substructure_1.1v.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "optical-world",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "from rdkit.Chem.Fragments import * \n",
    "from rdkit import Chem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c2d5d629-37ef-426e-90b4-5b61c6885933",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Python 3.8.13\n"
     ]
    }
   ],
   "source": [
    "!python -V"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "incorporate-apparel",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>spectrum_id</th>\n",
       "      <th>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
       "      <th>intensities</th>\n",
       "      <th>loss_mzs</th>\n",
       "      <th>loss_intensities</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CCMSLIB00005883221</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>243.088000</td>\n",
       "      <td>[91.054298, 95.049202, 103.054298, 104.0495, 1...</td>\n",
       "      <td>[0.04068640697166502, 0.01589638945223964, 0.2...</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NIST937042</td>\n",
       "      <td>[M-H2O+H]+</td>\n",
       "      <td>205.085900</td>\n",
       "      <td>[63.0231, 65.0387, 77.0386, 79.0543, 89.0387, ...</td>\n",
       "      <td>[0.0221021021021021, 0.24380380380380381, 0.06...</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>spec_id=107587</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>370.130000</td>\n",
       "      <td>[106.065, 113.072, 121.088, 137.056, 137.062, ...</td>\n",
       "      <td>[0.842, 0.599, 0.97, 1.0, 1.0, 1.0, 0.119, 0.0...</td>\n",
       "      <td>[20.004999999999995, 29.548000000000002, 30.49...</td>\n",
       "      <td>[0.387, 0.069, 0.011, 0.066, 0.159, 0.033, 1.0...</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Eriodictyol-7-O-glucoside_plasma_1981</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>451.123488</td>\n",
       "      <td>[67.01862, 69.03341, 79.01767, 80.06145, 89.03...</td>\n",
       "      <td>[0.084, 0.027, 0.013, 0.021, 0.048, 0.019, 0.0...</td>\n",
       "      <td>[163.059708, 164.07297800000003, 221.074678, 2...</td>\n",
       "      <td>[0.015, 0.023, 0.014, 0.023, 0.021, 0.013, 0.0...</td>\n",
       "      <td>RAFHNDRXYHOLSH-RGHIGTIISA-N</td>\n",
       "      <td>O=C1CC(c2ccc(O)c(O)c2)Oc2cc(OC3OC(CO)C(O)C(O)C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NIST297310</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>303.231900</td>\n",
       "      <td>[50.0151, 51.0228, 53.0385, 55.0177, 55.0541, ...</td>\n",
       "      <td>[0.061401401401401406, 0.2772972972972973, 0.2...</td>\n",
       "      <td>[18.01049999999998, 33.0342, 34.2534, 36.02109...</td>\n",
       "      <td>[1.0, 0.051301301301301304, 0.0665965965965966...</td>\n",
       "      <td>GCKMFJBGXUYNAG-MPRNQXESSA-N</td>\n",
       "      <td>CC12CCC(=O)C=C1CCC1C2CCC2(C)C1CCC2(C)O</td>\n",
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       "    <tr>\n",
       "      <th>83353</th>\n",
       "      <td>CCMSLIB00004704976</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>285.112000</td>\n",
       "      <td>[61.011341, 103.054558, 131.049133, 132.052399...</td>\n",
       "      <td>[0.036569120000000004, 0.020349529999999998, 0...</td>\n",
       "      <td>[92.15045200000003, 103.05926600000004, 104.06...</td>\n",
       "      <td>[0.01426239, 0.09765834999999999, 1.0, 0.03854...</td>\n",
       "      <td>IAFBOKYTDSDNHV-UHFFFAOYSA-N</td>\n",
       "      <td>COc1cc(OC)c2c(c1)OC(c1ccccc1)CC2=O</td>\n",
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       "      <td>CCMSLIB00004712186</td>\n",
       "      <td>[M+K]+</td>\n",
       "      <td>189.068000</td>\n",
       "      <td>[51.940292, 55.018112, 55.05452, 56.049725, 56...</td>\n",
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       "      <td>MGSRCZKZVOBKFT-UHFFFAOYSA-N</td>\n",
       "      <td>Cc1ccc(C(C)C)c(O)c1</td>\n",
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       "      <th>83355</th>\n",
       "      <td>CCMSLIB00010119259</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>271.096000</td>\n",
       "      <td>[79.054443, 81.033691, 96.020523, 103.053909, ...</td>\n",
       "      <td>[0.01896576750013369, 0.07313959617720532, 0.0...</td>\n",
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       "    <tr>\n",
       "      <th>83356</th>\n",
       "      <td>NIST256349</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>178.053200</td>\n",
       "      <td>[55.0179, 57.0208, 58.9949, 62.9898, 70.0287, ...</td>\n",
       "      <td>[0.20500500500500501, 0.28869869869869874, 0.0...</td>\n",
       "      <td>[17.026399999999995, 19.05709999999999, 35.037...</td>\n",
       "      <td>[0.055005005005005006, 1.0, 0.0183983983983983...</td>\n",
       "      <td>XUHLIQGRKRUKPH-ITZCMCNPSA-N</td>\n",
       "      <td>C=CCS(=O)CC(N)C(=O)O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83357</th>\n",
       "      <td>NIST140732</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>409.164600</td>\n",
       "      <td>[50.0148, 51.0226, 52.0843, 53.0019, 53.0383, ...</td>\n",
       "      <td>[0.6689989989989991, 1.0, 0.0278978978978979, ...</td>\n",
       "      <td>[15.024200000000008, 18.010100000000023, 30.04...</td>\n",
       "      <td>[0.011501501501501503, 0.05200200200200201, 0....</td>\n",
       "      <td>HQWHKELJHUFLGD-UHFFFAOYSA-N</td>\n",
       "      <td>COc1c(O)cc2oc3cc4c(c(O)c3c(=O)c2c1CC=C(C)C)C=C...</td>\n",
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       "<p>83358 rows × 9 columns</p>\n",
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      ],
      "text/plain": [
       "                                 spectrum_id      adduct  precursor_mz  \\\n",
       "0                         CCMSLIB00005883221      [M+H]+    243.088000   \n",
       "1                                 NIST937042  [M-H2O+H]+    205.085900   \n",
       "2                             spec_id=107587      [M+H]+    370.130000   \n",
       "3      Eriodictyol-7-O-glucoside_plasma_1981      [M+H]+    451.123488   \n",
       "4                                 NIST297310      [M+H]+    303.231900   \n",
       "...                                      ...         ...           ...   \n",
       "83353                     CCMSLIB00004704976      [M+H]+    285.112000   \n",
       "83354                     CCMSLIB00004712186      [M+K]+    189.068000   \n",
       "83355                     CCMSLIB00010119259      [M+H]+    271.096000   \n",
       "83356                             NIST256349      [M+H]+    178.053200   \n",
       "83357                             NIST140732      [M+H]+    409.164600   \n",
       "\n",
       "                                                     mzs  \\\n",
       "0      [91.054298, 95.049202, 103.054298, 104.0495, 1...   \n",
       "1      [63.0231, 65.0387, 77.0386, 79.0543, 89.0387, ...   \n",
       "2      [106.065, 113.072, 121.088, 137.056, 137.062, ...   \n",
       "3      [67.01862, 69.03341, 79.01767, 80.06145, 89.03...   \n",
       "4      [50.0151, 51.0228, 53.0385, 55.0177, 55.0541, ...   \n",
       "...                                                  ...   \n",
       "83353  [61.011341, 103.054558, 131.049133, 132.052399...   \n",
       "83354  [51.940292, 55.018112, 55.05452, 56.049725, 56...   \n",
       "83355  [79.054443, 81.033691, 96.020523, 103.053909, ...   \n",
       "83356  [55.0179, 57.0208, 58.9949, 62.9898, 70.0287, ...   \n",
       "83357  [50.0148, 51.0226, 52.0843, 53.0019, 53.0383, ...   \n",
       "\n",
       "                                             intensities  \\\n",
       "0      [0.04068640697166502, 0.01589638945223964, 0.2...   \n",
       "1      [0.0221021021021021, 0.24380380380380381, 0.06...   \n",
       "2      [0.842, 0.599, 0.97, 1.0, 1.0, 1.0, 0.119, 0.0...   \n",
       "3      [0.084, 0.027, 0.013, 0.021, 0.048, 0.019, 0.0...   \n",
       "4      [0.061401401401401406, 0.2772972972972973, 0.2...   \n",
       "...                                                  ...   \n",
       "83353  [0.036569120000000004, 0.020349529999999998, 0...   \n",
       "83354  [0.11617364000000001, 0.02121181, 0.1648827899...   \n",
       "83355  [0.01896576750013369, 0.07313959617720532, 0.0...   \n",
       "83356  [0.20500500500500501, 0.28869869869869874, 0.0...   \n",
       "83357  [0.6689989989989991, 1.0, 0.0278978978978979, ...   \n",
       "\n",
       "                                                loss_mzs  \\\n",
       "0      [26.007495000000006, 27.011003999999986, 43.00...   \n",
       "1      [17.0223, 18.010100000000023, 18.0305000000000...   \n",
       "2      [20.004999999999995, 29.548000000000002, 30.49...   \n",
       "3      [163.059708, 164.07297800000003, 221.074678, 2...   \n",
       "4      [18.01049999999998, 33.0342, 34.2534, 36.02109...   \n",
       "...                                                  ...   \n",
       "83353  [92.15045200000003, 103.05926600000004, 104.06...   \n",
       "83354  [29.116019000000023, 30.09127000000001, 30.122...   \n",
       "83355  [42.01059699999999, 102.03124199999999, 108.05...   \n",
       "83356  [17.026399999999995, 19.05709999999999, 35.037...   \n",
       "83357  [15.024200000000008, 18.010100000000023, 30.04...   \n",
       "\n",
       "                                        loss_intensities  \\\n",
       "0      [0.09251948915755456, 0.5639426077381412, 0.05...   \n",
       "1      [0.025495495495495495, 1.0, 0.0601001001001001...   \n",
       "2      [0.387, 0.069, 0.011, 0.066, 0.159, 0.033, 1.0...   \n",
       "3      [0.015, 0.023, 0.014, 0.023, 0.021, 0.013, 0.0...   \n",
       "4      [1.0, 0.051301301301301304, 0.0665965965965966...   \n",
       "...                                                  ...   \n",
       "83353  [0.01426239, 0.09765834999999999, 1.0, 0.03854...   \n",
       "83354  [0.063098, 0.013058350000000002, 0.0179634, 0....   \n",
       "83355  [0.04077342072895897, 0.01816400430866546, 0.0...   \n",
       "83356  [0.055005005005005006, 1.0, 0.0183983983983983...   \n",
       "83357  [0.011501501501501503, 0.05200200200200201, 0....   \n",
       "\n",
       "                          inchikey  \\\n",
       "0      ZJTJUVIJVLLGSP-UHFFFAOYSA-N   \n",
       "1      OHQFGTDAUDLCBG-UHFFFAOYSA-N   \n",
       "2      VPRBWEMXTXPBEY-UHFFFAOYSA-N   \n",
       "3      RAFHNDRXYHOLSH-RGHIGTIISA-N   \n",
       "4      GCKMFJBGXUYNAG-MPRNQXESSA-N   \n",
       "...                            ...   \n",
       "83353  IAFBOKYTDSDNHV-UHFFFAOYSA-N   \n",
       "83354  MGSRCZKZVOBKFT-UHFFFAOYSA-N   \n",
       "83355  ODLVGCCGMXGMGZ-RMKNXTFCSA-N   \n",
       "83356  XUHLIQGRKRUKPH-ITZCMCNPSA-N   \n",
       "83357  HQWHKELJHUFLGD-UHFFFAOYSA-N   \n",
       "\n",
       "                                     smiles_preprocessed  \n",
       "0                   Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C  \n",
       "1                           Cc1cccc(CC(CC(=O)O)C(=O)O)c1  \n",
       "2           Cc1c(C)c2ccc3c(c2oc1=O)CN(CCc1ccc(Cl)cc1)CO3  \n",
       "3      O=C1CC(c2ccc(O)c(O)c2)Oc2cc(OC3OC(CO)C(O)C(O)C...  \n",
       "4                 CC12CCC(=O)C=C1CCC1C2CCC2(C)C1CCC2(C)O  \n",
       "...                                                  ...  \n",
       "83353                 COc1cc(OC)c2c(c1)OC(c1ccccc1)CC2=O  \n",
       "83354                                Cc1ccc(C(C)C)c(O)c1  \n",
       "83355                     COc1ccccc1C=CC(=O)c1ccc(O)cc1O  \n",
       "83356                               C=CCS(=O)CC(N)C(=O)O  \n",
       "83357  COc1c(O)cc2oc3cc4c(c(O)c3c(=O)c2c1CC=C(C)C)C=C...  \n",
       "\n",
       "[83358 rows x 9 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#ames_df = pd.read_csv(\"example/mydata.csv\", index_col=0)\n",
    "# check cddd preprocessing to see how many smiles fail\n",
    "#ames_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/all-HRMS-loss-header-validation-refine.tsv\", index_col=\"id\",sep=\"\\t\")\n",
    "#ames_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/lipidblast-loss-header-train-refine.tsv\", index_col=\"id\",sep=\"\\t\")\n",
    "#ames_df = pd.read_csv(\"/Users/delser/downloads/all_CFM_loss_header.tsv\", index_col=\"id\",sep=\"\\t\")\n",
    "#ames_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/nist/all-HRMS-loss-header-train-refine.tsv\", index_col=\"id\",sep=\"\\t\")\n",
    "data_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/nist/all_HRMS_train_16122022_cddd_refine.tsv\",sep=\"\\t\")\n",
    "#data_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/nist/all_HRMS_validation_16122022_cddd_refine.tsv\",sep=\"\\t\")\n",
    "data_df=data_df.dropna()\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4a667cd1-dbaf-4ca5-a780-87cd5322ce20",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>spectrum_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C</td>\n",
       "      <td>CCMSLIB00005883221</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Cc1cccc(CC(CC(=O)O)C(=O)O)c1</td>\n",
       "      <td>NIST937042</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Cc1c(C)c2ccc3c(c2oc1=O)CN(CCc1ccc(Cl)cc1)CO3</td>\n",
       "      <td>spec_id=107587</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O=C1CC(c2ccc(O)c(O)c2)Oc2cc(OC3OC(CO)C(O)C(O)C...</td>\n",
       "      <td>Eriodictyol-7-O-glucoside_plasma_1981</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CC12CCC(=O)C=C1CCC1C2CCC2(C)C1CCC2(C)O</td>\n",
       "      <td>NIST297310</td>\n",
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       "      <th>...</th>\n",
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       "      <th>83353</th>\n",
       "      <td>COc1cc(OC)c2c(c1)OC(c1ccccc1)CC2=O</td>\n",
       "      <td>CCMSLIB00004704976</td>\n",
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       "    <tr>\n",
       "      <th>83354</th>\n",
       "      <td>Cc1ccc(C(C)C)c(O)c1</td>\n",
       "      <td>CCMSLIB00004712186</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83355</th>\n",
       "      <td>COc1ccccc1C=CC(=O)c1ccc(O)cc1O</td>\n",
       "      <td>CCMSLIB00010119259</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83356</th>\n",
       "      <td>C=CCS(=O)CC(N)C(=O)O</td>\n",
       "      <td>NIST256349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83357</th>\n",
       "      <td>COc1c(O)cc2oc3cc4c(c(O)c3c(=O)c2c1CC=C(C)C)C=C...</td>\n",
       "      <td>NIST140732</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     smiles_preprocessed  \\\n",
       "0                   Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C   \n",
       "1                           Cc1cccc(CC(CC(=O)O)C(=O)O)c1   \n",
       "2           Cc1c(C)c2ccc3c(c2oc1=O)CN(CCc1ccc(Cl)cc1)CO3   \n",
       "3      O=C1CC(c2ccc(O)c(O)c2)Oc2cc(OC3OC(CO)C(O)C(O)C...   \n",
       "4                 CC12CCC(=O)C=C1CCC1C2CCC2(C)C1CCC2(C)O   \n",
       "...                                                  ...   \n",
       "83353                 COc1cc(OC)c2c(c1)OC(c1ccccc1)CC2=O   \n",
       "83354                                Cc1ccc(C(C)C)c(O)c1   \n",
       "83355                     COc1ccccc1C=CC(=O)c1ccc(O)cc1O   \n",
       "83356                               C=CCS(=O)CC(N)C(=O)O   \n",
       "83357  COc1c(O)cc2oc3cc4c(c(O)c3c(=O)c2c1CC=C(C)C)C=C...   \n",
       "\n",
       "                                 spectrum_id  \n",
       "0                         CCMSLIB00005883221  \n",
       "1                                 NIST937042  \n",
       "2                             spec_id=107587  \n",
       "3      Eriodictyol-7-O-glucoside_plasma_1981  \n",
       "4                                 NIST297310  \n",
       "...                                      ...  \n",
       "83353                     CCMSLIB00004704976  \n",
       "83354                     CCMSLIB00004712186  \n",
       "83355                     CCMSLIB00010119259  \n",
       "83356                             NIST256349  \n",
       "83357                             NIST140732  \n",
       "\n",
       "[83358 rows x 2 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "smiles_exp=data_df[[\"smiles_preprocessed\",\"spectrum_id\"]]\n",
    "smiles_exp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "82935a20-73cb-4570-9d2c-fbdd9e7777c9",
   "metadata": {},
   "outputs": [],
   "source": [
    "smiles_exp.to_csv(\"/Users/delser/mass2smiles/retrain/all_HRMS_train_16122022_cddd_smiles.txt\",index=False,header=False,sep=\" \")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f7d5b49f-bce1-4a1c-8f1f-72f894c4dfb6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Sugar Removal Service Application starting. Evaluating command line arguments...\n",
      "All command line arguments valid. Executing application...\n",
      "\n",
      "Trying to load file at /Users/delser/mass2smiles/retrain/all_HRMS_train_16122022_cddd_smiles.txt\n",
      "Found SMILES file.\n",
      "Results will be written to: /Users/delser/mass2smiles/retrain/deglycosylation_results.txt\n",
      "Logging will be done in file at: /Users/delser/mass2smiles/retrain/Log.txt\n",
      "\n",
      "Given settings for Sugar Removal Utility:\n",
      "\tType of moieties to remove: circular AND linear sugars (3)\n",
      "\tDetect circular sugars only with O-glycosidic bond: false\n",
      "\tRemove only terminal sugar moieties: false\n",
      "\tPreservation mode setting: HEAVY_ATOM_COUNT (1)\n",
      "\tPreservation mode threshold: 5\n",
      "\tDetect circular sugars only with enough exocyclic oxygen atoms: true\n",
      "\tExocyclic oxygen atoms to atoms in ring ratio threshold: 0.5\n",
      "\tDetect linear sugars in rings: false\n",
      "\tLinear sugar candidate minimum size: 4 carbon atoms\n",
      "\tLinear sugar candidate maximum size: 7 carbon atoms\n",
      "\tDetect linear acidic sugars: false\n",
      "\tDetect spiro rings as circular sugars: false\n",
      "\tDetect circular sugars with keto groups: false\n",
      "\n",
      "Entering iteration of molecules...\n",
      "\n",
      "Finished analysis of molecules.\n",
      "\n",
      "83358 molecules were analysed.\n",
      "0 fatal exceptions occurred (molecule could not be read, was disconnected or could not be cloned).\n",
      "0 minor exceptions occurred (SMILES codes could not be generated etc.).\n",
      "6819 molecules contained sugar moieties.\n",
      "6259 molecules contained circular sugar moieties.\n",
      "567 molecules contained linear sugar moieties.\n",
      "452 molecules were basically sugars because they were completely removed.\n",
      "\n",
      "Execution successful. Analysis took 1.387 minutes.\n",
      "Application will now exit.\n"
     ]
    }
   ],
   "source": [
    "!java -jar \"SugarRemovalUtility-jar-with-dependencies.jar\" -i \"all_HRMS_train_16122022_cddd_smiles.txt\" -t \"3\" -remTerm \"false\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "f2b0067b-9999-4a85-a04d-3d3c89756bbd",
   "metadata": {},
   "outputs": [],
   "source": [
    "ScanList=[]\n",
    "with open(\"/Users/delser/mass2smiles/retrain/deglycosylation_results.txt\", 'r') as f:     \n",
    " counter=0\n",
    " for line in f:\n",
    "        line=line.strip('\\n')\n",
    "        ListID=line.split(';')\n",
    "        ScanList.append(ListID)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "35524017-89d6-4294-aafc-6e8b6a3dac61",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "745"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(ScanList)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "07ddc653-53ce-42ac-b1ec-4b37a2f18948",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Nr',\n",
       " 'ID',\n",
       " 'originalMoleculeSMILES',\n",
       " 'deglycosylatedMoleculeSMILES',\n",
       " 'hadOrHasSugars',\n",
       " 'SugarMoietySMILES']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ScanList[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "d37ec7d7-ff14-4ade-b3e0-c7c32b19e792",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['COC1=CC=C2C=C3C4=C(CCN3C(=O)C2=C1OC)C=C5C(=C4)OCO5', 'false']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ScanList[22][3:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "149d5469-9bcd-4f76-acdb-d4dd0effff47",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['22',\n",
       " 'spec_id=94556',\n",
       " 'COC1=CC=C2C=C3C4=C(CCN3C(=O)C2=C1OC)C=C5C(=C4)OCO5',\n",
       " 'COC1=CC=C2C=C3C4=C(CCN3C(=O)C2=C1OC)C=C5C(=C4)OCO5',\n",
       " 'false']"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ScanList[22]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "5d3d24c1-36c7-4995-a1ce-28d6a7b91e4a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "max([len(i[3:]) for i in ScanList])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "73c62431-1e0c-4e99-ba4a-08c20a9f4097",
   "metadata": {},
   "outputs": [],
   "source": [
    "sugars=[i for i in ScanList if 'true' in i]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "b123e4c6-552c-4975-be24-8c70ad00463d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6819"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(sugars)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "b1ff9d8f-74ad-44b1-8834-d0a6e188bc88",
   "metadata": {},
   "outputs": [],
   "source": [
    "sugars=[i for i in sugars if not '[empty]' in i]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "c41326e3-f280-4448-a40d-51219d654061",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6367"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(sugars)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "3a7fad85-2d02-47e2-b797-6107e502ece1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "max([len(i[5:]) for i in sugars])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "e93505f9-a3f7-425b-bcc6-174b0fc052f6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['305',\n",
       " 'isookanin-7-O-glucoside_plasma_1863',\n",
       " 'C1=C(C=C(C(=C1)O)O)C2CC(=O)C3=CC=C(C(=C3O2)O)OC4C(C(C(C(CO)O4)O)O)O',\n",
       " 'C1=C(C=C(C(=C1)O)O)C2CC(=O)C3=CC=C(C(=C3O2)O)O',\n",
       " 'true',\n",
       " '[CH]1[CH][CH]O[CH][CH]1']"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sugars[26]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "494abf76-65b4-4da5-a4a5-769cd8b9a2fa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6367"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test=[i for i in sugars if 'true' == i[4]]\n",
    "len(test)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "1579f787-2680-43eb-b98f-3a80a11d674b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'isookanin-7-O-glucoside_plasma_1863'"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sugars[26][1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "1e1b77e7-e835-4737-9fc2-12012ca29c30",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'C1=C(C=C(C(=C1)O)O)C2CC(=O)C3=CC=C(C(=C3O2)O)O'"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sugars[26][3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "29c00046-3d9c-43d3-a5db-b2d7fd6f67c6",
   "metadata": {},
   "outputs": [],
   "source": [
    "end=[[i[1].strip('\"'),i[3],len(i[5:])] for i in sugars]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "id": "24ed96b6-82c8-41f3-a9d4-603a65dadd65",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['CCMSLIB00004710931',\n",
       " 'C=C1C(CC2C(=COC(C12)OC3C(C(C(C(CO)O3)O)O)OC(=O)C=CC4=CC=C(C=C4)O)C(=O)O)O',\n",
       " 0]"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "end[6814]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "fc649a16-cfdf-446b-b038-e069ba4f08fa",
   "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>spectrum_id</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>num_of_sugars</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Eriodictyol-7-O-glucoside_plasma_1981</td>\n",
       "      <td>C1=C(C=C(C(=C1)O)O)C2CC(=O)C3=C(C=C(C=C3O)O)O2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CCMSLIB00004703056</td>\n",
       "      <td>COC1=CC=C(C=CC(=O)OC2C3C=COC(C3C4(CO)C2O4)O)C=C1O</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NP-000004(11)_plasma_2705</td>\n",
       "      <td>C1=CC(=CC=C1C2=CC(=O)C3=C(C=C(C(=C3O2)C4C(C(C(...</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>spec_id=75828</td>\n",
       "      <td>C1=CC=C(C=C1)C2=CC(=O)C3=C(C=C(C=C3O)O)O2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CCMSLIB00004708523</td>\n",
       "      <td>CC1=C(C(=O)O)C(C)(C)CCC1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6362</th>\n",
       "      <td>CCMSLIB00004715997</td>\n",
       "      <td>COC1=C(C=C2C3=C1OC(=O)C4=C3C(=C(C(=C4)O)OC)OC2...</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6363</th>\n",
       "      <td>CCMSLIB00004710931</td>\n",
       "      <td>C=C1C(CC2C(=COC(C12)O)C(=O)O)O.C1=C(C=CC(=C1)O...</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6364</th>\n",
       "      <td>CCMSLIB00006673475</td>\n",
       "      <td>C(CC(=O)O)C1=CC(=CC(=C1)O)O</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6365</th>\n",
       "      <td>CCMSLIB00004708972</td>\n",
       "      <td>CC1=CC=CC2=C1C(=CC(=O)O2)O</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6366</th>\n",
       "      <td>CCMSLIB00004702300</td>\n",
       "      <td>C1=CC(=C(C=C1)O)CO</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6367 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                spectrum_id  \\\n",
       "0     Eriodictyol-7-O-glucoside_plasma_1981   \n",
       "1                        CCMSLIB00004703056   \n",
       "2                 NP-000004(11)_plasma_2705   \n",
       "3                             spec_id=75828   \n",
       "4                        CCMSLIB00004708523   \n",
       "...                                     ...   \n",
       "6362                     CCMSLIB00004715997   \n",
       "6363                     CCMSLIB00004710931   \n",
       "6364                     CCMSLIB00006673475   \n",
       "6365                     CCMSLIB00004708972   \n",
       "6366                     CCMSLIB00004702300   \n",
       "\n",
       "                                    smiles_preprocessed  num_of_sugars  \n",
       "0        C1=C(C=C(C(=C1)O)O)C2CC(=O)C3=C(C=C(C=C3O)O)O2              1  \n",
       "1     COC1=CC=C(C=CC(=O)OC2C3C=COC(C3C4(CO)C2O4)O)C=C1O              1  \n",
       "2     C1=CC(=CC=C1C2=CC(=O)C3=C(C=C(C(=C3O2)C4C(C(C(...              1  \n",
       "3             C1=CC=C(C=C1)C2=CC(=O)C3=C(C=C(C=C3O)O)O2              2  \n",
       "4                              CC1=C(C(=O)O)C(C)(C)CCC1              2  \n",
       "...                                                 ...            ...  \n",
       "6362  COC1=C(C=C2C3=C1OC(=O)C4=C3C(=C(C(=C4)O)OC)OC2...              1  \n",
       "6363  C=C1C(CC2C(=COC(C12)O)C(=O)O)O.C1=C(C=CC(=C1)O...              1  \n",
       "6364                        C(CC(=O)O)C1=CC(=CC(=C1)O)O              1  \n",
       "6365                         CC1=CC=CC2=C1C(=CC(=O)O2)O              1  \n",
       "6366                                 C1=CC(=C(C=C1)O)CO              1  \n",
       "\n",
       "[6367 rows x 3 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.DataFrame(end, columns =['spectrum_id','smiles_preprocessed','num_of_sugars'])\n",
    "df "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "cc8b3417-3cdc-4ac5-8c03-9a0126034d1b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df['num_of_sugars'].max()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "2c7d1d61-e9eb-4386-81e9-bef313109ad8",
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       "1"
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     "execution_count": 20,
     "metadata": {},
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   "source": [
    "df['num_of_sugars'].min()"
   ]
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   "execution_count": 21,
   "id": "e624dcdf-9c7f-482c-9302-7493d2ec3da0",
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       "                                                                     smiles_preprocessed  \\\n",
       "spectrum_id                                                                                \n",
       "Eriodictyol-7-O-glucoside_plasma_1981     C1=C(C=C(C(=C1)O)O)C2CC(=O)C3=C(C=C(C=C3O)O)O2   \n",
       "CCMSLIB00004703056                     COC1=CC=C(C=CC(=O)OC2C3C=COC(C3C4(CO)C2O4)O)C=C1O   \n",
       "NP-000004(11)_plasma_2705              C1=CC(=CC=C1C2=CC(=O)C3=C(C=C(C(=C3O2)C4C(C(C(...   \n",
       "spec_id=75828                                  C1=CC=C(C=C1)C2=CC(=O)C3=C(C=C(C=C3O)O)O2   \n",
       "CCMSLIB00004708523                                              CC1=C(C(=O)O)C(C)(C)CCC1   \n",
       "...                                                                                  ...   \n",
       "CCMSLIB00004715997                     COC1=C(C=C2C3=C1OC(=O)C4=C3C(=C(C(=C4)O)OC)OC2...   \n",
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       "CCMSLIB00006673475                                           C(CC(=O)O)C1=CC(=CC(=C1)O)O   \n",
       "CCMSLIB00004708972                                            CC1=CC=CC2=C1C(=CC(=O)O2)O   \n",
       "CCMSLIB00004702300                                                    C1=CC(=C(C=C1)O)CO   \n",
       "\n",
       "                                       num_of_sugars  \n",
       "spectrum_id                                           \n",
       "Eriodictyol-7-O-glucoside_plasma_1981              1  \n",
       "CCMSLIB00004703056                                 1  \n",
       "NP-000004(11)_plasma_2705                          1  \n",
       "spec_id=75828                                      2  \n",
       "CCMSLIB00004708523                                 2  \n",
       "...                                              ...  \n",
       "CCMSLIB00004715997                                 1  \n",
       "CCMSLIB00004710931                                 1  \n",
       "CCMSLIB00006673475                                 1  \n",
       "CCMSLIB00004708972                                 1  \n",
       "CCMSLIB00004702300                                 1  \n",
       "\n",
       "[6367 rows x 2 columns]"
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     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
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    "df=df.set_index('spectrum_id')\n",
    "df"
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   "execution_count": 22,
   "id": "ee184a7a-c9f4-4f23-899e-a183bdee5a78",
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       "                                       num_of_sugars\n",
       "spectrum_id                                         \n",
       "Eriodictyol-7-O-glucoside_plasma_1981              1\n",
       "CCMSLIB00004703056                                 1\n",
       "NP-000004(11)_plasma_2705                          1\n",
       "spec_id=75828                                      2\n",
       "CCMSLIB00004708523                                 2\n",
       "...                                              ...\n",
       "CCMSLIB00004715997                                 1\n",
       "CCMSLIB00004710931                                 1\n",
       "CCMSLIB00006673475                                 1\n",
       "CCMSLIB00004708972                                 1\n",
       "CCMSLIB00004702300                                 1\n",
       "\n",
       "[6367 rows x 1 columns]"
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     "execution_count": 22,
     "metadata": {},
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   "source": [
    "df=df.drop([\"smiles_preprocessed\"], axis=1)\n",
    "df"
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   "execution_count": 23,
   "id": "f9edc8a3-792f-4e80-8031-244d4fd24e08",
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       "      <td>[0.061401401401401406, 0.2772972972972973, 0.2...</td>\n",
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       "      <td>[92.15045200000003, 103.05926600000004, 104.06...</td>\n",
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       "      <td>[29.116019000000023, 30.09127000000001, 30.122...</td>\n",
       "      <td>[0.063098, 0.013058350000000002, 0.0179634, 0....</td>\n",
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       "      <td>[79.054443, 81.033691, 96.020523, 103.053909, ...</td>\n",
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       "      <th>NIST140732</th>\n",
       "      <td>[M+H]+</td>\n",
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       "<p>83358 rows × 8 columns</p>\n",
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      ],
      "text/plain": [
       "                                           adduct  precursor_mz  \\\n",
       "spectrum_id                                                       \n",
       "CCMSLIB00005883221                         [M+H]+    243.088000   \n",
       "NIST937042                             [M-H2O+H]+    205.085900   \n",
       "spec_id=107587                             [M+H]+    370.130000   \n",
       "Eriodictyol-7-O-glucoside_plasma_1981      [M+H]+    451.123488   \n",
       "NIST297310                                 [M+H]+    303.231900   \n",
       "...                                           ...           ...   \n",
       "CCMSLIB00004704976                         [M+H]+    285.112000   \n",
       "CCMSLIB00004712186                         [M+K]+    189.068000   \n",
       "CCMSLIB00010119259                         [M+H]+    271.096000   \n",
       "NIST256349                                 [M+H]+    178.053200   \n",
       "NIST140732                                 [M+H]+    409.164600   \n",
       "\n",
       "                                                                                     mzs  \\\n",
       "spectrum_id                                                                                \n",
       "CCMSLIB00005883221                     [91.054298, 95.049202, 103.054298, 104.0495, 1...   \n",
       "NIST937042                             [63.0231, 65.0387, 77.0386, 79.0543, 89.0387, ...   \n",
       "spec_id=107587                         [106.065, 113.072, 121.088, 137.056, 137.062, ...   \n",
       "Eriodictyol-7-O-glucoside_plasma_1981  [67.01862, 69.03341, 79.01767, 80.06145, 89.03...   \n",
       "NIST297310                             [50.0151, 51.0228, 53.0385, 55.0177, 55.0541, ...   \n",
       "...                                                                                  ...   \n",
       "CCMSLIB00004704976                     [61.011341, 103.054558, 131.049133, 132.052399...   \n",
       "CCMSLIB00004712186                     [51.940292, 55.018112, 55.05452, 56.049725, 56...   \n",
       "CCMSLIB00010119259                     [79.054443, 81.033691, 96.020523, 103.053909, ...   \n",
       "NIST256349                             [55.0179, 57.0208, 58.9949, 62.9898, 70.0287, ...   \n",
       "NIST140732                             [50.0148, 51.0226, 52.0843, 53.0019, 53.0383, ...   \n",
       "\n",
       "                                                                             intensities  \\\n",
       "spectrum_id                                                                                \n",
       "CCMSLIB00005883221                     [0.04068640697166502, 0.01589638945223964, 0.2...   \n",
       "NIST937042                             [0.0221021021021021, 0.24380380380380381, 0.06...   \n",
       "spec_id=107587                         [0.842, 0.599, 0.97, 1.0, 1.0, 1.0, 0.119, 0.0...   \n",
       "Eriodictyol-7-O-glucoside_plasma_1981  [0.084, 0.027, 0.013, 0.021, 0.048, 0.019, 0.0...   \n",
       "NIST297310                             [0.061401401401401406, 0.2772972972972973, 0.2...   \n",
       "...                                                                                  ...   \n",
       "CCMSLIB00004704976                     [0.036569120000000004, 0.020349529999999998, 0...   \n",
       "CCMSLIB00004712186                     [0.11617364000000001, 0.02121181, 0.1648827899...   \n",
       "CCMSLIB00010119259                     [0.01896576750013369, 0.07313959617720532, 0.0...   \n",
       "NIST256349                             [0.20500500500500501, 0.28869869869869874, 0.0...   \n",
       "NIST140732                             [0.6689989989989991, 1.0, 0.0278978978978979, ...   \n",
       "\n",
       "                                                                                loss_mzs  \\\n",
       "spectrum_id                                                                                \n",
       "CCMSLIB00005883221                     [26.007495000000006, 27.011003999999986, 43.00...   \n",
       "NIST937042                             [17.0223, 18.010100000000023, 18.0305000000000...   \n",
       "spec_id=107587                         [20.004999999999995, 29.548000000000002, 30.49...   \n",
       "Eriodictyol-7-O-glucoside_plasma_1981  [163.059708, 164.07297800000003, 221.074678, 2...   \n",
       "NIST297310                             [18.01049999999998, 33.0342, 34.2534, 36.02109...   \n",
       "...                                                                                  ...   \n",
       "CCMSLIB00004704976                     [92.15045200000003, 103.05926600000004, 104.06...   \n",
       "CCMSLIB00004712186                     [29.116019000000023, 30.09127000000001, 30.122...   \n",
       "CCMSLIB00010119259                     [42.01059699999999, 102.03124199999999, 108.05...   \n",
       "NIST256349                             [17.026399999999995, 19.05709999999999, 35.037...   \n",
       "NIST140732                             [15.024200000000008, 18.010100000000023, 30.04...   \n",
       "\n",
       "                                                                        loss_intensities  \\\n",
       "spectrum_id                                                                                \n",
       "CCMSLIB00005883221                     [0.09251948915755456, 0.5639426077381412, 0.05...   \n",
       "NIST937042                             [0.025495495495495495, 1.0, 0.0601001001001001...   \n",
       "spec_id=107587                         [0.387, 0.069, 0.011, 0.066, 0.159, 0.033, 1.0...   \n",
       "Eriodictyol-7-O-glucoside_plasma_1981  [0.015, 0.023, 0.014, 0.023, 0.021, 0.013, 0.0...   \n",
       "NIST297310                             [1.0, 0.051301301301301304, 0.0665965965965966...   \n",
       "...                                                                                  ...   \n",
       "CCMSLIB00004704976                     [0.01426239, 0.09765834999999999, 1.0, 0.03854...   \n",
       "CCMSLIB00004712186                     [0.063098, 0.013058350000000002, 0.0179634, 0....   \n",
       "CCMSLIB00010119259                     [0.04077342072895897, 0.01816400430866546, 0.0...   \n",
       "NIST256349                             [0.055005005005005006, 1.0, 0.0183983983983983...   \n",
       "NIST140732                             [0.011501501501501503, 0.05200200200200201, 0....   \n",
       "\n",
       "                                                          inchikey  \\\n",
       "spectrum_id                                                          \n",
       "CCMSLIB00005883221                     ZJTJUVIJVLLGSP-UHFFFAOYSA-N   \n",
       "NIST937042                             OHQFGTDAUDLCBG-UHFFFAOYSA-N   \n",
       "spec_id=107587                         VPRBWEMXTXPBEY-UHFFFAOYSA-N   \n",
       "Eriodictyol-7-O-glucoside_plasma_1981  RAFHNDRXYHOLSH-RGHIGTIISA-N   \n",
       "NIST297310                             GCKMFJBGXUYNAG-MPRNQXESSA-N   \n",
       "...                                                            ...   \n",
       "CCMSLIB00004704976                     IAFBOKYTDSDNHV-UHFFFAOYSA-N   \n",
       "CCMSLIB00004712186                     MGSRCZKZVOBKFT-UHFFFAOYSA-N   \n",
       "CCMSLIB00010119259                     ODLVGCCGMXGMGZ-RMKNXTFCSA-N   \n",
       "NIST256349                             XUHLIQGRKRUKPH-ITZCMCNPSA-N   \n",
       "NIST140732                             HQWHKELJHUFLGD-UHFFFAOYSA-N   \n",
       "\n",
       "                                                                     smiles_preprocessed  \n",
       "spectrum_id                                                                               \n",
       "CCMSLIB00005883221                                  Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C  \n",
       "NIST937042                                                  Cc1cccc(CC(CC(=O)O)C(=O)O)c1  \n",
       "spec_id=107587                              Cc1c(C)c2ccc3c(c2oc1=O)CN(CCc1ccc(Cl)cc1)CO3  \n",
       "Eriodictyol-7-O-glucoside_plasma_1981  O=C1CC(c2ccc(O)c(O)c2)Oc2cc(OC3OC(CO)C(O)C(O)C...  \n",
       "NIST297310                                        CC12CCC(=O)C=C1CCC1C2CCC2(C)C1CCC2(C)O  \n",
       "...                                                                                  ...  \n",
       "CCMSLIB00004704976                                    COc1cc(OC)c2c(c1)OC(c1ccccc1)CC2=O  \n",
       "CCMSLIB00004712186                                                   Cc1ccc(C(C)C)c(O)c1  \n",
       "CCMSLIB00010119259                                        COc1ccccc1C=CC(=O)c1ccc(O)cc1O  \n",
       "NIST256349                                                          C=CCS(=O)CC(N)C(=O)O  \n",
       "NIST140732                             COc1c(O)cc2oc3cc4c(c(O)c3c(=O)c2c1CC=C(C)C)C=C...  \n",
       "\n",
       "[83358 rows x 8 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df=data_df.set_index('spectrum_id')\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "9cb6b7cd-8e42-489d-bdd8-19da72fc44d7",
   "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>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
       "      <th>intensities</th>\n",
       "      <th>loss_mzs</th>\n",
       "      <th>loss_intensities</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>num_of_sugars</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>spectrum_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1338</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.045, 159.04369, 163.04027, 173.0605, 179....</td>\n",
       "      <td>[0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...</td>\n",
       "      <td>[18.014429199999995, 30.038839199999984, 31.04...</td>\n",
       "      <td>[0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1340</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[275.0733, 305.08203, 323.09119, 324.09433, 35...</td>\n",
       "      <td>[0.017, 0.022, 0.028, 0.01, 1.0, 0.029]</td>\n",
       "      <td>[30.03926919999998, 31.04240920000001, 49.0515...</td>\n",
       "      <td>[0.01, 0.028, 0.022, 0.017]</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1343</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.04521, 143.05431, 159.04745, 161.0602, 16...</td>\n",
       "      <td>[0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...</td>\n",
       "      <td>[18.008909200000005, 31.031639199999972, 31.04...</td>\n",
       "      <td>[0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1346</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[103.05478, 118.06499, 131.04845, 135.04384, 1...</td>\n",
       "      <td>[0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...</td>\n",
       "      <td>[79.06267919999999, 106.06514919999998, 107.05...</td>\n",
       "      <td>[0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1349</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.03654, 135.04454, 159.04517, 163.03651, 1...</td>\n",
       "      <td>[0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...</td>\n",
       "      <td>[18.00828919999998, 30.03291919999998, 30.0438...</td>\n",
       "      <td>[0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3538</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.01796, 77.03296, 77.03867, 79.02107, 79.05...</td>\n",
       "      <td>[0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...</td>\n",
       "      <td>[15.022540799999973, 16.0322008, 17.0336207999...</td>\n",
       "      <td>[0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3540</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[65.03999, 75.02646, 77.02925, 77.03927, 78.04...</td>\n",
       "      <td>[0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...</td>\n",
       "      <td>[31.055850799999973, 45.04376079999997, 46.038...</td>\n",
       "      <td>[0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3542</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[91.05325, 103.0554, 105.07047, 107.05009, 111...</td>\n",
       "      <td>[0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...</td>\n",
       "      <td>[15.01973079999999, 31.012410799999998, 31.021...</td>\n",
       "      <td>[0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3544</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.02081, 68.99757, 77.03687, 77.04144, 77.04...</td>\n",
       "      <td>[0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...</td>\n",
       "      <td>[15.023320799999993, 16.02811079999998, 16.044...</td>\n",
       "      <td>[0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3546</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[51.02621, 68.99291, 75.02341, 77.03965, 78.04...</td>\n",
       "      <td>[0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...</td>\n",
       "      <td>[44.05670079999999, 45.03549079999999, 46.0800...</td>\n",
       "      <td>[0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 adduct  precursor_mz  \\\n",
       "spectrum_id                                             \n",
       "(+)-Chelidonine_plasma_1338      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1340      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1343      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1346      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1349      [M+H]+    354.133599   \n",
       "...                                 ...           ...   \n",
       "trans-pterostilbene_plasma_3538  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3540  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3542  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3544  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3546  [M+H]+    257.117221   \n",
       "\n",
       "                                                                               mzs  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [135.045, 159.04369, 163.04027, 173.0605, 179....   \n",
       "(+)-Chelidonine_plasma_1340      [275.0733, 305.08203, 323.09119, 324.09433, 35...   \n",
       "(+)-Chelidonine_plasma_1343      [135.04521, 143.05431, 159.04745, 161.0602, 16...   \n",
       "(+)-Chelidonine_plasma_1346      [103.05478, 118.06499, 131.04845, 135.04384, 1...   \n",
       "(+)-Chelidonine_plasma_1349      [135.03654, 135.04454, 159.04517, 163.03651, 1...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [55.01796, 77.03296, 77.03867, 79.02107, 79.05...   \n",
       "trans-pterostilbene_plasma_3540  [65.03999, 75.02646, 77.02925, 77.03927, 78.04...   \n",
       "trans-pterostilbene_plasma_3542  [91.05325, 103.0554, 105.07047, 107.05009, 111...   \n",
       "trans-pterostilbene_plasma_3544  [55.02081, 68.99757, 77.03687, 77.04144, 77.04...   \n",
       "trans-pterostilbene_plasma_3546  [51.02621, 68.99291, 75.02341, 77.03965, 78.04...   \n",
       "\n",
       "                                                                       intensities  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...   \n",
       "(+)-Chelidonine_plasma_1340                [0.017, 0.022, 0.028, 0.01, 1.0, 0.029]   \n",
       "(+)-Chelidonine_plasma_1343      [0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...   \n",
       "(+)-Chelidonine_plasma_1346      [0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...   \n",
       "(+)-Chelidonine_plasma_1349      [0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...   \n",
       "trans-pterostilbene_plasma_3540  [0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...   \n",
       "trans-pterostilbene_plasma_3542  [0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...   \n",
       "trans-pterostilbene_plasma_3544  [0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...   \n",
       "trans-pterostilbene_plasma_3546  [0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...   \n",
       "\n",
       "                                                                          loss_mzs  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [18.014429199999995, 30.038839199999984, 31.04...   \n",
       "(+)-Chelidonine_plasma_1340      [30.03926919999998, 31.04240920000001, 49.0515...   \n",
       "(+)-Chelidonine_plasma_1343      [18.008909200000005, 31.031639199999972, 31.04...   \n",
       "(+)-Chelidonine_plasma_1346      [79.06267919999999, 106.06514919999998, 107.05...   \n",
       "(+)-Chelidonine_plasma_1349      [18.00828919999998, 30.03291919999998, 30.0438...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [15.022540799999973, 16.0322008, 17.0336207999...   \n",
       "trans-pterostilbene_plasma_3540  [31.055850799999973, 45.04376079999997, 46.038...   \n",
       "trans-pterostilbene_plasma_3542  [15.01973079999999, 31.012410799999998, 31.021...   \n",
       "trans-pterostilbene_plasma_3544  [15.023320799999993, 16.02811079999998, 16.044...   \n",
       "trans-pterostilbene_plasma_3546  [44.05670079999999, 45.03549079999999, 46.0800...   \n",
       "\n",
       "                                                                  loss_intensities  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...   \n",
       "(+)-Chelidonine_plasma_1340                            [0.01, 0.028, 0.022, 0.017]   \n",
       "(+)-Chelidonine_plasma_1343      [0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...   \n",
       "(+)-Chelidonine_plasma_1346      [0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...   \n",
       "(+)-Chelidonine_plasma_1349      [0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...   \n",
       "trans-pterostilbene_plasma_3540  [0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...   \n",
       "trans-pterostilbene_plasma_3542  [0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...   \n",
       "trans-pterostilbene_plasma_3544  [0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...   \n",
       "trans-pterostilbene_plasma_3546  [0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...   \n",
       "\n",
       "                                                    inchikey  \\\n",
       "spectrum_id                                                    \n",
       "(+)-Chelidonine_plasma_1338      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1340      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1343      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1346      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1349      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "...                                                      ...   \n",
       "trans-pterostilbene_plasma_3538  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3540  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3542  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3544  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3546  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "\n",
       "                                                          smiles_preprocessed  \\\n",
       "spectrum_id                                                                     \n",
       "(+)-Chelidonine_plasma_1338      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1340      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1343      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1346      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1349      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "...                                                                       ...   \n",
       "trans-pterostilbene_plasma_3538                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3540                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3542                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3544                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3546                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "\n",
       "                                 num_of_sugars  \n",
       "spectrum_id                                     \n",
       "(+)-Chelidonine_plasma_1338                NaN  \n",
       "(+)-Chelidonine_plasma_1340                NaN  \n",
       "(+)-Chelidonine_plasma_1343                NaN  \n",
       "(+)-Chelidonine_plasma_1346                NaN  \n",
       "(+)-Chelidonine_plasma_1349                NaN  \n",
       "...                                        ...  \n",
       "trans-pterostilbene_plasma_3538            NaN  \n",
       "trans-pterostilbene_plasma_3540            NaN  \n",
       "trans-pterostilbene_plasma_3542            NaN  \n",
       "trans-pterostilbene_plasma_3544            NaN  \n",
       "trans-pterostilbene_plasma_3546            NaN  \n",
       "\n",
       "[83358 rows x 9 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df=data_df.join(df,how=\"outer\")\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "ff6e6bd8-80c0-49f2-bd57-7b63bd2faa89",
   "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>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
       "      <th>intensities</th>\n",
       "      <th>loss_mzs</th>\n",
       "      <th>loss_intensities</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>num_of_sugars</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>spectrum_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1338</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.045, 159.04369, 163.04027, 173.0605, 179....</td>\n",
       "      <td>[0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...</td>\n",
       "      <td>[18.014429199999995, 30.038839199999984, 31.04...</td>\n",
       "      <td>[0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1340</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[275.0733, 305.08203, 323.09119, 324.09433, 35...</td>\n",
       "      <td>[0.017, 0.022, 0.028, 0.01, 1.0, 0.029]</td>\n",
       "      <td>[30.03926919999998, 31.04240920000001, 49.0515...</td>\n",
       "      <td>[0.01, 0.028, 0.022, 0.017]</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1343</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.04521, 143.05431, 159.04745, 161.0602, 16...</td>\n",
       "      <td>[0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...</td>\n",
       "      <td>[18.008909200000005, 31.031639199999972, 31.04...</td>\n",
       "      <td>[0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1346</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[103.05478, 118.06499, 131.04845, 135.04384, 1...</td>\n",
       "      <td>[0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...</td>\n",
       "      <td>[79.06267919999999, 106.06514919999998, 107.05...</td>\n",
       "      <td>[0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1349</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.03654, 135.04454, 159.04517, 163.03651, 1...</td>\n",
       "      <td>[0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...</td>\n",
       "      <td>[18.00828919999998, 30.03291919999998, 30.0438...</td>\n",
       "      <td>[0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3538</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.01796, 77.03296, 77.03867, 79.02107, 79.05...</td>\n",
       "      <td>[0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...</td>\n",
       "      <td>[15.022540799999973, 16.0322008, 17.0336207999...</td>\n",
       "      <td>[0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3540</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[65.03999, 75.02646, 77.02925, 77.03927, 78.04...</td>\n",
       "      <td>[0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...</td>\n",
       "      <td>[31.055850799999973, 45.04376079999997, 46.038...</td>\n",
       "      <td>[0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3542</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[91.05325, 103.0554, 105.07047, 107.05009, 111...</td>\n",
       "      <td>[0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...</td>\n",
       "      <td>[15.01973079999999, 31.012410799999998, 31.021...</td>\n",
       "      <td>[0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3544</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.02081, 68.99757, 77.03687, 77.04144, 77.04...</td>\n",
       "      <td>[0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...</td>\n",
       "      <td>[15.023320799999993, 16.02811079999998, 16.044...</td>\n",
       "      <td>[0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3546</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[51.02621, 68.99291, 75.02341, 77.03965, 78.04...</td>\n",
       "      <td>[0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...</td>\n",
       "      <td>[44.05670079999999, 45.03549079999999, 46.0800...</td>\n",
       "      <td>[0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 adduct  precursor_mz  \\\n",
       "spectrum_id                                             \n",
       "(+)-Chelidonine_plasma_1338      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1340      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1343      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1346      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1349      [M+H]+    354.133599   \n",
       "...                                 ...           ...   \n",
       "trans-pterostilbene_plasma_3538  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3540  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3542  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3544  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3546  [M+H]+    257.117221   \n",
       "\n",
       "                                                                               mzs  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [135.045, 159.04369, 163.04027, 173.0605, 179....   \n",
       "(+)-Chelidonine_plasma_1340      [275.0733, 305.08203, 323.09119, 324.09433, 35...   \n",
       "(+)-Chelidonine_plasma_1343      [135.04521, 143.05431, 159.04745, 161.0602, 16...   \n",
       "(+)-Chelidonine_plasma_1346      [103.05478, 118.06499, 131.04845, 135.04384, 1...   \n",
       "(+)-Chelidonine_plasma_1349      [135.03654, 135.04454, 159.04517, 163.03651, 1...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [55.01796, 77.03296, 77.03867, 79.02107, 79.05...   \n",
       "trans-pterostilbene_plasma_3540  [65.03999, 75.02646, 77.02925, 77.03927, 78.04...   \n",
       "trans-pterostilbene_plasma_3542  [91.05325, 103.0554, 105.07047, 107.05009, 111...   \n",
       "trans-pterostilbene_plasma_3544  [55.02081, 68.99757, 77.03687, 77.04144, 77.04...   \n",
       "trans-pterostilbene_plasma_3546  [51.02621, 68.99291, 75.02341, 77.03965, 78.04...   \n",
       "\n",
       "                                                                       intensities  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...   \n",
       "(+)-Chelidonine_plasma_1340                [0.017, 0.022, 0.028, 0.01, 1.0, 0.029]   \n",
       "(+)-Chelidonine_plasma_1343      [0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...   \n",
       "(+)-Chelidonine_plasma_1346      [0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...   \n",
       "(+)-Chelidonine_plasma_1349      [0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...   \n",
       "trans-pterostilbene_plasma_3540  [0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...   \n",
       "trans-pterostilbene_plasma_3542  [0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...   \n",
       "trans-pterostilbene_plasma_3544  [0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...   \n",
       "trans-pterostilbene_plasma_3546  [0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...   \n",
       "\n",
       "                                                                          loss_mzs  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [18.014429199999995, 30.038839199999984, 31.04...   \n",
       "(+)-Chelidonine_plasma_1340      [30.03926919999998, 31.04240920000001, 49.0515...   \n",
       "(+)-Chelidonine_plasma_1343      [18.008909200000005, 31.031639199999972, 31.04...   \n",
       "(+)-Chelidonine_plasma_1346      [79.06267919999999, 106.06514919999998, 107.05...   \n",
       "(+)-Chelidonine_plasma_1349      [18.00828919999998, 30.03291919999998, 30.0438...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [15.022540799999973, 16.0322008, 17.0336207999...   \n",
       "trans-pterostilbene_plasma_3540  [31.055850799999973, 45.04376079999997, 46.038...   \n",
       "trans-pterostilbene_plasma_3542  [15.01973079999999, 31.012410799999998, 31.021...   \n",
       "trans-pterostilbene_plasma_3544  [15.023320799999993, 16.02811079999998, 16.044...   \n",
       "trans-pterostilbene_plasma_3546  [44.05670079999999, 45.03549079999999, 46.0800...   \n",
       "\n",
       "                                                                  loss_intensities  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...   \n",
       "(+)-Chelidonine_plasma_1340                            [0.01, 0.028, 0.022, 0.017]   \n",
       "(+)-Chelidonine_plasma_1343      [0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...   \n",
       "(+)-Chelidonine_plasma_1346      [0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...   \n",
       "(+)-Chelidonine_plasma_1349      [0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...   \n",
       "trans-pterostilbene_plasma_3540  [0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...   \n",
       "trans-pterostilbene_plasma_3542  [0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...   \n",
       "trans-pterostilbene_plasma_3544  [0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...   \n",
       "trans-pterostilbene_plasma_3546  [0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...   \n",
       "\n",
       "                                                    inchikey  \\\n",
       "spectrum_id                                                    \n",
       "(+)-Chelidonine_plasma_1338      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1340      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1343      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1346      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1349      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "...                                                      ...   \n",
       "trans-pterostilbene_plasma_3538  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3540  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3542  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3544  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3546  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "\n",
       "                                                          smiles_preprocessed  \\\n",
       "spectrum_id                                                                     \n",
       "(+)-Chelidonine_plasma_1338      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1340      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1343      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1346      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1349      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "...                                                                       ...   \n",
       "trans-pterostilbene_plasma_3538                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3540                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3542                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3544                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3546                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "\n",
       "                                 num_of_sugars  \n",
       "spectrum_id                                     \n",
       "(+)-Chelidonine_plasma_1338                0.0  \n",
       "(+)-Chelidonine_plasma_1340                0.0  \n",
       "(+)-Chelidonine_plasma_1343                0.0  \n",
       "(+)-Chelidonine_plasma_1346                0.0  \n",
       "(+)-Chelidonine_plasma_1349                0.0  \n",
       "...                                        ...  \n",
       "trans-pterostilbene_plasma_3538            0.0  \n",
       "trans-pterostilbene_plasma_3540            0.0  \n",
       "trans-pterostilbene_plasma_3542            0.0  \n",
       "trans-pterostilbene_plasma_3544            0.0  \n",
       "trans-pterostilbene_plasma_3546            0.0  \n",
       "\n",
       "[83358 rows x 9 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df['num_of_sugars'] = data_df['num_of_sugars'].fillna(0)\n",
    "data_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6e0c6c8e-8458-4b3b-9b33-b0be9b5e452f",
   "metadata": {
    "tags": []
   },
   "source": [
    "fr_Al_COO(mol)\n",
    "#Number of aliphatic carboxylic acids\n",
    "fr_Al_OH(mol)\n",
    "#Number of aliphatic hydroxyl groups\n",
    "\n",
    "fr_Al_OH_noTert(mol)\n",
    "#Number of aliphatic hydroxyl groups excluding tert-OH\n",
    "\n",
    "fr_ArN(mol)\n",
    "#Number of N functional groups attached to aromatics\n",
    "\n",
    "fr_Ar_COO(mol)\n",
    "#Number of Aromatic carboxylic acide\n",
    "\n",
    "fr_Ar_N(mol)\n",
    "#Number of aromatic nitrogens\n",
    "\n",
    "fr_Ar_NH(mol)\n",
    "#Number of aromatic amines\n",
    "\n",
    "fr_Ar_OH(mol)\n",
    "#Number of aromatic hydroxyl groups\n",
    "\n",
    "fr_COO(mol)\n",
    "#Number of carboxylic acids\n",
    "\n",
    "fr_COO2(mol)\n",
    "#Number of carboxylic acids\n",
    "\n",
    "fr_C_O(mol)\n",
    "#Number of carbonyl O\n",
    "\n",
    "fr_C_O_noCOO(mol)\n",
    "#Number of carbonyl O, excluding COOH\n",
    "\n",
    "fr_C_S(mol)\n",
    "#Number of thiocarbonyl\n",
    "\n",
    "fr_Imine(mol)\n",
    "#Number of Imines\n",
    "\n",
    "fr_NH0(mol)\n",
    "#Number of Tertiary amines\n",
    "\n",
    "fr_NH1(mol)\n",
    "#Number of Secondary amines\n",
    "\n",
    "fr_NH2(mol)\n",
    "#Number of Primary amines\n",
    "\n",
    "fr_N_O(mol)\n",
    "#Number of hydroxylamine groups\n",
    "\n",
    "fr_Ndealkylation2(mol)\n",
    "#Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)\n",
    "\n",
    "fr_Nhpyrrole(mol)\n",
    "#Number of H-pyrrole nitrogens\n",
    "\n",
    "fr_SH(mol)\n",
    "#Number of thiol groups\n",
    "\n",
    "fr_aldehyde(mol)\n",
    "#Number of aldehydes\n",
    "\n",
    "fr_alkyl_carbamate(mol)\n",
    "#Number of alkyl carbamates (subject to hydrolysis)\n",
    "\n",
    "fr_alkyl_halide(mol)\n",
    "#Number of alkyl halides\n",
    "\n",
    "fr_allylic_oxid(mol)\n",
    "#Number of allylic oxidation sites excluding steroid dienone\n",
    "\n",
    "fr_amide(mol)\n",
    "#Number of amides\n",
    "\n",
    "\n",
    "fr_aniline(mol)\n",
    "#Number of anilines\n",
    "\n",
    "fr_aryl_methyl(mol)\n",
    "#Number of aryl methyl sites for hydroxylation\n",
    "\n",
    "fr_azo(mol)\n",
    "#Number of azo groups\n",
    "\n",
    "\n",
    "fr_benzene(mol)\n",
    "#Number of benzene rings\n",
    "\n",
    "\n",
    "fr_bicyclic(mol)\n",
    "#Bicyclic\n",
    "\n",
    "\n",
    "fr_dihydropyridine(mol)\n",
    "#Number of dihydropyridines\n",
    "\n",
    "fr_epoxide(mol)\n",
    "#Number of epoxide rings\n",
    "\n",
    "fr_ester(mol)\n",
    "#Number of esters\n",
    "\n",
    "fr_ether(mol)\n",
    "#Number of ether oxygens (including phenoxy)\n",
    "\n",
    "fr_furan(mol)\n",
    "#Number of furan rings\n",
    "\n",
    "fr_guanido(mol)\n",
    "#Number of guanidine groups\n",
    "\n",
    "fr_halogen(mol)\n",
    "Number of halogens\n",
    "\n",
    "fr_imidazole(mol)\n",
    "#Number of imidazole rings\n",
    "\n",
    "fr_isothiocyan(mol)\n",
    "#Number of isothiocyanates\n",
    "\n",
    "fr_ketone(mol)\n",
    "#Number of ketones\n",
    "\n",
    "fr_ketone_Topliss(mol)\n",
    "#Number of ketones excluding diaryl, a,b-unsat. dienones, heteroatom on Calpha\n",
    "\n",
    "fr_lactam(mol)\n",
    "#Number of beta lactams\n",
    "\n",
    "fr_lactone(mol)\n",
    "#Number of cyclic esters (lactones)\n",
    "\n",
    "fr_methoxy(mol)\n",
    "#Number of methoxy groups -OCH3\n",
    "\n",
    "\n",
    "fr_nitrile(mol)\n",
    "#Number of nitriles\n",
    "\n",
    "fr_nitro(mol)\n",
    "#Number of nitro groups\n",
    "\n",
    "\n",
    "fr_oxazole(mol)\n",
    "#Number of oxazole rings\n",
    "\n",
    "fr_para_hydroxylation(mol)\n",
    "#Number of para-hydroxylation sites\n",
    "\n",
    "fr_phenol(mol)\n",
    "#Number of phenols\n",
    "\n",
    "fr_phos_acid(mol)\n",
    "#Number of phosphoric acid groups\n",
    "\n",
    "fr_phos_ester(mol)\n",
    "#Number of phosphoric ester groups\n",
    "\n",
    "fr_piperdine(mol)\n",
    "#Number of piperdine rings\n",
    "\n",
    "fr_priamide(mol)\n",
    "#Number of primary amides\n",
    "\n",
    "fr_pyridine(mol)\n",
    "#Number of pyridine rings\n",
    "\n",
    "fr_quatN(mol)\n",
    "#Number of quaternary nitrogens\n",
    "\n",
    "fr_sulfide(mol)\n",
    "#Number of thioether\n",
    "\n",
    "fr_thiazole(mol)\n",
    "#Number of thiazole rings\n",
    "\n",
    "fr_unbrch_alkane(mol)\n",
    "#Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "e1c1f2b6-29bc-423d-8bcc-665db550d431",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "def get_func_gr(mol):\n",
    "    mol=Chem.MolFromSmiles(mol)\n",
    "    gr=[fr_Al_COO(mol),\n",
    "     #Number of aliphatic carboxylic acids\n",
    "     fr_Al_OH(mol),\n",
    "     #Number of aliphatic hydroxyl groups\n",
    "     fr_Al_OH_noTert(mol),\n",
    "     #Number of aliphatic hydroxyl groups excluding tert-OH\n",
    "     fr_ArN(mol),\n",
    "     #Number of N functional groups attached to aromatics\n",
    "     fr_Ar_COO(mol),\n",
    "     #Number of Aromatic carboxylic acide\n",
    "     fr_Ar_N(mol),\n",
    "     #Number of aromatic nitrogens\n",
    "     fr_Ar_NH(mol),\n",
    "     #Number of aromatic amines\n",
    "     fr_Ar_OH(mol),\n",
    "     #Number of aromatic hydroxyl groups\n",
    "     fr_COO(mol),\n",
    "     #Number of carboxylic acids\n",
    "     fr_COO2(mol),\n",
    "     #Number of carboxylic acids\n",
    "     fr_C_O(mol),\n",
    "     #Number of carbonyl O\n",
    "     fr_C_O_noCOO(mol),\n",
    "     #Number of carbonyl O, excluding COOH\n",
    "     fr_C_S(mol),\n",
    "     #Number of thiocarbonyl\n",
    "     fr_Imine(mol),\n",
    "     #Number of Imines\n",
    "     fr_NH0(mol),\n",
    "     #Number of Tertiary amines\n",
    "     fr_NH1(mol),\n",
    "     #Number of Secondary amines\n",
    "     fr_NH2(mol),\n",
    "     #Number of Primary amines\n",
    "     fr_N_O(mol),\n",
    "     #Number of hydroxylamine groups\n",
    "     fr_Ndealkylation2(mol),\n",
    "     #Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)\n",
    "     fr_Nhpyrrole(mol),\n",
    "     #Number of H-pyrrole nitrogens\n",
    "     fr_SH(mol),\n",
    "     #Number of thiol groups\n",
    "     fr_aldehyde(mol),\n",
    "     #Number of aldehydes\n",
    "     fr_alkyl_carbamate(mol),\n",
    "     #Number of alkyl carbamates (subject to hydrolysis)\n",
    "     fr_alkyl_halide(mol),\n",
    "     #Number of alkyl halides\n",
    "     fr_allylic_oxid(mol),\n",
    "     #Number of allylic oxidation sites excluding steroid dienone\n",
    "     fr_amide(mol),\n",
    "     #Number of amides\n",
    "     fr_aniline(mol),\n",
    "     #Number of anilines\n",
    "     fr_aryl_methyl(mol),\n",
    "     #Number of aryl methyl sites for hydroxylation\n",
    "     fr_azo(mol),\n",
    "     #Number of azo groups\n",
    "     fr_benzene(mol),\n",
    "     #Number of benzene rings\n",
    "     fr_bicyclic(mol),\n",
    "     #Bicyclic\n",
    "     fr_dihydropyridine(mol),\n",
    "     #Number of dihydropyridines\n",
    "     fr_epoxide(mol),\n",
    "     #Number of epoxide rings\n",
    "     fr_ester(mol),\n",
    "     #Number of esters\n",
    "     fr_ether(mol),\n",
    "     #Number of ether oxygens (including phenoxy)\n",
    "     fr_furan(mol),\n",
    "     #Number of furan rings\n",
    "     fr_guanido(mol),\n",
    "     #Number of guanidine groups\n",
    "     fr_halogen(mol),\n",
    "     #Number of halogens\n",
    "     fr_imidazole(mol),\n",
    "     #Number of imidazole rings\n",
    "     fr_isothiocyan(mol),\n",
    "     #Number of isothiocyanates\n",
    "     fr_ketone(mol),\n",
    "     #Number of ketones\n",
    "     fr_ketone_Topliss(mol),\n",
    "     #Number of ketones excluding diaryl, a,b-unsat. dienones, heteroatom on Calpha\n",
    "     fr_lactam(mol),\n",
    "     #Number of beta lactams\n",
    "     fr_lactone(mol),\n",
    "     #Number of cyclic esters (lactones)\n",
    "     fr_methoxy(mol),\n",
    "     #Number of methoxy groups -OCH3\n",
    "     fr_nitrile(mol),\n",
    "     #Number of nitriles\n",
    "     fr_nitro(mol),\n",
    "     #Number of nitro groups\n",
    "     fr_oxazole(mol),\n",
    "     #Number of oxazole rings\n",
    "     fr_para_hydroxylation(mol),\n",
    "     #Number of para-hydroxylation sites\n",
    "     fr_phenol(mol),\n",
    "     #Number of phenols\n",
    "     fr_phos_acid(mol),\n",
    "     #Number of phosphoric acid groups\n",
    "     fr_phos_ester(mol),\n",
    "     #Number of phosphoric ester groups\n",
    "     fr_piperdine(mol),\n",
    "     #Number of piperdine rings\n",
    "     fr_priamide(mol),\n",
    "     #Number of primary amides\n",
    "     fr_pyridine(mol),\n",
    "     #Number of pyridine rings\n",
    "     fr_quatN(mol),\n",
    "     #Number of quaternary nitrogens\n",
    "     fr_sulfide(mol),\n",
    "     #Number of thioether\n",
    "     fr_thiazole(mol),\n",
    "     #Number of thiazole rings\n",
    "     fr_unbrch_alkane(mol)]\n",
    "     #Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)\n",
    "    return gr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "58510768-d66b-4939-9b55-fd1f6f010dfa",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "59"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(get_func_gr(\"OCC1(C(OC(CCCC)=O)C(OC(CCCCC)=O)C(COC(CCC)=O)O1)OC(O2)C(O)C(OC(CC)=O)C(O)C2COC(CC)=O\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "75af6b58-9e02-472b-a961-164cd19f6186",
   "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>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
       "      <th>intensities</th>\n",
       "      <th>loss_mzs</th>\n",
       "      <th>loss_intensities</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>num_of_sugars</th>\n",
       "      <th>groups</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>spectrum_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1338</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.045, 159.04369, 163.04027, 173.0605, 179....</td>\n",
       "      <td>[0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...</td>\n",
       "      <td>[18.014429199999995, 30.038839199999984, 31.04...</td>\n",
       "      <td>[0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1340</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[275.0733, 305.08203, 323.09119, 324.09433, 35...</td>\n",
       "      <td>[0.017, 0.022, 0.028, 0.01, 1.0, 0.029]</td>\n",
       "      <td>[30.03926919999998, 31.04240920000001, 49.0515...</td>\n",
       "      <td>[0.01, 0.028, 0.022, 0.017]</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1343</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.04521, 143.05431, 159.04745, 161.0602, 16...</td>\n",
       "      <td>[0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...</td>\n",
       "      <td>[18.008909200000005, 31.031639199999972, 31.04...</td>\n",
       "      <td>[0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1346</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[103.05478, 118.06499, 131.04845, 135.04384, 1...</td>\n",
       "      <td>[0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...</td>\n",
       "      <td>[79.06267919999999, 106.06514919999998, 107.05...</td>\n",
       "      <td>[0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(+)-Chelidonine_plasma_1349</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.03654, 135.04454, 159.04517, 163.03651, 1...</td>\n",
       "      <td>[0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...</td>\n",
       "      <td>[18.00828919999998, 30.03291919999998, 30.0438...</td>\n",
       "      <td>[0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3538</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.01796, 77.03296, 77.03867, 79.02107, 79.05...</td>\n",
       "      <td>[0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...</td>\n",
       "      <td>[15.022540799999973, 16.0322008, 17.0336207999...</td>\n",
       "      <td>[0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3540</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[65.03999, 75.02646, 77.02925, 77.03927, 78.04...</td>\n",
       "      <td>[0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...</td>\n",
       "      <td>[31.055850799999973, 45.04376079999997, 46.038...</td>\n",
       "      <td>[0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3542</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[91.05325, 103.0554, 105.07047, 107.05009, 111...</td>\n",
       "      <td>[0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...</td>\n",
       "      <td>[15.01973079999999, 31.012410799999998, 31.021...</td>\n",
       "      <td>[0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3544</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.02081, 68.99757, 77.03687, 77.04144, 77.04...</td>\n",
       "      <td>[0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...</td>\n",
       "      <td>[15.023320799999993, 16.02811079999998, 16.044...</td>\n",
       "      <td>[0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>trans-pterostilbene_plasma_3546</th>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[51.02621, 68.99291, 75.02341, 77.03965, 78.04...</td>\n",
       "      <td>[0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...</td>\n",
       "      <td>[44.05670079999999, 45.03549079999999, 46.0800...</td>\n",
       "      <td>[0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 adduct  precursor_mz  \\\n",
       "spectrum_id                                             \n",
       "(+)-Chelidonine_plasma_1338      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1340      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1343      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1346      [M+H]+    354.133599   \n",
       "(+)-Chelidonine_plasma_1349      [M+H]+    354.133599   \n",
       "...                                 ...           ...   \n",
       "trans-pterostilbene_plasma_3538  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3540  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3542  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3544  [M+H]+    257.117221   \n",
       "trans-pterostilbene_plasma_3546  [M+H]+    257.117221   \n",
       "\n",
       "                                                                               mzs  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [135.045, 159.04369, 163.04027, 173.0605, 179....   \n",
       "(+)-Chelidonine_plasma_1340      [275.0733, 305.08203, 323.09119, 324.09433, 35...   \n",
       "(+)-Chelidonine_plasma_1343      [135.04521, 143.05431, 159.04745, 161.0602, 16...   \n",
       "(+)-Chelidonine_plasma_1346      [103.05478, 118.06499, 131.04845, 135.04384, 1...   \n",
       "(+)-Chelidonine_plasma_1349      [135.03654, 135.04454, 159.04517, 163.03651, 1...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [55.01796, 77.03296, 77.03867, 79.02107, 79.05...   \n",
       "trans-pterostilbene_plasma_3540  [65.03999, 75.02646, 77.02925, 77.03927, 78.04...   \n",
       "trans-pterostilbene_plasma_3542  [91.05325, 103.0554, 105.07047, 107.05009, 111...   \n",
       "trans-pterostilbene_plasma_3544  [55.02081, 68.99757, 77.03687, 77.04144, 77.04...   \n",
       "trans-pterostilbene_plasma_3546  [51.02621, 68.99291, 75.02341, 77.03965, 78.04...   \n",
       "\n",
       "                                                                       intensities  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...   \n",
       "(+)-Chelidonine_plasma_1340                [0.017, 0.022, 0.028, 0.01, 1.0, 0.029]   \n",
       "(+)-Chelidonine_plasma_1343      [0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...   \n",
       "(+)-Chelidonine_plasma_1346      [0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...   \n",
       "(+)-Chelidonine_plasma_1349      [0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...   \n",
       "trans-pterostilbene_plasma_3540  [0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...   \n",
       "trans-pterostilbene_plasma_3542  [0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...   \n",
       "trans-pterostilbene_plasma_3544  [0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...   \n",
       "trans-pterostilbene_plasma_3546  [0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...   \n",
       "\n",
       "                                                                          loss_mzs  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [18.014429199999995, 30.038839199999984, 31.04...   \n",
       "(+)-Chelidonine_plasma_1340      [30.03926919999998, 31.04240920000001, 49.0515...   \n",
       "(+)-Chelidonine_plasma_1343      [18.008909200000005, 31.031639199999972, 31.04...   \n",
       "(+)-Chelidonine_plasma_1346      [79.06267919999999, 106.06514919999998, 107.05...   \n",
       "(+)-Chelidonine_plasma_1349      [18.00828919999998, 30.03291919999998, 30.0438...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [15.022540799999973, 16.0322008, 17.0336207999...   \n",
       "trans-pterostilbene_plasma_3540  [31.055850799999973, 45.04376079999997, 46.038...   \n",
       "trans-pterostilbene_plasma_3542  [15.01973079999999, 31.012410799999998, 31.021...   \n",
       "trans-pterostilbene_plasma_3544  [15.023320799999993, 16.02811079999998, 16.044...   \n",
       "trans-pterostilbene_plasma_3546  [44.05670079999999, 45.03549079999999, 46.0800...   \n",
       "\n",
       "                                                                  loss_intensities  \\\n",
       "spectrum_id                                                                          \n",
       "(+)-Chelidonine_plasma_1338      [0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...   \n",
       "(+)-Chelidonine_plasma_1340                            [0.01, 0.028, 0.022, 0.017]   \n",
       "(+)-Chelidonine_plasma_1343      [0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...   \n",
       "(+)-Chelidonine_plasma_1346      [0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...   \n",
       "(+)-Chelidonine_plasma_1349      [0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...   \n",
       "...                                                                            ...   \n",
       "trans-pterostilbene_plasma_3538  [0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...   \n",
       "trans-pterostilbene_plasma_3540  [0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...   \n",
       "trans-pterostilbene_plasma_3542  [0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...   \n",
       "trans-pterostilbene_plasma_3544  [0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...   \n",
       "trans-pterostilbene_plasma_3546  [0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...   \n",
       "\n",
       "                                                    inchikey  \\\n",
       "spectrum_id                                                    \n",
       "(+)-Chelidonine_plasma_1338      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1340      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1343      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1346      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "(+)-Chelidonine_plasma_1349      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "...                                                      ...   \n",
       "trans-pterostilbene_plasma_3538  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3540  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3542  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3544  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "trans-pterostilbene_plasma_3546  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "\n",
       "                                                          smiles_preprocessed  \\\n",
       "spectrum_id                                                                     \n",
       "(+)-Chelidonine_plasma_1338      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1340      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1343      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1346      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "(+)-Chelidonine_plasma_1349      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4   \n",
       "...                                                                       ...   \n",
       "trans-pterostilbene_plasma_3538                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3540                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3542                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3544                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "trans-pterostilbene_plasma_3546                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1   \n",
       "\n",
       "                                 num_of_sugars  \\\n",
       "spectrum_id                                      \n",
       "(+)-Chelidonine_plasma_1338                0.0   \n",
       "(+)-Chelidonine_plasma_1340                0.0   \n",
       "(+)-Chelidonine_plasma_1343                0.0   \n",
       "(+)-Chelidonine_plasma_1346                0.0   \n",
       "(+)-Chelidonine_plasma_1349                0.0   \n",
       "...                                        ...   \n",
       "trans-pterostilbene_plasma_3538            0.0   \n",
       "trans-pterostilbene_plasma_3540            0.0   \n",
       "trans-pterostilbene_plasma_3542            0.0   \n",
       "trans-pterostilbene_plasma_3544            0.0   \n",
       "trans-pterostilbene_plasma_3546            0.0   \n",
       "\n",
       "                                                                            groups  \n",
       "spectrum_id                                                                         \n",
       "(+)-Chelidonine_plasma_1338      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "(+)-Chelidonine_plasma_1340      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "(+)-Chelidonine_plasma_1343      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "(+)-Chelidonine_plasma_1346      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "(+)-Chelidonine_plasma_1349      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "...                                                                            ...  \n",
       "trans-pterostilbene_plasma_3538  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "trans-pterostilbene_plasma_3540  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "trans-pterostilbene_plasma_3542  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "trans-pterostilbene_plasma_3544  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "trans-pterostilbene_plasma_3546  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "\n",
       "[83358 rows x 10 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df['groups'] = data_df.apply(lambda x: get_func_gr(x.smiles_preprocessed), axis=1)\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "d1c5ea07-2f54-4ab6-923f-25ef133610f8",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "funct=[\"Number of aliphatic carboxylic acids\",\n",
    " \"Number of aliphatic hydroxyl groups\",\n",
    " \"Number of aliphatic hydroxyl groups excluding tert-OH\",\n",
    " \"Number of N functional groups attached to aromatics\",\n",
    " \"Number of Aromatic carboxylic acides\",\n",
    " \"Number of aromatic nitrogens\",\n",
    " \"Number of aromatic amines\",\n",
    " \"Number of aromatic hydroxyl groups\",\n",
    " \"Number of carboxylic acids\",\n",
    " \"Number of carboxylic acids\",\n",
    " \"Number of carbonyl O\",\n",
    " \"Number of carbonyl O, excluding COOH\",\n",
    " \"Number of thiocarbonyl\",\n",
    " \"Number of Imines\",\n",
    " \"Number of Tertiary amines\",\n",
    " \"Number of Secondary amines\",\n",
    " \"Number of Primary amines\",\n",
    " \"Number of hydroxylamine groups\",\n",
    " \"Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)\",\n",
    " \"Number of H-pyrrole nitrogens\",\n",
    " \"Number of thiol groups\",\n",
    " \"Number of aldehydes\",\n",
    " \"Number of alkyl carbamates (subject to hydrolysis)\",\n",
    " \"Number of alkyl halides\",\n",
    " \"Number of allylic oxidation sites excluding steroid dienone\",\n",
    " \"Number of amides\",\n",
    " \"Number of anilines\",\n",
    " \"Number of aryl methyl sites for hydroxylation\",\n",
    " \"Number of azo groups\",\n",
    " \"Number of benzene rings\",\n",
    " \"Bicyclic\",\n",
    " \"Number of dihydropyridines\",\n",
    " \"Number of epoxide rings\",\n",
    " \"Number of esters\",\n",
    " \"Number of ether oxygens (including phenoxy)\",\n",
    " \"Number of furan rings\",\n",
    " \"Number of guanidine groups\",\n",
    " \"Number of halogens\",\n",
    " \"Number of imidazole rings\",\n",
    " \"Number of isothiocyanates\",\n",
    " \"Number of ketones\",\n",
    " \"Number of ketones excluding diaryl, a,b-unsat. dienones, heteroatom on Calpha\",\n",
    " \"Number of beta lactams\",\n",
    " \"Number of cyclic esters (lactones)\",\n",
    " \"Number of methoxy groups -OCH3\",\n",
    " \"Number of nitriles\",\n",
    " \"Number of nitro groups\",\n",
    " \"Number of oxazole rings\",\n",
    " \"Number of para-hydroxylation sites\",\n",
    " \"Number of phenols\",\n",
    " \"Number of phosphoric acid groups\",\n",
    " \"Number of phosphoric ester groups\",\n",
    " \"Number of piperdine rings\",\n",
    " \"Number of primary amides\",\n",
    " \"Number of pyridine rings\",\n",
    " \"Number of quaternary nitrogens\",\n",
    " \"Number of thioether\",\n",
    " \"Number of thiazole rings\",\n",
    " \"Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)\"]"
   ]
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  {
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      ],
      "text/plain": [
       "       Number of aliphatic carboxylic acids  \\\n",
       "0                                         0   \n",
       "1                                         0   \n",
       "2                                         0   \n",
       "3                                         0   \n",
       "4                                         0   \n",
       "...                                     ...   \n",
       "83353                                     0   \n",
       "83354                                     0   \n",
       "83355                                     0   \n",
       "83356                                     0   \n",
       "83357                                     0   \n",
       "\n",
       "       Number of aliphatic hydroxyl groups  \\\n",
       "0                                        1   \n",
       "1                                        1   \n",
       "2                                        1   \n",
       "3                                        1   \n",
       "4                                        1   \n",
       "...                                    ...   \n",
       "83353                                    0   \n",
       "83354                                    0   \n",
       "83355                                    0   \n",
       "83356                                    0   \n",
       "83357                                    0   \n",
       "\n",
       "       Number of aliphatic hydroxyl groups excluding tert-OH  \\\n",
       "0                                                      1       \n",
       "1                                                      1       \n",
       "2                                                      1       \n",
       "3                                                      1       \n",
       "4                                                      1       \n",
       "...                                                  ...       \n",
       "83353                                                  0       \n",
       "83354                                                  0       \n",
       "83355                                                  0       \n",
       "83356                                                  0       \n",
       "83357                                                  0       \n",
       "\n",
       "       Number of N functional groups attached to aromatics  \\\n",
       "0                                                      0     \n",
       "1                                                      0     \n",
       "2                                                      0     \n",
       "3                                                      0     \n",
       "4                                                      0     \n",
       "...                                                  ...     \n",
       "83353                                                  0     \n",
       "83354                                                  0     \n",
       "83355                                                  0     \n",
       "83356                                                  0     \n",
       "83357                                                  0     \n",
       "\n",
       "       Number of Aromatic carboxylic acides  Number of aromatic nitrogens  \\\n",
       "0                                         0                             0   \n",
       "1                                         0                             0   \n",
       "2                                         0                             0   \n",
       "3                                         0                             0   \n",
       "4                                         0                             0   \n",
       "...                                     ...                           ...   \n",
       "83353                                     0                             0   \n",
       "83354                                     0                             0   \n",
       "83355                                     0                             0   \n",
       "83356                                     0                             0   \n",
       "83357                                     0                             0   \n",
       "\n",
       "       Number of aromatic amines  Number of aromatic hydroxyl groups  \\\n",
       "0                              0                                   0   \n",
       "1                              0                                   0   \n",
       "2                              0                                   0   \n",
       "3                              0                                   0   \n",
       "4                              0                                   0   \n",
       "...                          ...                                 ...   \n",
       "83353                          0                                   1   \n",
       "83354                          0                                   1   \n",
       "83355                          0                                   1   \n",
       "83356                          0                                   1   \n",
       "83357                          0                                   1   \n",
       "\n",
       "       Number of carboxylic acids  Number of carboxylic acids  ...  \\\n",
       "0                               0                           0  ...   \n",
       "1                               0                           0  ...   \n",
       "2                               0                           0  ...   \n",
       "3                               0                           0  ...   \n",
       "4                               0                           0  ...   \n",
       "...                           ...                         ...  ...   \n",
       "83353                           0                           0  ...   \n",
       "83354                           0                           0  ...   \n",
       "83355                           0                           0  ...   \n",
       "83356                           0                           0  ...   \n",
       "83357                           0                           0  ...   \n",
       "\n",
       "       Number of phenols  Number of phosphoric acid groups  \\\n",
       "0                      0                                 0   \n",
       "1                      0                                 0   \n",
       "2                      0                                 0   \n",
       "3                      0                                 0   \n",
       "4                      0                                 0   \n",
       "...                  ...                               ...   \n",
       "83353                  1                                 0   \n",
       "83354                  1                                 0   \n",
       "83355                  1                                 0   \n",
       "83356                  1                                 0   \n",
       "83357                  1                                 0   \n",
       "\n",
       "       Number of phosphoric ester groups  Number of piperdine rings  \\\n",
       "0                                      0                          0   \n",
       "1                                      0                          0   \n",
       "2                                      0                          0   \n",
       "3                                      0                          0   \n",
       "4                                      0                          0   \n",
       "...                                  ...                        ...   \n",
       "83353                                  0                          0   \n",
       "83354                                  0                          0   \n",
       "83355                                  0                          0   \n",
       "83356                                  0                          0   \n",
       "83357                                  0                          0   \n",
       "\n",
       "       Number of primary amides  Number of pyridine rings  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             0                         0   \n",
       "...                         ...                       ...   \n",
       "83353                         0                         0   \n",
       "83354                         0                         0   \n",
       "83355                         0                         0   \n",
       "83356                         0                         0   \n",
       "83357                         0                         0   \n",
       "\n",
       "       Number of quaternary nitrogens  Number of thioether  \\\n",
       "0                                   0                    0   \n",
       "1                                   0                    0   \n",
       "2                                   0                    0   \n",
       "3                                   0                    0   \n",
       "4                                   0                    0   \n",
       "...                               ...                  ...   \n",
       "83353                               0                    0   \n",
       "83354                               0                    0   \n",
       "83355                               0                    0   \n",
       "83356                               0                    0   \n",
       "83357                               0                    0   \n",
       "\n",
       "       Number of thiazole rings  \\\n",
       "0                             0   \n",
       "1                             0   \n",
       "2                             0   \n",
       "3                             0   \n",
       "4                             0   \n",
       "...                         ...   \n",
       "83353                         0   \n",
       "83354                         0   \n",
       "83355                         0   \n",
       "83356                         0   \n",
       "83357                         0   \n",
       "\n",
       "       Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)  \n",
       "0                                                      0                                  \n",
       "1                                                      0                                  \n",
       "2                                                      0                                  \n",
       "3                                                      0                                  \n",
       "4                                                      0                                  \n",
       "...                                                  ...                                  \n",
       "83353                                                  0                                  \n",
       "83354                                                  0                                  \n",
       "83355                                                  0                                  \n",
       "83356                                                  0                                  \n",
       "83357                                                  0                                  \n",
       "\n",
       "[83358 rows x 59 columns]"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "groups_df = pd.DataFrame(data_df['groups'].to_list(), columns=funct)\n",
    "groups_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "76a746ae-398f-4144-8cbe-b9b4be036647",
   "metadata": {},
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       "      <td>[18.014429199999995, 30.038839199999984, 31.04...</td>\n",
       "      <td>[0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>(+)-Chelidonine_plasma_1340</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[275.0733, 305.08203, 323.09119, 324.09433, 35...</td>\n",
       "      <td>[0.017, 0.022, 0.028, 0.01, 1.0, 0.029]</td>\n",
       "      <td>[30.03926919999998, 31.04240920000001, 49.0515...</td>\n",
       "      <td>[0.01, 0.028, 0.022, 0.017]</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>(+)-Chelidonine_plasma_1343</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.04521, 143.05431, 159.04745, 161.0602, 16...</td>\n",
       "      <td>[0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...</td>\n",
       "      <td>[18.008909200000005, 31.031639199999972, 31.04...</td>\n",
       "      <td>[0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>(+)-Chelidonine_plasma_1346</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[103.05478, 118.06499, 131.04845, 135.04384, 1...</td>\n",
       "      <td>[0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...</td>\n",
       "      <td>[79.06267919999999, 106.06514919999998, 107.05...</td>\n",
       "      <td>[0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>(+)-Chelidonine_plasma_1349</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.03654, 135.04454, 159.04517, 163.03651, 1...</td>\n",
       "      <td>[0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...</td>\n",
       "      <td>[18.00828919999998, 30.03291919999998, 30.0438...</td>\n",
       "      <td>[0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83353</th>\n",
       "      <td>trans-pterostilbene_plasma_3538</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.01796, 77.03296, 77.03867, 79.02107, 79.05...</td>\n",
       "      <td>[0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...</td>\n",
       "      <td>[15.022540799999973, 16.0322008, 17.0336207999...</td>\n",
       "      <td>[0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83354</th>\n",
       "      <td>trans-pterostilbene_plasma_3540</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[65.03999, 75.02646, 77.02925, 77.03927, 78.04...</td>\n",
       "      <td>[0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...</td>\n",
       "      <td>[31.055850799999973, 45.04376079999997, 46.038...</td>\n",
       "      <td>[0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83355</th>\n",
       "      <td>trans-pterostilbene_plasma_3542</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[91.05325, 103.0554, 105.07047, 107.05009, 111...</td>\n",
       "      <td>[0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...</td>\n",
       "      <td>[15.01973079999999, 31.012410799999998, 31.021...</td>\n",
       "      <td>[0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83356</th>\n",
       "      <td>trans-pterostilbene_plasma_3544</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.02081, 68.99757, 77.03687, 77.04144, 77.04...</td>\n",
       "      <td>[0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...</td>\n",
       "      <td>[15.023320799999993, 16.02811079999998, 16.044...</td>\n",
       "      <td>[0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83357</th>\n",
       "      <td>trans-pterostilbene_plasma_3546</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[51.02621, 68.99291, 75.02341, 77.03965, 78.04...</td>\n",
       "      <td>[0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...</td>\n",
       "      <td>[44.05670079999999, 45.03549079999999, 46.0800...</td>\n",
       "      <td>[0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           spectrum_id  adduct  precursor_mz  \\\n",
       "0          (+)-Chelidonine_plasma_1338  [M+H]+    354.133599   \n",
       "1          (+)-Chelidonine_plasma_1340  [M+H]+    354.133599   \n",
       "2          (+)-Chelidonine_plasma_1343  [M+H]+    354.133599   \n",
       "3          (+)-Chelidonine_plasma_1346  [M+H]+    354.133599   \n",
       "4          (+)-Chelidonine_plasma_1349  [M+H]+    354.133599   \n",
       "...                                ...     ...           ...   \n",
       "83353  trans-pterostilbene_plasma_3538  [M+H]+    257.117221   \n",
       "83354  trans-pterostilbene_plasma_3540  [M+H]+    257.117221   \n",
       "83355  trans-pterostilbene_plasma_3542  [M+H]+    257.117221   \n",
       "83356  trans-pterostilbene_plasma_3544  [M+H]+    257.117221   \n",
       "83357  trans-pterostilbene_plasma_3546  [M+H]+    257.117221   \n",
       "\n",
       "                                                     mzs  \\\n",
       "0      [135.045, 159.04369, 163.04027, 173.0605, 179....   \n",
       "1      [275.0733, 305.08203, 323.09119, 324.09433, 35...   \n",
       "2      [135.04521, 143.05431, 159.04745, 161.0602, 16...   \n",
       "3      [103.05478, 118.06499, 131.04845, 135.04384, 1...   \n",
       "4      [135.03654, 135.04454, 159.04517, 163.03651, 1...   \n",
       "...                                                  ...   \n",
       "83353  [55.01796, 77.03296, 77.03867, 79.02107, 79.05...   \n",
       "83354  [65.03999, 75.02646, 77.02925, 77.03927, 78.04...   \n",
       "83355  [91.05325, 103.0554, 105.07047, 107.05009, 111...   \n",
       "83356  [55.02081, 68.99757, 77.03687, 77.04144, 77.04...   \n",
       "83357  [51.02621, 68.99291, 75.02341, 77.03965, 78.04...   \n",
       "\n",
       "                                             intensities  \\\n",
       "0      [0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...   \n",
       "1                [0.017, 0.022, 0.028, 0.01, 1.0, 0.029]   \n",
       "2      [0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...   \n",
       "3      [0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...   \n",
       "4      [0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...   \n",
       "...                                                  ...   \n",
       "83353  [0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...   \n",
       "83354  [0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...   \n",
       "83355  [0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...   \n",
       "83356  [0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...   \n",
       "83357  [0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...   \n",
       "\n",
       "                                                loss_mzs  \\\n",
       "0      [18.014429199999995, 30.038839199999984, 31.04...   \n",
       "1      [30.03926919999998, 31.04240920000001, 49.0515...   \n",
       "2      [18.008909200000005, 31.031639199999972, 31.04...   \n",
       "3      [79.06267919999999, 106.06514919999998, 107.05...   \n",
       "4      [18.00828919999998, 30.03291919999998, 30.0438...   \n",
       "...                                                  ...   \n",
       "83353  [15.022540799999973, 16.0322008, 17.0336207999...   \n",
       "83354  [31.055850799999973, 45.04376079999997, 46.038...   \n",
       "83355  [15.01973079999999, 31.012410799999998, 31.021...   \n",
       "83356  [15.023320799999993, 16.02811079999998, 16.044...   \n",
       "83357  [44.05670079999999, 45.03549079999999, 46.0800...   \n",
       "\n",
       "                                        loss_intensities  \\\n",
       "0      [0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...   \n",
       "1                            [0.01, 0.028, 0.022, 0.017]   \n",
       "2      [0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...   \n",
       "3      [0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...   \n",
       "4      [0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...   \n",
       "...                                                  ...   \n",
       "83353  [0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...   \n",
       "83354  [0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...   \n",
       "83355  [0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...   \n",
       "83356  [0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...   \n",
       "83357  [0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...   \n",
       "\n",
       "                          inchikey  \\\n",
       "0      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "1      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "2      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "3      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "4      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "...                            ...   \n",
       "83353  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83354  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83355  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83356  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83357  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "\n",
       "                                smiles_preprocessed  num_of_sugars  \\\n",
       "0      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0   \n",
       "1      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0   \n",
       "2      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0   \n",
       "3      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0   \n",
       "4      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0   \n",
       "...                                             ...            ...   \n",
       "83353                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0   \n",
       "83354                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0   \n",
       "83355                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0   \n",
       "83356                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0   \n",
       "83357                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0   \n",
       "\n",
       "                                                  groups  \n",
       "0      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "1      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "2      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "3      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "4      [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, ...  \n",
       "...                                                  ...  \n",
       "83353  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "83354  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "83355  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "83356  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "83357  [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, ...  \n",
       "\n",
       "[83358 rows x 11 columns]"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df=data_df.reset_index()\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "ffa9978f-aa89-49f8-a360-d8f7bd3d9422",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>spectrum_id</th>\n",
       "      <th>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
       "      <th>intensities</th>\n",
       "      <th>loss_mzs</th>\n",
       "      <th>loss_intensities</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>num_of_sugars</th>\n",
       "      <th>...</th>\n",
       "      <th>Number of phenols</th>\n",
       "      <th>Number of phosphoric acid groups</th>\n",
       "      <th>Number of phosphoric ester groups</th>\n",
       "      <th>Number of piperdine rings</th>\n",
       "      <th>Number of primary amides</th>\n",
       "      <th>Number of pyridine rings</th>\n",
       "      <th>Number of quaternary nitrogens</th>\n",
       "      <th>Number of thioether</th>\n",
       "      <th>Number of thiazole rings</th>\n",
       "      <th>Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>(+)-Chelidonine_plasma_1338</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.045, 159.04369, 163.04027, 173.0605, 179....</td>\n",
       "      <td>[0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...</td>\n",
       "      <td>[18.014429199999995, 30.038839199999984, 31.04...</td>\n",
       "      <td>[0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>(+)-Chelidonine_plasma_1340</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[275.0733, 305.08203, 323.09119, 324.09433, 35...</td>\n",
       "      <td>[0.017, 0.022, 0.028, 0.01, 1.0, 0.029]</td>\n",
       "      <td>[30.03926919999998, 31.04240920000001, 49.0515...</td>\n",
       "      <td>[0.01, 0.028, 0.022, 0.017]</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>(+)-Chelidonine_plasma_1343</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.04521, 143.05431, 159.04745, 161.0602, 16...</td>\n",
       "      <td>[0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...</td>\n",
       "      <td>[18.008909200000005, 31.031639199999972, 31.04...</td>\n",
       "      <td>[0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>(+)-Chelidonine_plasma_1346</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[103.05478, 118.06499, 131.04845, 135.04384, 1...</td>\n",
       "      <td>[0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...</td>\n",
       "      <td>[79.06267919999999, 106.06514919999998, 107.05...</td>\n",
       "      <td>[0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>(+)-Chelidonine_plasma_1349</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.03654, 135.04454, 159.04517, 163.03651, 1...</td>\n",
       "      <td>[0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...</td>\n",
       "      <td>[18.00828919999998, 30.03291919999998, 30.0438...</td>\n",
       "      <td>[0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83353</th>\n",
       "      <td>trans-pterostilbene_plasma_3538</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.01796, 77.03296, 77.03867, 79.02107, 79.05...</td>\n",
       "      <td>[0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...</td>\n",
       "      <td>[15.022540799999973, 16.0322008, 17.0336207999...</td>\n",
       "      <td>[0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83354</th>\n",
       "      <td>trans-pterostilbene_plasma_3540</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[65.03999, 75.02646, 77.02925, 77.03927, 78.04...</td>\n",
       "      <td>[0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...</td>\n",
       "      <td>[31.055850799999973, 45.04376079999997, 46.038...</td>\n",
       "      <td>[0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83355</th>\n",
       "      <td>trans-pterostilbene_plasma_3542</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[91.05325, 103.0554, 105.07047, 107.05009, 111...</td>\n",
       "      <td>[0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...</td>\n",
       "      <td>[15.01973079999999, 31.012410799999998, 31.021...</td>\n",
       "      <td>[0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83356</th>\n",
       "      <td>trans-pterostilbene_plasma_3544</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.02081, 68.99757, 77.03687, 77.04144, 77.04...</td>\n",
       "      <td>[0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...</td>\n",
       "      <td>[15.023320799999993, 16.02811079999998, 16.044...</td>\n",
       "      <td>[0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83357</th>\n",
       "      <td>trans-pterostilbene_plasma_3546</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[51.02621, 68.99291, 75.02341, 77.03965, 78.04...</td>\n",
       "      <td>[0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...</td>\n",
       "      <td>[44.05670079999999, 45.03549079999999, 46.0800...</td>\n",
       "      <td>[0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 70 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           spectrum_id  adduct  precursor_mz  \\\n",
       "0          (+)-Chelidonine_plasma_1338  [M+H]+    354.133599   \n",
       "1          (+)-Chelidonine_plasma_1340  [M+H]+    354.133599   \n",
       "2          (+)-Chelidonine_plasma_1343  [M+H]+    354.133599   \n",
       "3          (+)-Chelidonine_plasma_1346  [M+H]+    354.133599   \n",
       "4          (+)-Chelidonine_plasma_1349  [M+H]+    354.133599   \n",
       "...                                ...     ...           ...   \n",
       "83353  trans-pterostilbene_plasma_3538  [M+H]+    257.117221   \n",
       "83354  trans-pterostilbene_plasma_3540  [M+H]+    257.117221   \n",
       "83355  trans-pterostilbene_plasma_3542  [M+H]+    257.117221   \n",
       "83356  trans-pterostilbene_plasma_3544  [M+H]+    257.117221   \n",
       "83357  trans-pterostilbene_plasma_3546  [M+H]+    257.117221   \n",
       "\n",
       "                                                     mzs  \\\n",
       "0      [135.045, 159.04369, 163.04027, 173.0605, 179....   \n",
       "1      [275.0733, 305.08203, 323.09119, 324.09433, 35...   \n",
       "2      [135.04521, 143.05431, 159.04745, 161.0602, 16...   \n",
       "3      [103.05478, 118.06499, 131.04845, 135.04384, 1...   \n",
       "4      [135.03654, 135.04454, 159.04517, 163.03651, 1...   \n",
       "...                                                  ...   \n",
       "83353  [55.01796, 77.03296, 77.03867, 79.02107, 79.05...   \n",
       "83354  [65.03999, 75.02646, 77.02925, 77.03927, 78.04...   \n",
       "83355  [91.05325, 103.0554, 105.07047, 107.05009, 111...   \n",
       "83356  [55.02081, 68.99757, 77.03687, 77.04144, 77.04...   \n",
       "83357  [51.02621, 68.99291, 75.02341, 77.03965, 78.04...   \n",
       "\n",
       "                                             intensities  \\\n",
       "0      [0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...   \n",
       "1                [0.017, 0.022, 0.028, 0.01, 1.0, 0.029]   \n",
       "2      [0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...   \n",
       "3      [0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...   \n",
       "4      [0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...   \n",
       "...                                                  ...   \n",
       "83353  [0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...   \n",
       "83354  [0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...   \n",
       "83355  [0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...   \n",
       "83356  [0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...   \n",
       "83357  [0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...   \n",
       "\n",
       "                                                loss_mzs  \\\n",
       "0      [18.014429199999995, 30.038839199999984, 31.04...   \n",
       "1      [30.03926919999998, 31.04240920000001, 49.0515...   \n",
       "2      [18.008909200000005, 31.031639199999972, 31.04...   \n",
       "3      [79.06267919999999, 106.06514919999998, 107.05...   \n",
       "4      [18.00828919999998, 30.03291919999998, 30.0438...   \n",
       "...                                                  ...   \n",
       "83353  [15.022540799999973, 16.0322008, 17.0336207999...   \n",
       "83354  [31.055850799999973, 45.04376079999997, 46.038...   \n",
       "83355  [15.01973079999999, 31.012410799999998, 31.021...   \n",
       "83356  [15.023320799999993, 16.02811079999998, 16.044...   \n",
       "83357  [44.05670079999999, 45.03549079999999, 46.0800...   \n",
       "\n",
       "                                        loss_intensities  \\\n",
       "0      [0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...   \n",
       "1                            [0.01, 0.028, 0.022, 0.017]   \n",
       "2      [0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...   \n",
       "3      [0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...   \n",
       "4      [0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...   \n",
       "...                                                  ...   \n",
       "83353  [0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...   \n",
       "83354  [0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...   \n",
       "83355  [0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...   \n",
       "83356  [0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...   \n",
       "83357  [0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...   \n",
       "\n",
       "                          inchikey  \\\n",
       "0      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "1      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "2      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "3      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "4      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "...                            ...   \n",
       "83353  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83354  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83355  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83356  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83357  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "\n",
       "                                smiles_preprocessed  num_of_sugars  ...  \\\n",
       "0      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "1      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "2      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "3      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "4      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "...                                             ...            ...  ...   \n",
       "83353                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83354                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83355                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83356                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83357                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "\n",
       "      Number of phenols  Number of phosphoric acid groups  \\\n",
       "0                     0                                 0   \n",
       "1                     0                                 0   \n",
       "2                     0                                 0   \n",
       "3                     0                                 0   \n",
       "4                     0                                 0   \n",
       "...                 ...                               ...   \n",
       "83353                 1                                 0   \n",
       "83354                 1                                 0   \n",
       "83355                 1                                 0   \n",
       "83356                 1                                 0   \n",
       "83357                 1                                 0   \n",
       "\n",
       "       Number of phosphoric ester groups  Number of piperdine rings  \\\n",
       "0                                      0                          0   \n",
       "1                                      0                          0   \n",
       "2                                      0                          0   \n",
       "3                                      0                          0   \n",
       "4                                      0                          0   \n",
       "...                                  ...                        ...   \n",
       "83353                                  0                          0   \n",
       "83354                                  0                          0   \n",
       "83355                                  0                          0   \n",
       "83356                                  0                          0   \n",
       "83357                                  0                          0   \n",
       "\n",
       "       Number of primary amides  Number of pyridine rings  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             0                         0   \n",
       "...                         ...                       ...   \n",
       "83353                         0                         0   \n",
       "83354                         0                         0   \n",
       "83355                         0                         0   \n",
       "83356                         0                         0   \n",
       "83357                         0                         0   \n",
       "\n",
       "       Number of quaternary nitrogens  Number of thioether  \\\n",
       "0                                   0                    0   \n",
       "1                                   0                    0   \n",
       "2                                   0                    0   \n",
       "3                                   0                    0   \n",
       "4                                   0                    0   \n",
       "...                               ...                  ...   \n",
       "83353                               0                    0   \n",
       "83354                               0                    0   \n",
       "83355                               0                    0   \n",
       "83356                               0                    0   \n",
       "83357                               0                    0   \n",
       "\n",
       "       Number of thiazole rings  \\\n",
       "0                             0   \n",
       "1                             0   \n",
       "2                             0   \n",
       "3                             0   \n",
       "4                             0   \n",
       "...                         ...   \n",
       "83353                         0   \n",
       "83354                         0   \n",
       "83355                         0   \n",
       "83356                         0   \n",
       "83357                         0   \n",
       "\n",
       "       Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)  \n",
       "0                                                      0                                  \n",
       "1                                                      0                                  \n",
       "2                                                      0                                  \n",
       "3                                                      0                                  \n",
       "4                                                      0                                  \n",
       "...                                                  ...                                  \n",
       "83353                                                  0                                  \n",
       "83354                                                  0                                  \n",
       "83355                                                  0                                  \n",
       "83356                                                  0                                  \n",
       "83357                                                  0                                  \n",
       "\n",
       "[83358 rows x 70 columns]"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df=data_df.join(groups_df,how=\"outer\")\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "ee6d07fe-e58d-4871-9387-3df55e2012c3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
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       "        ... \n",
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       "83354    0.0\n",
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       "Name: num_of_sugars, Length: 83358, dtype: float64"
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     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df.iloc[:, 9]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "17720b83-9653-41a7-aaca-74450cdfd44b",
   "metadata": {},
   "outputs": [
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       "      <th></th>\n",
       "      <th>spectrum_id</th>\n",
       "      <th>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
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       "      <td>(+)-Chelidonine_plasma_1338</td>\n",
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       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
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       "      <td>[0.017, 0.022, 0.028, 0.01, 1.0, 0.029]</td>\n",
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       "      <td>[0.01, 0.028, 0.022, 0.017]</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>(+)-Chelidonine_plasma_1343</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.04521, 143.05431, 159.04745, 161.0602, 16...</td>\n",
       "      <td>[0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...</td>\n",
       "      <td>[18.008909200000005, 31.031639199999972, 31.04...</td>\n",
       "      <td>[0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
       "      <td>CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>(+)-Chelidonine_plasma_1346</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[103.05478, 118.06499, 131.04845, 135.04384, 1...</td>\n",
       "      <td>[0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...</td>\n",
       "      <td>[79.06267919999999, 106.06514919999998, 107.05...</td>\n",
       "      <td>[0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...</td>\n",
       "      <td>GHKISGDRQRSCII-UHFFFAOYNA-N</td>\n",
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       "      <th>4</th>\n",
       "      <td>(+)-Chelidonine_plasma_1349</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>354.133599</td>\n",
       "      <td>[135.03654, 135.04454, 159.04517, 163.03651, 1...</td>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>83353</th>\n",
       "      <td>trans-pterostilbene_plasma_3538</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.01796, 77.03296, 77.03867, 79.02107, 79.05...</td>\n",
       "      <td>[0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...</td>\n",
       "      <td>[15.022540799999973, 16.0322008, 17.0336207999...</td>\n",
       "      <td>[0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>83354</th>\n",
       "      <td>trans-pterostilbene_plasma_3540</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[65.03999, 75.02646, 77.02925, 77.03927, 78.04...</td>\n",
       "      <td>[0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...</td>\n",
       "      <td>[31.055850799999973, 45.04376079999997, 46.038...</td>\n",
       "      <td>[0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>83355</th>\n",
       "      <td>trans-pterostilbene_plasma_3542</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[91.05325, 103.0554, 105.07047, 107.05009, 111...</td>\n",
       "      <td>[0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...</td>\n",
       "      <td>[15.01973079999999, 31.012410799999998, 31.021...</td>\n",
       "      <td>[0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83356</th>\n",
       "      <td>trans-pterostilbene_plasma_3544</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[55.02081, 68.99757, 77.03687, 77.04144, 77.04...</td>\n",
       "      <td>[0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...</td>\n",
       "      <td>[15.023320799999993, 16.02811079999998, 16.044...</td>\n",
       "      <td>[0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83357</th>\n",
       "      <td>trans-pterostilbene_plasma_3546</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>257.117221</td>\n",
       "      <td>[51.02621, 68.99291, 75.02341, 77.03965, 78.04...</td>\n",
       "      <td>[0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...</td>\n",
       "      <td>[44.05670079999999, 45.03549079999999, 46.0800...</td>\n",
       "      <td>[0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...</td>\n",
       "      <td>VLEUZFDZJKSGMX-ONEGZZNKSA-N</td>\n",
       "      <td>COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
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       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 69 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           spectrum_id  adduct  precursor_mz  \\\n",
       "0          (+)-Chelidonine_plasma_1338  [M+H]+    354.133599   \n",
       "1          (+)-Chelidonine_plasma_1340  [M+H]+    354.133599   \n",
       "2          (+)-Chelidonine_plasma_1343  [M+H]+    354.133599   \n",
       "3          (+)-Chelidonine_plasma_1346  [M+H]+    354.133599   \n",
       "4          (+)-Chelidonine_plasma_1349  [M+H]+    354.133599   \n",
       "...                                ...     ...           ...   \n",
       "83353  trans-pterostilbene_plasma_3538  [M+H]+    257.117221   \n",
       "83354  trans-pterostilbene_plasma_3540  [M+H]+    257.117221   \n",
       "83355  trans-pterostilbene_plasma_3542  [M+H]+    257.117221   \n",
       "83356  trans-pterostilbene_plasma_3544  [M+H]+    257.117221   \n",
       "83357  trans-pterostilbene_plasma_3546  [M+H]+    257.117221   \n",
       "\n",
       "                                                     mzs  \\\n",
       "0      [135.045, 159.04369, 163.04027, 173.0605, 179....   \n",
       "1      [275.0733, 305.08203, 323.09119, 324.09433, 35...   \n",
       "2      [135.04521, 143.05431, 159.04745, 161.0602, 16...   \n",
       "3      [103.05478, 118.06499, 131.04845, 135.04384, 1...   \n",
       "4      [135.03654, 135.04454, 159.04517, 163.03651, 1...   \n",
       "...                                                  ...   \n",
       "83353  [55.01796, 77.03296, 77.03867, 79.02107, 79.05...   \n",
       "83354  [65.03999, 75.02646, 77.02925, 77.03927, 78.04...   \n",
       "83355  [91.05325, 103.0554, 105.07047, 107.05009, 111...   \n",
       "83356  [55.02081, 68.99757, 77.03687, 77.04144, 77.04...   \n",
       "83357  [51.02621, 68.99291, 75.02341, 77.03965, 78.04...   \n",
       "\n",
       "                                             intensities  \\\n",
       "0      [0.053, 0.011, 0.027, 0.015, 0.011, 0.034, 0.1...   \n",
       "1                [0.017, 0.022, 0.028, 0.01, 1.0, 0.029]   \n",
       "2      [0.101, 0.011, 0.012, 0.035, 0.081, 0.013, 0.0...   \n",
       "3      [0.016, 0.01, 0.027, 0.034, 0.01, 0.016, 0.01,...   \n",
       "4      [0.01, 0.047, 0.011, 0.016, 0.017, 0.014, 0.11...   \n",
       "...                                                  ...   \n",
       "83353  [0.021, 0.021, 0.046, 0.011, 0.046, 0.02, 0.01...   \n",
       "83354  [0.057, 0.011, 0.011, 0.115, 0.013, 0.043, 0.0...   \n",
       "83355  [0.015, 0.01, 0.058, 0.021, 0.034, 0.02, 0.015...   \n",
       "83356  [0.011, 0.01, 0.021, 0.018, 0.011, 0.013, 0.03...   \n",
       "83357  [0.021, 0.018, 0.022, 0.198, 0.021, 0.027, 0.0...   \n",
       "\n",
       "                                                loss_mzs  \\\n",
       "0      [18.014429199999995, 30.038839199999984, 31.04...   \n",
       "1      [30.03926919999998, 31.04240920000001, 49.0515...   \n",
       "2      [18.008909200000005, 31.031639199999972, 31.04...   \n",
       "3      [79.06267919999999, 106.06514919999998, 107.05...   \n",
       "4      [18.00828919999998, 30.03291919999998, 30.0438...   \n",
       "...                                                  ...   \n",
       "83353  [15.022540799999973, 16.0322008, 17.0336207999...   \n",
       "83354  [31.055850799999973, 45.04376079999997, 46.038...   \n",
       "83355  [15.01973079999999, 31.012410799999998, 31.021...   \n",
       "83356  [15.023320799999993, 16.02811079999998, 16.044...   \n",
       "83357  [44.05670079999999, 45.03549079999999, 46.0800...   \n",
       "\n",
       "                                        loss_intensities  \\\n",
       "0      [0.02, 0.045, 0.166, 0.026, 0.146, 0.041, 0.01...   \n",
       "1                            [0.01, 0.028, 0.022, 0.017]   \n",
       "2      [0.016, 0.02, 0.012, 0.013, 0.028, 0.023, 0.01...   \n",
       "3      [0.023, 0.02, 0.063, 0.065, 0.038, 0.014, 0.01...   \n",
       "4      [0.028, 0.025, 0.015, 0.148, 0.03, 0.126, 0.04...   \n",
       "...                                                  ...   \n",
       "83353  [0.259, 0.209, 0.02, 0.017, 0.034, 0.038, 0.01...   \n",
       "83354  [0.026, 0.011, 0.012, 0.013, 0.037, 0.016, 0.0...   \n",
       "83355  [0.043, 0.016, 0.018, 0.046, 0.012, 0.03, 0.03...   \n",
       "83356  [0.231, 0.163, 0.02, 0.01, 0.225, 0.011, 0.014...   \n",
       "83357  [0.021, 0.017, 0.033, 0.024, 0.021, 0.017, 0.0...   \n",
       "\n",
       "                          inchikey  \\\n",
       "0      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "1      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "2      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "3      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "4      GHKISGDRQRSCII-UHFFFAOYNA-N   \n",
       "...                            ...   \n",
       "83353  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83354  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83355  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83356  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "83357  VLEUZFDZJKSGMX-ONEGZZNKSA-N   \n",
       "\n",
       "                                smiles_preprocessed  num_of_sugars  ...  \\\n",
       "0      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "1      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "2      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "3      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "4      CN1Cc2c(ccc3c2OCO3)C2C(O)Cc3cc4c(cc3C21)OCO4            0.0  ...   \n",
       "...                                             ...            ...  ...   \n",
       "83353                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83354                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83355                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83356                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "83357                COc1cc(C=Cc2ccc(O)cc2)cc(OC)c1            0.0  ...   \n",
       "\n",
       "       Number of phenols  Number of phosphoric acid groups  \\\n",
       "0                      0                                 0   \n",
       "1                      0                                 0   \n",
       "2                      0                                 0   \n",
       "3                      0                                 0   \n",
       "4                      0                                 0   \n",
       "...                  ...                               ...   \n",
       "83353                  1                                 0   \n",
       "83354                  1                                 0   \n",
       "83355                  1                                 0   \n",
       "83356                  1                                 0   \n",
       "83357                  1                                 0   \n",
       "\n",
       "       Number of phosphoric ester groups  Number of piperdine rings  \\\n",
       "0                                      0                          0   \n",
       "1                                      0                          0   \n",
       "2                                      0                          0   \n",
       "3                                      0                          0   \n",
       "4                                      0                          0   \n",
       "...                                  ...                        ...   \n",
       "83353                                  0                          0   \n",
       "83354                                  0                          0   \n",
       "83355                                  0                          0   \n",
       "83356                                  0                          0   \n",
       "83357                                  0                          0   \n",
       "\n",
       "       Number of primary amides  Number of pyridine rings  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             0                         0   \n",
       "...                         ...                       ...   \n",
       "83353                         0                         0   \n",
       "83354                         0                         0   \n",
       "83355                         0                         0   \n",
       "83356                         0                         0   \n",
       "83357                         0                         0   \n",
       "\n",
       "       Number of quaternary nitrogens  Number of thioether  \\\n",
       "0                                   0                    0   \n",
       "1                                   0                    0   \n",
       "2                                   0                    0   \n",
       "3                                   0                    0   \n",
       "4                                   0                    0   \n",
       "...                               ...                  ...   \n",
       "83353                               0                    0   \n",
       "83354                               0                    0   \n",
       "83355                               0                    0   \n",
       "83356                               0                    0   \n",
       "83357                               0                    0   \n",
       "\n",
       "       Number of thiazole rings  \\\n",
       "0                             0   \n",
       "1                             0   \n",
       "2                             0   \n",
       "3                             0   \n",
       "4                             0   \n",
       "...                         ...   \n",
       "83353                         0   \n",
       "83354                         0   \n",
       "83355                         0   \n",
       "83356                         0   \n",
       "83357                         0   \n",
       "\n",
       "       Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)  \n",
       "0                                                      0                                  \n",
       "1                                                      0                                  \n",
       "2                                                      0                                  \n",
       "3                                                      0                                  \n",
       "4                                                      0                                  \n",
       "...                                                  ...                                  \n",
       "83353                                                  0                                  \n",
       "83354                                                  0                                  \n",
       "83355                                                  0                                  \n",
       "83356                                                  0                                  \n",
       "83357                                                  0                                  \n",
       "\n",
       "[83358 rows x 69 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df=data_df.drop([\"groups\"], axis=1)\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "9cef894d-ed35-4890-b285-ab58f3141ecc",
   "metadata": {},
   "outputs": [],
   "source": [
    "group_array=data_df.iloc[:, 9:]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "3e0445fe-57f2-468b-ae56-693185e34c95",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "23.0"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "group_array.to_numpy().max()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "4eac99c3-72b4-4075-bc14-21b36bae2df8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(83358, 60)"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "group_array.to_numpy().shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "bcaf7863-1859-4216-adce-5b89b3e028e3",
   "metadata": {},
   "outputs": [],
   "source": [
    "train_int=group_array.to_numpy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "9bd5b60e-8afb-4097-906c-7700e733f9fc",
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "def make_float_targets(k):\n",
    "  targets = np.zeros(k, dtype=np.float32)\n",
    "  start = 1.0 / (2 * k)  # like 0.125\n",
    "  delta = 1.0 / k        # like 0.250\n",
    "  for i in range(k):\n",
    "    targets[i] = start + (i * delta) \n",
    "  return targets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "7365d5dc-2439-4535-917b-4ecfe7d83eef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0.02083333, 0.0625    , 0.10416666, 0.14583333, 0.1875    ,\n",
       "       0.22916667, 0.27083334, 0.3125    , 0.35416666, 0.39583334,\n",
       "       0.4375    , 0.47916666, 0.5208333 , 0.5625    , 0.6041667 ,\n",
       "       0.6458333 , 0.6875    , 0.7291667 , 0.7708333 , 0.8125    ,\n",
       "       0.8541667 , 0.8958333 , 0.9375    , 0.9791667 ], dtype=float32)"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "make_float_targets(24)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "8493780d-a13a-48f4-85c5-3b119a4c9cb1",
   "metadata": {},
   "outputs": [],
   "source": [
    "ordinal=make_float_targets(24)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "6008ecab-bbb4-428a-be9a-206f060e7959",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.104166664"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ordinal[2]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ace47012-0c76-4f4b-89dc-dd05a5b7b9f7",
   "metadata": {
    "tags": []
   },
   "source": [
    "#data_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/nist/tcn_seq/all_HRMS_train_17012023_cddd_refine_s.tsv\",sep=\"\\t\")\n",
    "data_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/nist/tcn_seq/all_HRMS_valid_17012023_cddd_refine.tsv\",sep=\"\\t\")\n",
    "#data_df = pd.read_csv(\"/Users/delser/mass2smiles/retrain/nist/all_HRMS_validation_16122022_cddd_refine.tsv\",sep=\"\\t\")\n",
    "data_df=data_df.dropna()\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "id": "ad505791-43bf-48ae-9f06-1fdcb9c8678f",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
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       "      <th>spectrum_id</th>\n",
       "      <th>adduct</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>mzs</th>\n",
       "      <th>intensities</th>\n",
       "      <th>loss_mzs</th>\n",
       "      <th>loss_intensities</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>smiles_preprocessed</th>\n",
       "      <th>num_of_sugars</th>\n",
       "      <th>...</th>\n",
       "      <th>Number of phenols</th>\n",
       "      <th>Number of phosphoric acid groups</th>\n",
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       "      <th>Number of piperdine rings</th>\n",
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       "      <th>Number of pyridine rings</th>\n",
       "      <th>Number of quaternary nitrogens</th>\n",
       "      <th>Number of thioether</th>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42002</th>\n",
       "      <td>CCMSLIB00006673970</td>\n",
       "      <td>[M-H2O+H]+</td>\n",
       "      <td>120.04400</td>\n",
       "      <td>[50.716675, 52.040119, 54.318787, 54.323826, 5...</td>\n",
       "      <td>[0.024994948916947344, 0.02298565382566748, 0....</td>\n",
       "      <td>[16.09871799999999, 22.15638899999999, 22.1781...</td>\n",
       "      <td>[0.025422772046311003, 0.027329820729600093, 0...</td>\n",
       "      <td>RWZYAGGXGHYGMB-UHFFFAOYSA-N</td>\n",
       "      <td>Nc1ccccc1C(=O)O</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77441</th>\n",
       "      <td>NIST900303</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>174.05500</td>\n",
       "      <td>[50.0153, 51.0231, 52.0184, 53.0388, 61.0075, ...</td>\n",
       "      <td>[0.2785985985985986, 1.0, 0.016596596596596593...</td>\n",
       "      <td>[27.994699999999995, 44.01480000000001, 45.010...</td>\n",
       "      <td>[1.0, 0.07220220220220219, 0.4573973973973974,...</td>\n",
       "      <td>KVMMIDQDXZOPAB-UHFFFAOYSA-N</td>\n",
       "      <td>O=C(O)c1cc2ccccc2cn1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54204</th>\n",
       "      <td>DB#=MSBNK-Stacey_Reinke_ECU-Stacey_Reinke_pos_...</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>133.09715</td>\n",
       "      <td>[53.0028, 56.3404, 59.9308, 73.1201, 114.372, ...</td>\n",
       "      <td>[1.0, 0.644, 0.6709999999999999, 0.738, 0.65, ...</td>\n",
       "      <td>[18.72515, 59.977050000000006, 73.16635, 76.75...</td>\n",
       "      <td>[0.65, 0.738, 0.6709999999999999, 0.644, 1.0]</td>\n",
       "      <td>AHLPHDHHMVZTML-UHFFFAOYSA-N</td>\n",
       "      <td>NCCCC(N)C(=O)O</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63496</th>\n",
       "      <td>NIST323648</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>384.99490</td>\n",
       "      <td>[51.9398, 55.9342, 59.9663, 62.945, 63.0262, 6...</td>\n",
       "      <td>[0.0365965965965966, 0.0662962962962963, 0.024...</td>\n",
       "      <td>[34.12209999999999, 35.12299999999999, 45.1438...</td>\n",
       "      <td>[0.017197197197197197, 0.027797797797797796, 0...</td>\n",
       "      <td>RIZMRRKBZQXFOY-UHFFFAOYSA-N</td>\n",
       "      <td>CCOP(=S)(OCC)SCSP(=S)(OCC)OCC</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>78013</th>\n",
       "      <td>NIST923817</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>245.16480</td>\n",
       "      <td>[50.0153, 51.0232, 53.0388, 54.034, 55.0545, 5...</td>\n",
       "      <td>[0.031901901901901904, 0.1926026026026026, 0.0...</td>\n",
       "      <td>[26.99090000000001, 27.994400000000013, 45.020...</td>\n",
       "      <td>[0.0198998998998999, 1.0, 0.263003003003003, 0...</td>\n",
       "      <td>CUANCTHYEDWUMU-KBPBESRZSA-N</td>\n",
       "      <td>O=C1NC(Cc2ccccc2)CN2CCCCC12</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83358 rows × 69 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                             spectrum_id      adduct  \\\n",
       "24219                                 CCMSLIB00005726986      [M+H]+   \n",
       "36520                                 CCMSLIB00006115565      [M+H]+   \n",
       "57525                                         NIST114555      [M+H]+   \n",
       "18453                                 CCMSLIB00004714529      [M+H]+   \n",
       "57589                                         NIST116969      [M+H]+   \n",
       "...                                                  ...         ...   \n",
       "42002                                 CCMSLIB00006673970  [M-H2O+H]+   \n",
       "77441                                         NIST900303      [M+H]+   \n",
       "54204  DB#=MSBNK-Stacey_Reinke_ECU-Stacey_Reinke_pos_...      [M+H]+   \n",
       "63496                                         NIST323648      [M+H]+   \n",
       "78013                                         NIST923817      [M+H]+   \n",
       "\n",
       "       precursor_mz                                                mzs  \\\n",
       "24219     342.07700  [53.002701, 69.069901, 70.039902, 122.999496, ...   \n",
       "36520     466.31700  [55.0541, 60.922901, 67.054001, 70.752098, 71....   \n",
       "57525     420.96970  [50.0148, 51.0227, 53.002, 53.0383, 55.0175, 5...   \n",
       "18453     485.31100  [53.038925, 55.018158, 55.05455, 56.049793, 56...   \n",
       "57589     311.15540  [50.0149, 51.0227, 54.0336, 57.0132, 58.065, 5...   \n",
       "...             ...                                                ...   \n",
       "42002     120.04400  [50.716675, 52.040119, 54.318787, 54.323826, 5...   \n",
       "77441     174.05500  [50.0153, 51.0231, 52.0184, 53.0388, 61.0075, ...   \n",
       "54204     133.09715  [53.0028, 56.3404, 59.9308, 73.1201, 114.372, ...   \n",
       "63496     384.99490  [51.9398, 55.9342, 59.9663, 62.945, 63.0262, 6...   \n",
       "78013     245.16480  [50.0153, 51.0232, 53.0388, 54.034, 55.0545, 5...   \n",
       "\n",
       "                                             intensities  \\\n",
       "24219  [0.010063446472489251, 0.09171604559744392, 0....   \n",
       "36520  [0.16146962465733394, 0.06493402643554223, 0.0...   \n",
       "57525  [0.032002002002002, 0.07480480480480481, 0.011...   \n",
       "18453  [0.056912830000000005, 0.02006357, 0.355427699...   \n",
       "57589  [0.023103103103103102, 0.0355955955955956, 0.0...   \n",
       "...                                                  ...   \n",
       "42002  [0.024994948916947344, 0.02298565382566748, 0....   \n",
       "77441  [0.2785985985985986, 1.0, 0.016596596596596593...   \n",
       "54204  [1.0, 0.644, 0.6709999999999999, 0.738, 0.65, ...   \n",
       "63496  [0.0365965965965966, 0.0662962962962963, 0.024...   \n",
       "78013  [0.031901901901901904, 0.1926026026026026, 0.0...   \n",
       "\n",
       "                                                loss_mzs  \\\n",
       "24219  [151.11110299999999, 169.110798, 169.121601, 1...   \n",
       "36520  [54.03019599999999, 80.65830900000003, 129.063...   \n",
       "57525  [18.01139999999998, 32.03190000000001, 36.0030...   \n",
       "18453  [244.40157599999998, 246.13166299999997, 258.1...   \n",
       "57589  [17.007499999999993, 18.010699999999986, 31.04...   \n",
       "...                                                  ...   \n",
       "42002  [16.09871799999999, 22.15638899999999, 22.1781...   \n",
       "77441  [27.994699999999995, 44.01480000000001, 45.010...   \n",
       "54204  [18.72515, 59.977050000000006, 73.16635, 76.75...   \n",
       "63496  [34.12209999999999, 35.12299999999999, 45.1438...   \n",
       "78013  [26.99090000000001, 27.994400000000013, 45.020...   \n",
       "\n",
       "                                        loss_intensities  \\\n",
       "24219  [0.014194703372154123, 0.014742377244715292, 0...   \n",
       "36520  [0.28292792134215433, 0.08448161553784861, 0.3...   \n",
       "57525  [1.0, 1.0, 0.0533033033033033, 0.0147047047047...   \n",
       "18453  [0.024042059999999997, 0.03417382, 0.02122381,...   \n",
       "57589  [0.035005005005005, 1.0, 0.2139039039039039, 0...   \n",
       "...                                                  ...   \n",
       "42002  [0.025422772046311003, 0.027329820729600093, 0...   \n",
       "77441  [1.0, 0.07220220220220219, 0.4573973973973974,...   \n",
       "54204      [0.65, 0.738, 0.6709999999999999, 0.644, 1.0]   \n",
       "63496  [0.017197197197197197, 0.027797797797797796, 0...   \n",
       "78013  [0.0198998998998999, 1.0, 0.263003003003003, 0...   \n",
       "\n",
       "                          inchikey  \\\n",
       "24219  STJLVHWMYQXCPB-UHFFFAOYSA-N   \n",
       "36520  RFDAIACWWDREDC-FRVQLJSFSA-N   \n",
       "57525  GKDKOMAJZATYAY-XCMZKKERSA-N   \n",
       "18453  JECOCDKQCZSANH-RFKAOMIISA-N   \n",
       "57589  PTJADDMMFYXMMG-IBGZPJMESA-N   \n",
       "...                            ...   \n",
       "42002  RWZYAGGXGHYGMB-UHFFFAOYSA-N   \n",
       "77441  KVMMIDQDXZOPAB-UHFFFAOYSA-N   \n",
       "54204  AHLPHDHHMVZTML-UHFFFAOYSA-N   \n",
       "63496  RIZMRRKBZQXFOY-UHFFFAOYSA-N   \n",
       "78013  CUANCTHYEDWUMU-KBPBESRZSA-N   \n",
       "\n",
       "                                     smiles_preprocessed  num_of_sugars  ...  \\\n",
       "24219               CCCC1COC(Cn2cncn2)(c2ccc(Cl)cc2Cl)O1            0.0  ...   \n",
       "36520  CC(CCC(=O)NCC(=O)O)C1CCC2C3C(O)CC4CC(O)CCC4(C)...            0.0  ...   \n",
       "57525  O=P(O)(O)OC1C(O)C(O)C(O)C(OP(=O)(O)O)C1OP(=O)(O)O            0.0  ...   \n",
       "18453  C=C1C(OC2OC(CO)C(O)C(O)C2O)CC2C(C)(C)C(O)CCC2(...            1.0  ...   \n",
       "57589               CNCCCC1(c2ccc(F)cc2)OCc2cc(C#N)ccc21            0.0  ...   \n",
       "...                                                  ...            ...  ...   \n",
       "42002                                    Nc1ccccc1C(=O)O            0.0  ...   \n",
       "77441                               O=C(O)c1cc2ccccc2cn1            0.0  ...   \n",
       "54204                                     NCCCC(N)C(=O)O            0.0  ...   \n",
       "63496                      CCOP(=S)(OCC)SCSP(=S)(OCC)OCC            0.0  ...   \n",
       "78013                        O=C1NC(Cc2ccccc2)CN2CCCCC12            0.0  ...   \n",
       "\n",
       "       Number of phenols  Number of phosphoric acid groups  \\\n",
       "24219                  0                                 0   \n",
       "36520                  0                                 0   \n",
       "57525                  0                                 3   \n",
       "18453                  0                                 0   \n",
       "57589                  0                                 0   \n",
       "...                  ...                               ...   \n",
       "42002                  0                                 0   \n",
       "77441                  0                                 0   \n",
       "54204                  0                                 0   \n",
       "63496                  0                                 0   \n",
       "78013                  0                                 0   \n",
       "\n",
       "       Number of phosphoric ester groups  Number of piperdine rings  \\\n",
       "24219                                  0                          0   \n",
       "36520                                  0                          0   \n",
       "57525                                  3                          0   \n",
       "18453                                  0                          0   \n",
       "57589                                  0                          0   \n",
       "...                                  ...                        ...   \n",
       "42002                                  0                          0   \n",
       "77441                                  0                          0   \n",
       "54204                                  0                          0   \n",
       "63496                                  0                          0   \n",
       "78013                                  0                          1   \n",
       "\n",
       "       Number of primary amides  Number of pyridine rings  \\\n",
       "24219                         0                         0   \n",
       "36520                         0                         0   \n",
       "57525                         0                         0   \n",
       "18453                         0                         0   \n",
       "57589                         0                         0   \n",
       "...                         ...                       ...   \n",
       "42002                         0                         0   \n",
       "77441                         0                         1   \n",
       "54204                         0                         0   \n",
       "63496                         0                         0   \n",
       "78013                         0                         0   \n",
       "\n",
       "       Number of quaternary nitrogens  Number of thioether  \\\n",
       "24219                               0                    0   \n",
       "36520                               0                    0   \n",
       "57525                               0                    0   \n",
       "18453                               0                    0   \n",
       "57589                               0                    0   \n",
       "...                               ...                  ...   \n",
       "42002                               0                    0   \n",
       "77441                               0                    0   \n",
       "54204                               0                    0   \n",
       "63496                               0                    0   \n",
       "78013                               0                    0   \n",
       "\n",
       "       Number of thiazole rings  \\\n",
       "24219                         0   \n",
       "36520                         0   \n",
       "57525                         0   \n",
       "18453                         0   \n",
       "57589                         0   \n",
       "...                         ...   \n",
       "42002                         0   \n",
       "77441                         0   \n",
       "54204                         0   \n",
       "63496                         0   \n",
       "78013                         0   \n",
       "\n",
       "       Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)  \n",
       "24219                                                  0                                  \n",
       "36520                                                  0                                  \n",
       "57525                                                  0                                  \n",
       "18453                                                  0                                  \n",
       "57589                                                  1                                  \n",
       "...                                                  ...                                  \n",
       "42002                                                  0                                  \n",
       "77441                                                  0                                  \n",
       "54204                                                  0                                  \n",
       "63496                                                  0                                  \n",
       "78013                                                  0                                  \n",
       "\n",
       "[83358 rows x 69 columns]"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data_df = data_df.sample(frac = 1)\n",
    "data_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6ccee1e1-c67d-4333-a550-c2631f9d800e",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "3db3752f-f386-421a-87ba-7f774e3c84f1",
   "metadata": {},
   "outputs": [],
   "source": [
    "data_df.to_csv('/Users/delser/mass2smiles/retrain/nist/tcn_seq/all_HRMS_train_24012023_cddd_refine_s.tsv',sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "id": "0a4f7a1b-e86b-4eb8-8604-e71d5b2ec20a",
   "metadata": {},
   "outputs": [],
   "source": [
    "#data_df=data_df.drop([\"Unnamed: 0\"], axis=1)\n",
    "\n",
    "group_array=data_df.iloc[:, 9:]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "id": "a370897c-0005-4112-9d71-cd454d274000",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(83358, 60)"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "train_int=group_array.to_numpy()\n",
    "ordinal=make_float_targets(24)\n",
    "all_arr=[]\n",
    "for sample in train_int:\n",
    "    cache=[]\n",
    "    for i in sample:\n",
    "        cache.append(ordinal[int(i)])\n",
    "    x=np.array(cache)\n",
    "    all_arr.append(x)\n",
    "    \n",
    "train_y=np.stack(all_arr)   \n",
    "train_y.shape  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "id": "76eaccbe-6e34-4609-9a74-6c5c976f28f3",
   "metadata": {},
   "outputs": [],
   "source": [
    "np.save('y1_all_HRMS_train_24012023_cddd.npy',train_y)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d9a45c45-3669-4b3e-8495-9311feeb004b",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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