_all['Metadata_Plate'].apply(str)\n",
    "df_all['Metadata_Well'] = df_all['Metadata_Well'].str.upper()\n",
    "df_all[\"SAMPLE_KEY\"]= df_all[['Metadata_Plate', 'Metadata_Well']].agg('-'.join, axis=1)\n",
    "df_all_small = pd.concat([df_all[['SAMPLE_KEY', 'Metadata_broad_sample']],df_all.iloc[:,17:-1]], axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_smiles = pd.read_csv(\"csv/chemical_annotations.csv\")\n",
    "df_smiles = df_smiles.rename(columns={\"BROAD_ID\":\"Metadata_broad_sample\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.inchi import MolToInchiKey\n",
    "\n",
    "def smiles_to_mol(smiles):\n",
    "    \"\"\" Convert a SMILES string to INCHIKEY\n",
    "    \"\"\"\n",
    "    if not smiles:\n",
    "        return \"\"\n",
    "    try:\n",
    "        m = Chem.MolFromSmiles(smiles)\n",
    "    except:\n",
    "        return \"\"\n",
    "    inchikey = MolToInchiKey(m)\n",
    "    return inchikey"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_merge = pd.merge(df_smiles[[\"Metadata_broad_sample\", \"CPD_SMILES\"]], \n",
    "         df_all_small[df_all_small[\"Metadata_broad_sample\"]!=\"DMSO\"], \n",
    "         how = \"right\",\n",
    "         on=\"Metadata_broad_sample\")\n",
    "df_merge.insert(0,'INCHIKEY','')\n",
    "df_merge['INCHIKEY'] = df_merge['CPD_SMILES'].apply(smiles_to_mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_merge = df_merge.drop(columns=\"Metadata_broad_sample\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>INCHIKEY</th>\n",
       "      <th>CPD_SMILES</th>\n",
       "      <th>SAMPLE_KEY</th>\n",
       "      <th>Cells_AreaShape_Area</th>\n",
       "      <th>Cells_AreaShape_Center_X</th>\n",
       "      <th>Cells_AreaShape_Center_Y</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>Cells_AreaShape_Eccentricity</th>\n",
       "      <th>Cells_AreaShape_EulerNumber</th>\n",
       "      <th>Cells_AreaShape_Extent</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_DNA_5_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_3_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_5_0</th>\n",
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       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>PRTMXUMLGYLWPX-UHFFFAOYSA-N</td>\n",
       "      <td>Cc1ccccc1C(=O)NNC(=S)NC(=O)c1ccccc1</td>\n",
       "      <td>25372-A03</td>\n",
       "      <td>5438.0</td>\n",
       "      <td>352.0</td>\n",
       "      <td>220.0</td>\n",
       "      <td>1.341633</td>\n",
       "      <td>0.852598</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.548659</td>\n",
       "      <td>...</td>\n",
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       "      <td>1.406476</td>\n",
       "      <td>1.530319</td>\n",
       "      <td>1.495116</td>\n",
       "      <td>1.711729</td>\n",
       "      <td>1.930069</td>\n",
       "      <td>1.870354</td>\n",
       "      <td>2.698786</td>\n",
       "      <td>2.544510</td>\n",
       "      <td>2.573773</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>JQIGIYGSOWUONU-UHFFFAOYSA-N</td>\n",
       "      <td>Clc1ccc(Cn2nc(-c3ccccc3)c(cc2=O)N2CCCCC2)cc1</td>\n",
       "      <td>25372-A04</td>\n",
       "      <td>4347.0</td>\n",
       "      <td>350.0</td>\n",
       "      <td>247.0</td>\n",
       "      <td>1.400722</td>\n",
       "      <td>0.860154</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.529412</td>\n",
       "      <td>...</td>\n",
       "      <td>3.593072</td>\n",
       "      <td>1.205263</td>\n",
       "      <td>1.282520</td>\n",
       "      <td>1.231165</td>\n",
       "      <td>1.668451</td>\n",
       "      <td>1.774585</td>\n",
       "      <td>1.712926</td>\n",
       "      <td>2.602744</td>\n",
       "      <td>2.441468</td>\n",
       "      <td>2.532226</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>JBZPLGMTBVEFIZ-UHFFFAOYSA-N</td>\n",
       "      <td>COc1ccc(cc1)-c1c[n+]2CC(=C3CCCCn1c23)c1ccc(Br)cc1</td>\n",
       "      <td>25372-A05</td>\n",
       "      <td>4150.0</td>\n",
       "      <td>428.0</td>\n",
       "      <td>261.0</td>\n",
       "      <td>1.367345</td>\n",
       "      <td>0.863943</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.553578</td>\n",
       "      <td>...</td>\n",
       "      <td>4.311241</td>\n",
       "      <td>1.363952</td>\n",
       "      <td>1.356302</td>\n",
       "      <td>1.329784</td>\n",
       "      <td>2.600722</td>\n",
       "      <td>2.386389</td>\n",
       "      <td>2.381538</td>\n",
       "      <td>2.554461</td>\n",
       "      <td>2.387792</td>\n",
       "      <td>2.455155</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UFNAEUOXECFKRF-UHFFFAOYSA-N</td>\n",
       "      <td>CC(C)NC(=O)ON=C(C)c1sc(nc1C)-c1ccccc1</td>\n",
       "      <td>25372-A06</td>\n",
       "      <td>1681.0</td>\n",
       "      <td>314.0</td>\n",
       "      <td>261.0</td>\n",
       "      <td>1.239217</td>\n",
       "      <td>0.786957</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.557732</td>\n",
       "      <td>...</td>\n",
       "      <td>3.457100</td>\n",
       "      <td>1.790952</td>\n",
       "      <td>1.786865</td>\n",
       "      <td>1.766933</td>\n",
       "      <td>1.729822</td>\n",
       "      <td>1.871437</td>\n",
       "      <td>1.840501</td>\n",
       "      <td>2.169722</td>\n",
       "      <td>2.261197</td>\n",
       "      <td>2.277600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>PXIJCSZNPGOKCC-UHFFFAOYSA-O</td>\n",
       "      <td>CC\\C(Nc1ccccc1)=C/c1oc2cc3ccccc3cc2[n+]1CC</td>\n",
       "      <td>25372-A07</td>\n",
       "      <td>3631.0</td>\n",
       "      <td>364.0</td>\n",
       "      <td>254.0</td>\n",
       "      <td>1.318691</td>\n",
       "      <td>0.845600</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.543647</td>\n",
       "      <td>...</td>\n",
       "      <td>3.456242</td>\n",
       "      <td>1.558367</td>\n",
       "      <td>1.628596</td>\n",
       "      <td>1.596774</td>\n",
       "      <td>1.642393</td>\n",
       "      <td>1.751831</td>\n",
       "      <td>1.706001</td>\n",
       "      <td>2.514233</td>\n",
       "      <td>2.434023</td>\n",
       "      <td>2.468646</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <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",
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       "    <tr>\n",
       "      <th>126793</th>\n",
       "      <td>DAHNEQAICFEUKA-RZIGYZOXSA-N</td>\n",
       "      <td>C[C@@H](CO)N1C[C@@H](C)[C@@H](CN(C)Cc2ccc(cc2)...</td>\n",
       "      <td>24740-P20</td>\n",
       "      <td>3348.0</td>\n",
       "      <td>347.5</td>\n",
       "      <td>253.0</td>\n",
       "      <td>1.335052</td>\n",
       "      <td>0.844260</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.530161</td>\n",
       "      <td>...</td>\n",
       "      <td>2.644437</td>\n",
       "      <td>1.553295</td>\n",
       "      <td>1.595929</td>\n",
       "      <td>1.595249</td>\n",
       "      <td>1.468006</td>\n",
       "      <td>1.574379</td>\n",
       "      <td>1.541481</td>\n",
       "      <td>2.288113</td>\n",
       "      <td>2.361514</td>\n",
       "      <td>2.413726</td>\n",
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       "    <tr>\n",
       "      <th>126794</th>\n",
       "      <td>DSHXGOUIOHRIOZ-DNVFCKCGSA-N</td>\n",
       "      <td>COc1ccc(CN(C)C[C@H]2OCc3cn(CCCC(=O)N(C[C@H]2C)...</td>\n",
       "      <td>24740-P21</td>\n",
       "      <td>3866.5</td>\n",
       "      <td>389.0</td>\n",
       "      <td>285.5</td>\n",
       "      <td>1.340830</td>\n",
       "      <td>0.838347</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.548940</td>\n",
       "      <td>...</td>\n",
       "      <td>2.651812</td>\n",
       "      <td>1.530398</td>\n",
       "      <td>1.451356</td>\n",
       "      <td>1.481157</td>\n",
       "      <td>1.734706</td>\n",
       "      <td>1.745322</td>\n",
       "      <td>1.746123</td>\n",
       "      <td>2.255154</td>\n",
       "      <td>2.228869</td>\n",
       "      <td>2.270517</td>\n",
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       "    <tr>\n",
       "      <th>126795</th>\n",
       "      <td>QVHCTLOUCAXGOY-UMEGOILYSA-N</td>\n",
       "      <td>C[C@H](CO)N1C[C@@H](C)[C@@H](CN(C)S(=O)(=O)c2c...</td>\n",
       "      <td>24740-P22</td>\n",
       "      <td>3471.5</td>\n",
       "      <td>399.0</td>\n",
       "      <td>257.0</td>\n",
       "      <td>1.390091</td>\n",
       "      <td>0.864196</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.530796</td>\n",
       "      <td>...</td>\n",
       "      <td>2.692879</td>\n",
       "      <td>1.644374</td>\n",
       "      <td>1.620638</td>\n",
       "      <td>1.657840</td>\n",
       "      <td>1.400277</td>\n",
       "      <td>1.449004</td>\n",
       "      <td>1.414502</td>\n",
       "      <td>2.360146</td>\n",
       "      <td>2.342338</td>\n",
       "      <td>2.390572</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126796</th>\n",
       "      <td>DSHXGOUIOHRIOZ-YDHSSHFGSA-N</td>\n",
       "      <td>COc1ccc(CN(C)C[C@@H]2OCc3cn(CCCC(=O)N(C[C@@H]2...</td>\n",
       "      <td>24740-P23</td>\n",
       "      <td>3696.0</td>\n",
       "      <td>355.0</td>\n",
       "      <td>253.0</td>\n",
       "      <td>1.298613</td>\n",
       "      <td>0.818742</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.556117</td>\n",
       "      <td>...</td>\n",
       "      <td>2.608098</td>\n",
       "      <td>1.409582</td>\n",
       "      <td>1.466746</td>\n",
       "      <td>1.503614</td>\n",
       "      <td>1.530055</td>\n",
       "      <td>1.739891</td>\n",
       "      <td>1.662961</td>\n",
       "      <td>2.218604</td>\n",
       "      <td>2.336516</td>\n",
       "      <td>2.393916</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126797</th>\n",
       "      <td>YNSZNIPNNMZZOV-HMFYCAOWSA-N</td>\n",
       "      <td>C[C@H](CO)N1C[C@@H](C)[C@H](CN(C)Cc2ccc(O)cc2)...</td>\n",
       "      <td>24740-P24</td>\n",
       "      <td>3718.0</td>\n",
       "      <td>358.0</td>\n",
       "      <td>267.0</td>\n",
       "      <td>1.347765</td>\n",
       "      <td>0.849602</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.536983</td>\n",
       "      <td>...</td>\n",
       "      <td>2.644039</td>\n",
       "      <td>1.621899</td>\n",
       "      <td>1.596862</td>\n",
       "      <td>1.594147</td>\n",
       "      <td>1.448064</td>\n",
       "      <td>1.551916</td>\n",
       "      <td>1.529037</td>\n",
       "      <td>2.096578</td>\n",
       "      <td>2.196672</td>\n",
       "      <td>2.205802</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>126798 rows × 1786 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           INCHIKEY  \\\n",
       "0       PRTMXUMLGYLWPX-UHFFFAOYSA-N   \n",
       "1       JQIGIYGSOWUONU-UHFFFAOYSA-N   \n",
       "2       JBZPLGMTBVEFIZ-UHFFFAOYSA-N   \n",
       "3       UFNAEUOXECFKRF-UHFFFAOYSA-N   \n",
       "4       PXIJCSZNPGOKCC-UHFFFAOYSA-O   \n",
       "...                             ...   \n",
       "126793  DAHNEQAICFEUKA-RZIGYZOXSA-N   \n",
       "126794  DSHXGOUIOHRIOZ-DNVFCKCGSA-N   \n",
       "126795  QVHCTLOUCAXGOY-UMEGOILYSA-N   \n",
       "126796  DSHXGOUIOHRIOZ-YDHSSHFGSA-N   \n",
       "126797  YNSZNIPNNMZZOV-HMFYCAOWSA-N   \n",
       "\n",
       "                                               CPD_SMILES SAMPLE_KEY  \\\n",
       "0                     Cc1ccccc1C(=O)NNC(=S)NC(=O)c1ccccc1  25372-A03   \n",
       "1            Clc1ccc(Cn2nc(-c3ccccc3)c(cc2=O)N2CCCCC2)cc1  25372-A04   \n",
       "2       COc1ccc(cc1)-c1c[n+]2CC(=C3CCCCn1c23)c1ccc(Br)cc1  25372-A05   \n",
       "3                   CC(C)NC(=O)ON=C(C)c1sc(nc1C)-c1ccccc1  25372-A06   \n",
       "4              CC\\C(Nc1ccccc1)=C/c1oc2cc3ccccc3cc2[n+]1CC  25372-A07   \n",
       "...                                                   ...        ...   \n",
       "126793  C[C@@H](CO)N1C[C@@H](C)[C@@H](CN(C)Cc2ccc(cc2)...  24740-P20   \n",
       "126794  COc1ccc(CN(C)C[C@H]2OCc3cn(CCCC(=O)N(C[C@H]2C)...  24740-P21   \n",
       "126795  C[C@H](CO)N1C[C@@H](C)[C@@H](CN(C)S(=O)(=O)c2c...  24740-P22   \n",
       "126796  COc1ccc(CN(C)C[C@@H]2OCc3cn(CCCC(=O)N(C[C@@H]2...  24740-P23   \n",
       "126797  C[C@H](CO)N1C[C@@H](C)[C@H](CN(C)Cc2ccc(O)cc2)...  24740-P24   \n",
       "\n",
       "        Cells_AreaShape_Area  Cells_AreaShape_Center_X  \\\n",
       "0                     5438.0                     352.0   \n",
       "1                     4347.0                     350.0   \n",
       "2                     4150.0                     428.0   \n",
       "3                     1681.0                     314.0   \n",
       "4                     3631.0                     364.0   \n",
       "...                      ...                       ...   \n",
       "126793                3348.0                     347.5   \n",
       "126794                3866.5                     389.0   \n",
       "126795                3471.5                     399.0   \n",
       "126796                3696.0                     355.0   \n",
       "126797                3718.0                     358.0   \n",
       "\n",
       "        Cells_AreaShape_Center_Y  Cells_AreaShape_Compactness  \\\n",
       "0                          220.0                     1.341633   \n",
       "1                          247.0                     1.400722   \n",
       "2                          261.0                     1.367345   \n",
       "3                          261.0                     1.239217   \n",
       "4                          254.0                     1.318691   \n",
       "...                          ...                          ...   \n",
       "126793                     253.0                     1.335052   \n",
       "126794                     285.5                     1.340830   \n",
       "126795                     257.0                     1.390091   \n",
       "126796                     253.0                     1.298613   \n",
       "126797                     267.0                     1.347765   \n",
       "\n",
       "        Cells_AreaShape_Eccentricity  Cells_AreaShape_EulerNumber  \\\n",
       "0                           0.852598                          1.0   \n",
       "1                           0.860154                          1.0   \n",
       "2                           0.863943                          1.0   \n",
       "3                           0.786957                          1.0   \n",
       "4                           0.845600                          1.0   \n",
       "...                              ...                          ...   \n",
       "126793                      0.844260                          1.0   \n",
       "126794                      0.838347                          1.0   \n",
       "126795                      0.864196                          1.0   \n",
       "126796                      0.818742                          1.0   \n",
       "126797                      0.849602                          1.0   \n",
       "\n",
       "        Cells_AreaShape_Extent  ...  Nuclei_Texture_Variance_DNA_5_0  \\\n",
       "0                     0.548659  ...                         3.865420   \n",
       "1                     0.529412  ...                         3.593072   \n",
       "2                     0.553578  ...                         4.311241   \n",
       "3                     0.557732  ...                         3.457100   \n",
       "4                     0.543647  ...                         3.456242   \n",
       "...                        ...  ...                              ...   \n",
       "126793                0.530161  ...                         2.644437   \n",
       "126794                0.548940  ...                         2.651812   \n",
       "126795                0.530796  ...                         2.692879   \n",
       "126796                0.556117  ...                         2.608098   \n",
       "126797                0.536983  ...                         2.644039   \n",
       "\n",
       "        Nuclei_Texture_Variance_ER_10_0  Nuclei_Texture_Variance_ER_3_0  \\\n",
       "0                              1.406476                        1.530319   \n",
       "1                              1.205263                        1.282520   \n",
       "2                              1.363952                        1.356302   \n",
       "3                              1.790952                        1.786865   \n",
       "4                              1.558367                        1.628596   \n",
       "...                                 ...                             ...   \n",
       "126793                         1.553295                        1.595929   \n",
       "126794                         1.530398                        1.451356   \n",
       "126795                         1.644374                        1.620638   \n",
       "126796                         1.409582                        1.466746   \n",
       "126797                         1.621899                        1.596862   \n",
       "\n",
       "        Nuclei_Texture_Variance_ER_5_0  Nuclei_Texture_Variance_Mito_10_0  \\\n",
       "0                             1.495116                           1.711729   \n",
       "1                             1.231165                           1.668451   \n",
       "2                             1.329784                           2.600722   \n",
       "3                             1.766933                           1.729822   \n",
       "4                             1.596774                           1.642393   \n",
       "...                                ...                                ...   \n",
       "126793                        1.595249                           1.468006   \n",
       "126794                        1.481157                           1.734706   \n",
       "126795                        1.657840                           1.400277   \n",
       "126796                        1.503614                           1.530055   \n",
       "126797                        1.594147                           1.448064   \n",
       "\n",
       "        Nuclei_Texture_Variance_Mito_3_0  Nuclei_Texture_Variance_Mito_5_0  \\\n",
       "0                               1.930069                          1.870354   \n",
       "1                               1.774585                          1.712926   \n",
       "2                               2.386389                          2.381538   \n",
       "3                               1.871437                          1.840501   \n",
       "4                               1.751831                          1.706001   \n",
       "...                                  ...                               ...   \n",
       "126793                          1.574379                          1.541481   \n",
       "126794                          1.745322                          1.746123   \n",
       "126795                          1.449004                          1.414502   \n",
       "126796                          1.739891                          1.662961   \n",
       "126797                          1.551916                          1.529037   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_10_0  Nuclei_Texture_Variance_RNA_3_0  \\\n",
       "0                               2.698786                         2.544510   \n",
       "1                               2.602744                         2.441468   \n",
       "2                               2.554461                         2.387792   \n",
       "3                               2.169722                         2.261197   \n",
       "4                               2.514233                         2.434023   \n",
       "...                                  ...                              ...   \n",
       "126793                          2.288113                         2.361514   \n",
       "126794                          2.255154                         2.228869   \n",
       "126795                          2.360146                         2.342338   \n",
       "126796                          2.218604                         2.336516   \n",
       "126797                          2.096578                         2.196672   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_5_0  \n",
       "0                              2.573773  \n",
       "1                              2.532226  \n",
       "2                              2.455155  \n",
       "3                              2.277600  \n",
       "4                              2.468646  \n",
       "...                                 ...  \n",
       "126793                         2.413726  \n",
       "126794                         2.270517  \n",
       "126795                         2.390572  \n",
       "126796                         2.393916  \n",
       "126797                         2.205802  \n",
       "\n",
       "[126798 rows x 1786 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_merge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_merge.to_csv(\"temp/cellpainting-index.csv\", index=False)"
   ]
  }
 ],
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