hin_generation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import networkx as nx\n",
    "\n",
    "path = 'path-to-data-repository'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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>doi</th>\n",
       "      <th>bioActivity</th>\n",
       "      <th>collectionSpecie</th>\n",
       "      <th>collectionSite</th>\n",
       "      <th>collectionType</th>\n",
       "      <th>molType</th>\n",
       "      <th>molecularMass</th>\n",
       "      <th>monoisotropicMass</th>\n",
       "      <th>cLogP</th>\n",
       "      <th>tpsa</th>\n",
       "      <th>numberOfLipinskiViolations</th>\n",
       "      <th>numberOfH_bondAcceptors</th>\n",
       "      <th>numberOfH_bondDonors</th>\n",
       "      <th>numberOfRotableBonds</th>\n",
       "      <th>molecularVolume</th>\n",
       "      <th>smile</th>\n",
       "      <th>name</th>\n",
       "      <th>file_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Inhibition of Protease</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/AromaticDerivative</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Inhibition of Protease</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/ChemicalCompound</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Inhibition of Protease</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/ChemicalSubstance</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Antiviral</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/AromaticDerivative</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Antiviral</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/ChemicalCompound</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
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       "      <td>10.1016/S0031-9422(00)94671-5</td>\n",
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       "      <td>10.1016@S0031-9422(00)94671-5.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>10.1016/S0031-9422(00)80444-6</td>\n",
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       "      <td>10.1016@S0031-9422(00)80444-6.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2301</th>\n",
       "      <td>10.1021/np50032a021</td>\n",
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       "      <td>10.1016@0031-9422(80)83208-0.pdf</td>\n",
       "    </tr>\n",
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       "<p>2304 rows × 18 columns</p>\n",
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      ],
      "text/plain": [
       "                                 doi             bioActivity  \\\n",
       "0     10.1016/j.biortech.2010.01.041  Inhibition of Protease   \n",
       "1     10.1016/j.biortech.2010.01.041  Inhibition of Protease   \n",
       "2     10.1016/j.biortech.2010.01.041  Inhibition of Protease   \n",
       "3     10.1016/j.biortech.2010.01.041               Antiviral   \n",
       "4     10.1016/j.biortech.2010.01.041               Antiviral   \n",
       "...                              ...                     ...   \n",
       "2299   10.1016/S0031-9422(00)94671-5                           \n",
       "2300   10.1016/S0031-9422(00)80444-6                           \n",
       "2301             10.1021/np50032a021                           \n",
       "2302   10.1016/S0031-9422(00)83467-6                           \n",
       "2303    10.1016/0031-9422(80)83208-0                           \n",
       "\n",
       "                      collectionSpecie collectionSite  \\\n",
       "0     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "1     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "2     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "3     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "4     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "...                                ...            ...   \n",
       "2299                                                    \n",
       "2300                                                    \n",
       "2301                                                    \n",
       "2302                                                    \n",
       "2303                                                    \n",
       "\n",
       "                 collectionType                             molType  \\\n",
       "0     Biotransformation Product  http://nubbe.db/AromaticDerivative   \n",
       "1     Biotransformation Product    http://nubbe.db/ChemicalCompound   \n",
       "2     Biotransformation Product   http://nubbe.db/ChemicalSubstance   \n",
       "3     Biotransformation Product  http://nubbe.db/AromaticDerivative   \n",
       "4     Biotransformation Product    http://nubbe.db/ChemicalCompound   \n",
       "...                         ...                                 ...   \n",
       "2299                                                                  \n",
       "2300                                                                  \n",
       "2301                                                                  \n",
       "2302                                                                  \n",
       "2303                                                                  \n",
       "\n",
       "     molecularMass monoisotropicMass        cLogP         tpsa  \\\n",
       "0       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "1       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "2       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "3       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "4       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "...            ...               ...          ...          ...   \n",
       "2299                                                             \n",
       "2300                                                             \n",
       "2301                                                             \n",
       "2302                                                             \n",
       "2303                                                             \n",
       "\n",
       "     numberOfLipinskiViolations numberOfH_bondAcceptors numberOfH_bondDonors  \\\n",
       "0                           0.0                     4.0                  2.0   \n",
       "1                           0.0                     4.0                  2.0   \n",
       "2                           0.0                     4.0                  2.0   \n",
       "3                           0.0                     4.0                  2.0   \n",
       "4                           0.0                     4.0                  2.0   \n",
       "...                         ...                     ...                  ...   \n",
       "2299                                                                           \n",
       "2300                                                                           \n",
       "2301                                                                           \n",
       "2302                                                                           \n",
       "2303                                                                           \n",
       "\n",
       "     numberOfRotableBonds molecularVolume  \\\n",
       "0                     7.0     282,9689941   \n",
       "1                     7.0     282,9689941   \n",
       "2                     7.0     282,9689941   \n",
       "3                     7.0     282,9689941   \n",
       "4                     7.0     282,9689941   \n",
       "...                   ...             ...   \n",
       "2299                                        \n",
       "2300                                        \n",
       "2301                                        \n",
       "2302                                        \n",
       "2303                                        \n",
       "\n",
       "                                            smile  \\\n",
       "0     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "1     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "2     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "3     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "4     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "...                                           ...   \n",
       "2299                                                \n",
       "2300                                                \n",
       "2301                                                \n",
       "2302                                                \n",
       "2303                                                \n",
       "\n",
       "                                         name  \\\n",
       "0     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "1     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "2     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "3     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "4     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "...                                       ...   \n",
       "2299                                            \n",
       "2300                                            \n",
       "2301                                            \n",
       "2302                                            \n",
       "2303                                            \n",
       "\n",
       "                               file_name  \n",
       "0     10.1016@j.biortech.2010.01.041.pdf  \n",
       "1     10.1016@j.biortech.2010.01.041.pdf  \n",
       "2     10.1016@j.biortech.2010.01.041.pdf  \n",
       "3     10.1016@j.biortech.2010.01.041.pdf  \n",
       "4     10.1016@j.biortech.2010.01.041.pdf  \n",
       "...                                  ...  \n",
       "2299   10.1016@S0031-9422(00)94671-5.pdf  \n",
       "2300   10.1016@S0031-9422(00)80444-6.pdf  \n",
       "2301             10.1021@np50032a021.pdf  \n",
       "2302   10.1016@S0031-9422(00)83467-6.pdf  \n",
       "2303    10.1016@0031-9422(80)83208-0.pdf  \n",
       "\n",
       "[2304 rows x 18 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_parquet('{}file-name_query03-05.parquet'.format(path))\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>doi</th>\n",
       "      <th>file_name</th>\n",
       "      <th>text</th>\n",
       "      <th>phrases</th>\n",
       "      <th>topics</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "      <td>Geranylation of benzoic acid derivatives by en...</td>\n",
       "      <td>[Geranylation of benzoic acid derivatives by e...</td>\n",
       "      <td>[128, 131, 137, 9, 25, 42, 50, 51, 52, 70, 106...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.1590/S0100-40422010000200017</td>\n",
       "      <td>10.1590@S0100-40422010000200017.pdf</td>\n",
       "      <td>Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Arti...</td>\n",
       "      <td>[Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Art...</td>\n",
       "      <td>[140, 50, 89, 106]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.1590/S0103-50532006000500017</td>\n",
       "      <td>10.1590@S0103-50532006000500017.pdf</td>\n",
       "      <td>J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934, ...</td>\n",
       "      <td>[J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934,...</td>\n",
       "      <td>[137, 140, 27, 51, 63, 75, 115]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.1002/pca.818</td>\n",
       "      <td>10.1002@pca.818.pdf</td>\n",
       "      <td>FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM CR...</td>\n",
       "      <td>[FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM C...</td>\n",
       "      <td>[137, 140, 16, 50, 51, 66, 90, 100]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10.1002/ps.478</td>\n",
       "      <td>10.1002@ps.478.pdf</td>\n",
       "      <td>Biological activity of astilbin from ���������...</td>\n",
       "      <td>[Biological activity of astilbin from ��������...</td>\n",
       "      <td>[1, 7, 140, 17, 23, 25, 29, 31, 36, 37, 50, 57...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>385</th>\n",
       "      <td>10.1016/S0031-9422(00)94671-5</td>\n",
       "      <td>10.1016@S0031-9422(00)94671-5.pdf</td>\n",
       "      <td>Short Reports  1671  Dichrographe Mark III, R....</td>\n",
       "      <td>[Short Reports  1671  Dichrographe Mark III, R...</td>\n",
       "      <td>[15, 64, 70, 124, 126]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>386</th>\n",
       "      <td>10.1016/S0031-9422(00)80444-6</td>\n",
       "      <td>10.1016@S0031-9422(00)80444-6.pdf</td>\n",
       "      <td>Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296,...</td>\n",
       "      <td>[Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296...</td>\n",
       "      <td>[35, 51, 63]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>387</th>\n",
       "      <td>10.1021/np50032a021</td>\n",
       "      <td>10.1021@np50032a021.pdf</td>\n",
       "      <td>Journal of Natural Products  Vol. 47. No. 2. p...</td>\n",
       "      <td>[Journal of Natural Products  Vol. 47. No. 2. ...</td>\n",
       "      <td>[90]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>388</th>\n",
       "      <td>10.1016/S0031-9422(00)83467-6</td>\n",
       "      <td>10.1016@S0031-9422(00)83467-6.pdf</td>\n",
       "      <td>Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679,...</td>\n",
       "      <td>[Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679...</td>\n",
       "      <td>[137, 31, 51, 82, 89, 90]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>389</th>\n",
       "      <td>10.1016/0031-9422(80)83208-0</td>\n",
       "      <td>10.1016@0031-9422(80)83208-0.pdf</td>\n",
       "      <td>Phytochemistry, 1980, Vol. 19, pp. 474-476. © ...</td>\n",
       "      <td>[Phytochemistry, 1980, Vol. 19, pp. 474-476. ©...</td>\n",
       "      <td>[140, 22, 40, 49, 65, 70, 115]</td>\n",
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       "2    10.1590/S0103-50532006000500017  10.1590@S0103-50532006000500017.pdf   \n",
       "3                    10.1002/pca.818                  10.1002@pca.818.pdf   \n",
       "4                     10.1002/ps.478                   10.1002@ps.478.pdf   \n",
       "..                               ...                                  ...   \n",
       "385    10.1016/S0031-9422(00)94671-5    10.1016@S0031-9422(00)94671-5.pdf   \n",
       "386    10.1016/S0031-9422(00)80444-6    10.1016@S0031-9422(00)80444-6.pdf   \n",
       "387              10.1021/np50032a021              10.1021@np50032a021.pdf   \n",
       "388    10.1016/S0031-9422(00)83467-6    10.1016@S0031-9422(00)83467-6.pdf   \n",
       "389     10.1016/0031-9422(80)83208-0     10.1016@0031-9422(80)83208-0.pdf   \n",
       "\n",
       "                                                  text  \\\n",
       "0    Geranylation of benzoic acid derivatives by en...   \n",
       "1    Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Arti...   \n",
       "2    J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934, ...   \n",
       "3    FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM CR...   \n",
       "4    Biological activity of astilbin from ���������...   \n",
       "..                                                 ...   \n",
       "385  Short Reports  1671  Dichrographe Mark III, R....   \n",
       "386  Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296,...   \n",
       "387  Journal of Natural Products  Vol. 47. No. 2. p...   \n",
       "388  Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679,...   \n",
       "389  Phytochemistry, 1980, Vol. 19, pp. 474-476. © ...   \n",
       "\n",
       "                                               phrases  \\\n",
       "0    [Geranylation of benzoic acid derivatives by e...   \n",
       "1    [Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Art...   \n",
       "2    [J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934,...   \n",
       "3    [FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM C...   \n",
       "4    [Biological activity of astilbin from ��������...   \n",
       "..                                                 ...   \n",
       "385  [Short Reports  1671  Dichrographe Mark III, R...   \n",
       "386  [Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296...   \n",
       "387  [Journal of Natural Products  Vol. 47. No. 2. ...   \n",
       "388  [Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679...   \n",
       "389  [Phytochemistry, 1980, Vol. 19, pp. 474-476. ©...   \n",
       "\n",
       "                                                topics  \n",
       "0    [128, 131, 137, 9, 25, 42, 50, 51, 52, 70, 106...  \n",
       "1                                   [140, 50, 89, 106]  \n",
       "2                      [137, 140, 27, 51, 63, 75, 115]  \n",
       "3                  [137, 140, 16, 50, 51, 66, 90, 100]  \n",
       "4    [1, 7, 140, 17, 23, 25, 29, 31, 36, 37, 50, 57...  \n",
       "..                                                 ...  \n",
       "385                             [15, 64, 70, 124, 126]  \n",
       "386                                       [35, 51, 63]  \n",
       "387                                               [90]  \n",
       "388                          [137, 31, 51, 82, 89, 90]  \n",
       "389                     [140, 22, 40, 49, 65, 70, 115]  \n",
       "\n",
       "[390 rows x 5 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "texts_df = pd.read_parquet('{}topics03-05.parquet'.format(path))\n",
    "texts_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-05-05 10:22:04 - Load pretrained SentenceTransformer: sentence-transformers/distiluse-base-multilingual-cased-v2\n",
      "2022-05-05 10:22:13 - Use pytorch device: cpu\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "1eaa2d494fd0489595f9b7f255bef770",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "0it [00:00, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
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     "data": {
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       "      <th></th>\n",
       "      <th>doi</th>\n",
       "      <th>file_name</th>\n",
       "      <th>text</th>\n",
       "      <th>phrases</th>\n",
       "      <th>topics</th>\n",
       "      <th>embedding</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "      <td>Geranylation of benzoic acid derivatives by en...</td>\n",
       "      <td>[Geranylation of benzoic acid derivatives by e...</td>\n",
       "      <td>[128, 131, 137, 9, 25, 42, 50, 51, 52, 70, 106...</td>\n",
       "      <td>[-0.8950119113142136, 0.6137956916936673, 0.44...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.1590/S0100-40422010000200017</td>\n",
       "      <td>10.1590@S0100-40422010000200017.pdf</td>\n",
       "      <td>Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Arti...</td>\n",
       "      <td>[Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Art...</td>\n",
       "      <td>[140, 50, 89, 106]</td>\n",
       "      <td>[0.04050083481706679, 0.44275644212029874, -0....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.1590/S0103-50532006000500017</td>\n",
       "      <td>10.1590@S0103-50532006000500017.pdf</td>\n",
       "      <td>J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934, ...</td>\n",
       "      <td>[J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934,...</td>\n",
       "      <td>[137, 140, 27, 51, 63, 75, 115]</td>\n",
       "      <td>[-0.31248263019369915, 0.45146785129327327, -0...</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.1002/pca.818</td>\n",
       "      <td>10.1002@pca.818.pdf</td>\n",
       "      <td>FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM CR...</td>\n",
       "      <td>[FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM C...</td>\n",
       "      <td>[137, 140, 16, 50, 51, 66, 90, 100]</td>\n",
       "      <td>[-0.1364280374837108, 0.9625890320166945, -0.2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10.1002/ps.478</td>\n",
       "      <td>10.1002@ps.478.pdf</td>\n",
       "      <td>Biological activity of astilbin from ���������...</td>\n",
       "      <td>[Biological activity of astilbin from ��������...</td>\n",
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       "      <td>[0.3284126768121496, -0.26284046075306833, -1....</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>385</th>\n",
       "      <td>10.1016/S0031-9422(00)94671-5</td>\n",
       "      <td>10.1016@S0031-9422(00)94671-5.pdf</td>\n",
       "      <td>Short Reports  1671  Dichrographe Mark III, R....</td>\n",
       "      <td>[Short Reports  1671  Dichrographe Mark III, R...</td>\n",
       "      <td>[15, 64, 70, 124, 126]</td>\n",
       "      <td>[-0.21970844618044794, 0.33494939119555056, 0....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>386</th>\n",
       "      <td>10.1016/S0031-9422(00)80444-6</td>\n",
       "      <td>10.1016@S0031-9422(00)80444-6.pdf</td>\n",
       "      <td>Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296,...</td>\n",
       "      <td>[Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296...</td>\n",
       "      <td>[35, 51, 63]</td>\n",
       "      <td>[-0.217852107307408, 0.9152514797169715, -0.47...</td>\n",
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       "    <tr>\n",
       "      <th>387</th>\n",
       "      <td>10.1021/np50032a021</td>\n",
       "      <td>10.1021@np50032a021.pdf</td>\n",
       "      <td>Journal of Natural Products  Vol. 47. No. 2. p...</td>\n",
       "      <td>[Journal of Natural Products  Vol. 47. No. 2. ...</td>\n",
       "      <td>[90]</td>\n",
       "      <td>[-0.3095813561230898, 0.12105271965265274, -0....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>388</th>\n",
       "      <td>10.1016/S0031-9422(00)83467-6</td>\n",
       "      <td>10.1016@S0031-9422(00)83467-6.pdf</td>\n",
       "      <td>Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679,...</td>\n",
       "      <td>[Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679...</td>\n",
       "      <td>[137, 31, 51, 82, 89, 90]</td>\n",
       "      <td>[-0.25929326261393726, 0.36754298279993236, -0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>389</th>\n",
       "      <td>10.1016/0031-9422(80)83208-0</td>\n",
       "      <td>10.1016@0031-9422(80)83208-0.pdf</td>\n",
       "      <td>Phytochemistry, 1980, Vol. 19, pp. 474-476. © ...</td>\n",
       "      <td>[Phytochemistry, 1980, Vol. 19, pp. 474-476. ©...</td>\n",
       "      <td>[140, 22, 40, 49, 65, 70, 115]</td>\n",
       "      <td>[-0.48299791174940765, 0.4926577670266852, -0....</td>\n",
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       "                                 doi                            file_name  \\\n",
       "0     10.1016/j.biortech.2010.01.041   10.1016@j.biortech.2010.01.041.pdf   \n",
       "1    10.1590/S0100-40422010000200017  10.1590@S0100-40422010000200017.pdf   \n",
       "2    10.1590/S0103-50532006000500017  10.1590@S0103-50532006000500017.pdf   \n",
       "3                    10.1002/pca.818                  10.1002@pca.818.pdf   \n",
       "4                     10.1002/ps.478                   10.1002@ps.478.pdf   \n",
       "..                               ...                                  ...   \n",
       "385    10.1016/S0031-9422(00)94671-5    10.1016@S0031-9422(00)94671-5.pdf   \n",
       "386    10.1016/S0031-9422(00)80444-6    10.1016@S0031-9422(00)80444-6.pdf   \n",
       "387              10.1021/np50032a021              10.1021@np50032a021.pdf   \n",
       "388    10.1016/S0031-9422(00)83467-6    10.1016@S0031-9422(00)83467-6.pdf   \n",
       "389     10.1016/0031-9422(80)83208-0     10.1016@0031-9422(80)83208-0.pdf   \n",
       "\n",
       "                                                  text  \\\n",
       "0    Geranylation of benzoic acid derivatives by en...   \n",
       "1    Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Arti...   \n",
       "2    J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934, ...   \n",
       "3    FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM CR...   \n",
       "4    Biological activity of astilbin from ���������...   \n",
       "..                                                 ...   \n",
       "385  Short Reports  1671  Dichrographe Mark III, R....   \n",
       "386  Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296,...   \n",
       "387  Journal of Natural Products  Vol. 47. No. 2. p...   \n",
       "388  Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679,...   \n",
       "389  Phytochemistry, 1980, Vol. 19, pp. 474-476. © ...   \n",
       "\n",
       "                                               phrases  \\\n",
       "0    [Geranylation of benzoic acid derivatives by e...   \n",
       "1    [Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Art...   \n",
       "2    [J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934,...   \n",
       "3    [FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM C...   \n",
       "4    [Biological activity of astilbin from ��������...   \n",
       "..                                                 ...   \n",
       "385  [Short Reports  1671  Dichrographe Mark III, R...   \n",
       "386  [Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296...   \n",
       "387  [Journal of Natural Products  Vol. 47. No. 2. ...   \n",
       "388  [Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679...   \n",
       "389  [Phytochemistry, 1980, Vol. 19, pp. 474-476. ©...   \n",
       "\n",
       "                                                topics  \\\n",
       "0    [128, 131, 137, 9, 25, 42, 50, 51, 52, 70, 106...   \n",
       "1                                   [140, 50, 89, 106]   \n",
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       "3                  [137, 140, 16, 50, 51, 66, 90, 100]   \n",
       "4    [1, 7, 140, 17, 23, 25, 29, 31, 36, 37, 50, 57...   \n",
       "..                                                 ...   \n",
       "385                             [15, 64, 70, 124, 126]   \n",
       "386                                       [35, 51, 63]   \n",
       "387                                               [90]   \n",
       "388                          [137, 31, 51, 82, 89, 90]   \n",
       "389                     [140, 22, 40, 49, 65, 70, 115]   \n",
       "\n",
       "                                             embedding  \n",
       "0    [-0.8950119113142136, 0.6137956916936673, 0.44...  \n",
       "1    [0.04050083481706679, 0.44275644212029874, -0....  \n",
       "2    [-0.31248263019369915, 0.45146785129327327, -0...  \n",
       "3    [-0.1364280374837108, 0.9625890320166945, -0.2...  \n",
       "4    [0.3284126768121496, -0.26284046075306833, -1....  \n",
       "..                                                 ...  \n",
       "385  [-0.21970844618044794, 0.33494939119555056, 0....  \n",
       "386  [-0.217852107307408, 0.9152514797169715, -0.47...  \n",
       "387  [-0.3095813561230898, 0.12105271965265274, -0....  \n",
       "388  [-0.25929326261393726, 0.36754298279993236, -0...  \n",
       "389  [-0.48299791174940765, 0.4926577670266852, -0....  \n",
       "\n",
       "[390 rows x 6 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from sentence_transformers import SentenceTransformer, LoggingHandler\n",
    "import numpy as np\n",
    "from tqdm.notebook import tqdm\n",
    "import logging\n",
    "\n",
    "#### Just some code to print debug information to stdout\n",
    "np.set_printoptions(threshold=100)\n",
    "\n",
    "logging.basicConfig(format='%(asctime)s - %(message)s',\n",
    "                    datefmt='%Y-%m-%d %H:%M:%S',\n",
    "                    level=logging.INFO,\n",
    "                    handlers=[LoggingHandler()])\n",
    "\n",
    "# Load Sentence model (based on BERT) from URL\n",
    "model = SentenceTransformer('sentence-transformers/distiluse-base-multilingual-cased-v2')\n",
    "\n",
    "def model_encode(model):\n",
    "    embeddings = []\n",
    "    for _, phrases in tqdm(texts_df['phrases'].iteritems()):\n",
    "        embedding = np.zeros(512)\n",
    "        for phrase in phrases:\n",
    "            embedding += model.encode(phrase, show_progress_bar=False)\n",
    "        embeddings.append(embedding)\n",
    "    return embeddings\n",
    "\n",
    "texts_df['embedding'] = model_encode(model)\n",
    "texts_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "texts_df.to_parquet('{}topics_embeddings03-05.parquet'.format(path))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>doi</th>\n",
       "      <th>file_name</th>\n",
       "      <th>text</th>\n",
       "      <th>phrases</th>\n",
       "      <th>topics</th>\n",
       "      <th>embedding</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "      <td>Geranylation of benzoic acid derivatives by en...</td>\n",
       "      <td>[Geranylation of benzoic acid derivatives by e...</td>\n",
       "      <td>[128, 131, 137, 9, 25, 42, 50, 51, 52, 70, 106...</td>\n",
       "      <td>[-0.8950119113142136, 0.6137956916936673, 0.44...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.1590/S0100-40422010000200017</td>\n",
       "      <td>10.1590@S0100-40422010000200017.pdf</td>\n",
       "      <td>Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Arti...</td>\n",
       "      <td>[Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Art...</td>\n",
       "      <td>[140, 50, 89, 106]</td>\n",
       "      <td>[0.04050083481706679, 0.44275644212029874, -0....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.1590/S0103-50532006000500017</td>\n",
       "      <td>10.1590@S0103-50532006000500017.pdf</td>\n",
       "      <td>J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934, ...</td>\n",
       "      <td>[J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934,...</td>\n",
       "      <td>[137, 140, 27, 51, 63, 75, 115]</td>\n",
       "      <td>[-0.31248263019369915, 0.45146785129327327, -0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.1002/pca.818</td>\n",
       "      <td>10.1002@pca.818.pdf</td>\n",
       "      <td>FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM CR...</td>\n",
       "      <td>[FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM C...</td>\n",
       "      <td>[137, 140, 16, 50, 51, 66, 90, 100]</td>\n",
       "      <td>[-0.1364280374837108, 0.9625890320166945, -0.2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10.1002/ps.478</td>\n",
       "      <td>10.1002@ps.478.pdf</td>\n",
       "      <td>Biological activity of astilbin from ���������...</td>\n",
       "      <td>[Biological activity of astilbin from ��������...</td>\n",
       "      <td>[1, 7, 140, 17, 23, 25, 29, 31, 36, 37, 50, 57...</td>\n",
       "      <td>[0.3284126768121496, -0.26284046075306833, -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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>385</th>\n",
       "      <td>10.1016/S0031-9422(00)94671-5</td>\n",
       "      <td>10.1016@S0031-9422(00)94671-5.pdf</td>\n",
       "      <td>Short Reports  1671  Dichrographe Mark III, R....</td>\n",
       "      <td>[Short Reports  1671  Dichrographe Mark III, R...</td>\n",
       "      <td>[15, 64, 70, 124, 126]</td>\n",
       "      <td>[-0.21970844618044794, 0.33494939119555056, 0....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>386</th>\n",
       "      <td>10.1016/S0031-9422(00)80444-6</td>\n",
       "      <td>10.1016@S0031-9422(00)80444-6.pdf</td>\n",
       "      <td>Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296,...</td>\n",
       "      <td>[Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296...</td>\n",
       "      <td>[35, 51, 63]</td>\n",
       "      <td>[-0.217852107307408, 0.9152514797169715, -0.47...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>387</th>\n",
       "      <td>10.1021/np50032a021</td>\n",
       "      <td>10.1021@np50032a021.pdf</td>\n",
       "      <td>Journal of Natural Products  Vol. 47. No. 2. p...</td>\n",
       "      <td>[Journal of Natural Products  Vol. 47. No. 2. ...</td>\n",
       "      <td>[90]</td>\n",
       "      <td>[-0.3095813561230898, 0.12105271965265274, -0....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>388</th>\n",
       "      <td>10.1016/S0031-9422(00)83467-6</td>\n",
       "      <td>10.1016@S0031-9422(00)83467-6.pdf</td>\n",
       "      <td>Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679,...</td>\n",
       "      <td>[Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679...</td>\n",
       "      <td>[137, 31, 51, 82, 89, 90]</td>\n",
       "      <td>[-0.25929326261393726, 0.36754298279993236, -0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>389</th>\n",
       "      <td>10.1016/0031-9422(80)83208-0</td>\n",
       "      <td>10.1016@0031-9422(80)83208-0.pdf</td>\n",
       "      <td>Phytochemistry, 1980, Vol. 19, pp. 474-476. © ...</td>\n",
       "      <td>[Phytochemistry, 1980, Vol. 19, pp. 474-476. ©...</td>\n",
       "      <td>[140, 22, 40, 49, 65, 70, 115]</td>\n",
       "      <td>[-0.48299791174940765, 0.4926577670266852, -0....</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>390 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 doi                            file_name  \\\n",
       "0     10.1016/j.biortech.2010.01.041   10.1016@j.biortech.2010.01.041.pdf   \n",
       "1    10.1590/S0100-40422010000200017  10.1590@S0100-40422010000200017.pdf   \n",
       "2    10.1590/S0103-50532006000500017  10.1590@S0103-50532006000500017.pdf   \n",
       "3                    10.1002/pca.818                  10.1002@pca.818.pdf   \n",
       "4                     10.1002/ps.478                   10.1002@ps.478.pdf   \n",
       "..                               ...                                  ...   \n",
       "385    10.1016/S0031-9422(00)94671-5    10.1016@S0031-9422(00)94671-5.pdf   \n",
       "386    10.1016/S0031-9422(00)80444-6    10.1016@S0031-9422(00)80444-6.pdf   \n",
       "387              10.1021/np50032a021              10.1021@np50032a021.pdf   \n",
       "388    10.1016/S0031-9422(00)83467-6    10.1016@S0031-9422(00)83467-6.pdf   \n",
       "389     10.1016/0031-9422(80)83208-0     10.1016@0031-9422(80)83208-0.pdf   \n",
       "\n",
       "                                                  text  \\\n",
       "0    Geranylation of benzoic acid derivatives by en...   \n",
       "1    Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Arti...   \n",
       "2    J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934, ...   \n",
       "3    FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM CR...   \n",
       "4    Biological activity of astilbin from ���������...   \n",
       "..                                                 ...   \n",
       "385  Short Reports  1671  Dichrographe Mark III, R....   \n",
       "386  Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296,...   \n",
       "387  Journal of Natural Products  Vol. 47. No. 2. p...   \n",
       "388  Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679,...   \n",
       "389  Phytochemistry, 1980, Vol. 19, pp. 474-476. © ...   \n",
       "\n",
       "                                               phrases  \\\n",
       "0    [Geranylation of benzoic acid derivatives by e...   \n",
       "1    [Quim. Nova, Vol. 33, No. 2, 321-323, 2010 Art...   \n",
       "2    [J. Braz. Chem. Soc., Vol. 17, No. 5, 929-934,...   \n",
       "3    [FLAVONOID GLYCOSIDES AND STYRYLPYRONES FROM C...   \n",
       "4    [Biological activity of astilbin from ��������...   \n",
       "..                                                 ...   \n",
       "385  [Short Reports  1671  Dichrographe Mark III, R...   \n",
       "386  [Phytochemrstry,  Vol. 23, No 6, pp. 1X33-1296...   \n",
       "387  [Journal of Natural Products  Vol. 47. No. 2. ...   \n",
       "388  [Phytockmistry,  Vol. 23, No. 8, pp. 1677-1679...   \n",
       "389  [Phytochemistry, 1980, Vol. 19, pp. 474-476. ©...   \n",
       "\n",
       "                                                topics  \\\n",
       "0    [128, 131, 137, 9, 25, 42, 50, 51, 52, 70, 106...   \n",
       "1                                   [140, 50, 89, 106]   \n",
       "2                      [137, 140, 27, 51, 63, 75, 115]   \n",
       "3                  [137, 140, 16, 50, 51, 66, 90, 100]   \n",
       "4    [1, 7, 140, 17, 23, 25, 29, 31, 36, 37, 50, 57...   \n",
       "..                                                 ...   \n",
       "385                             [15, 64, 70, 124, 126]   \n",
       "386                                       [35, 51, 63]   \n",
       "387                                               [90]   \n",
       "388                          [137, 31, 51, 82, 89, 90]   \n",
       "389                     [140, 22, 40, 49, 65, 70, 115]   \n",
       "\n",
       "                                             embedding  \n",
       "0    [-0.8950119113142136, 0.6137956916936673, 0.44...  \n",
       "1    [0.04050083481706679, 0.44275644212029874, -0....  \n",
       "2    [-0.31248263019369915, 0.45146785129327327, -0...  \n",
       "3    [-0.1364280374837108, 0.9625890320166945, -0.2...  \n",
       "4    [0.3284126768121496, -0.26284046075306833, -1....  \n",
       "..                                                 ...  \n",
       "385  [-0.21970844618044794, 0.33494939119555056, 0....  \n",
       "386  [-0.217852107307408, 0.9152514797169715, -0.47...  \n",
       "387  [-0.3095813561230898, 0.12105271965265274, -0....  \n",
       "388  [-0.25929326261393726, 0.36754298279993236, -0...  \n",
       "389  [-0.48299791174940765, 0.4926577670266852, -0....  \n",
       "\n",
       "[390 rows x 6 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# if texts df with embeddings already saved\n",
    "texts_df = pd.read_parquet('{}topics_embeddings03-05.parquet'.format(path))\n",
    "texts_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "doi                                     10.1002/chin.200552195\n",
       "file_name                           10.1002@chin.200552195.pdf\n",
       "text         2005 Other bioactive products U 1300 Isolation...\n",
       "phrases      [2005 Other bioactive products U 1300 Isolatio...\n",
       "topics                                                      []\n",
       "embedding    [-0.020641377195715904, 0.01006641797721386, 0...\n",
       "Name: 215, dtype: object"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "texts_df[texts_df['doi'] == '10.1002/chin.200552195'].iloc[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "from bertopic import BERTopic\n",
    "\n",
    "topic_model = BERTopic.load('{}topic_model03-05'.format(path))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "attribute_feature: smile, feature_value: , attribute_value: C[C@@H](C5=O)[C@H]([C@@]([C@@H](N3[H])CC1=CC=CC=C1)([C@@]([C@]3=O)([C@H]5/C=C\\C[C@@H](C4=O)C)[C@H](OC(C)=O)[C@H]2[C@H]([C@](C)4O)O2)[H])C\n",
      "attribute_feature: smile, feature_value: , attribute_value: C[C@@H](C5=O)[C@H]([C@@]([C@@H](N3[H])CC1=CC=CC=C1)([C@@]([C@]3=O)([C@H]5/C=C\\C[C@@H](C4=O)C)[C@H](OC(C)=O)[C@H]2[C@H]([C@](C)4O)O2)[H])C\n",
      "attribute_feature: smile, feature_value: , attribute_value: C[C@@H](C5=O)[C@H]([C@@]([C@@H](N3[H])CC1=CC=CC=C1)([C@@]([C@]3=O)([C@H]5/C=C\\C[C@@H](C4=O)C)[C@H](OC(C)=O)[C@H]2[C@H]([C@](C)4O)O2)[H])C\n",
      "doi 10.1002/chin.200552195 has no connections\n",
      "doi 10.1016/S0031-9422(00)85714-3 has no connections\n",
      "doi 10.1016/0031-9422(74)80106-8 has no connections\n"
     ]
    }
   ],
   "source": [
    "def make_networkx(df, texts_df, topic_model,\n",
    "                    id_feature='doi', special_attributes={'name': 'smile'}, list_features=[\n",
    "                        'bioActivity', 'molType', 'collectionSpecie', 'collectionSite', 'collectionType', 'molecularMass', 'monoisotropicMass', 'cLogP', 'tpsa', \n",
    "                        'numberOfLipinskiViolations', 'numberOfH_bondAcceptors', 'numberOfH_bondDonors', 'numberOfRotableBonds', 'molecularVolume', 'name'\n",
    "                    ],\n",
    "):\n",
    "    def create_edge(value1, value2, group1, group2, node_from):            \n",
    "        if value1 != '' and value2 != '':\n",
    "            G.add_edge(value1, value2, edge_group=f'{group1}_{group2}')\n",
    "            G.nodes[value1]['group'] = group1\n",
    "            G.nodes[value2]['group'] = group2\n",
    "            G.nodes[value2]['node_from'] = node_from\n",
    "    \n",
    "    def create_attribute(attribute_feature, feature_value, attribute_value):\n",
    "        if attribute_value != '':\n",
    "            try:\n",
    "                G.nodes[feature_value][attribute_feature] = attribute_value\n",
    "            except:\n",
    "                print('attribute_feature: {}, feature_value: {}, attribute_value: {}'. format(attribute_feature, feature_value, attribute_value))\n",
    "\n",
    "    G = nx.Graph()\n",
    "    for _, row in df.iterrows():\n",
    "        for feature in list_features:\n",
    "            create_edge(row[id_feature], row[feature], id_feature, feature, 'nubbe')\n",
    "            if feature in special_attributes:\n",
    "                create_attribute(special_attributes[feature], row[feature], row[special_attributes[feature]])\n",
    "    for _, row in texts_df.iterrows():\n",
    "        for topic in row['topics']:\n",
    "            create_edge(row[id_feature], topic_model.get_topic_info(topic)['Name'].iloc[0], id_feature, 'topic', 'pdf')\n",
    "        try:\n",
    "            G.nodes[row[id_feature]]['embedding'] = row['embedding']\n",
    "        except:\n",
    "            print('doi {} has no connections'.format(row[id_feature]))\n",
    "\n",
    "    return G\n",
    "\n",
    "G = make_networkx(df, texts_df, topic_model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['128_rat_protein_grandisin_microsomes',\n",
       " '131_stress_mpo_antioxidant_diseases',\n",
       " '137_brt_153_105_125',\n",
       " '9_cruzi_trypanocidal_trypanosoma_disease',\n",
       " '25_antimicrobial_candida_aureus_against',\n",
       " '42_mixture_stirred_added_was',\n",
       " '50_phase_ml_lpme_acceptor',\n",
       " '51_29_56_147_55',\n",
       " '52_fapesp_biota_virtual_cnpq',\n",
       " '70_sugar_anomeric_aglycone_açúcar',\n",
       " '106_gave_chci_residue_evaporated',\n",
       " '113_drying_extrato_evaporador_oven',\n",
       " '140_sementes_óleos_óleo_com',\n",
       " '89_extract_hexane_pressure_under',\n",
       " '27_electron_elétrons_transport_fsii',\n",
       " '63_crystals_nm_sh_000',\n",
       " '75_part_series_ref_brazilian',\n",
       " '115_endophytic_fungus_endophyte_stierle',\n",
       " '16_precision_accuracy_rsd_day',\n",
       " '66_days_fermented_ﬁve_trans',\n",
       " '90_espectrômetro_foram_espectros_em',\n",
       " '100_oh_ome_flavona_flavanone',\n",
       " '1_introduction___',\n",
       " '7_nm_ms_ord_loo',\n",
       " '17_correlations_noe_between_orientation',\n",
       " '23_brazil_universidade_de_sp',\n",
       " '29_stereochemistry_the_ring_be',\n",
       " '31_support_pessoal_financial_capes',\n",
       " '36_amorphous_λmax_uv_meoh',\n",
       " '37_11_18_107_12',\n",
       " '57_uv_log_nm_cm',\n",
       " '60_min_temperature_oc_temperatura',\n",
       " '83_os_dados_de_sesquichamaenol',\n",
       " '94_sinal_sinais_em_carbonos',\n",
       " '104_pesquisa_cnpq_estado_conselho',\n",
       " '121_corilagin_niruri_pad_hplc',\n",
       " '124_sl_population_individuals_seidelii',\n",
       " '125_uv_spectrum_showed_spectra',\n",
       " '47_electrode_glassy_caffeic_voltammograms',\n",
       " '107_sterol_4a_jamaican_sterols',\n",
       " '34_em_foi_mg_fração',\n",
       " '35_spectrum_absorption_at_cm',\n",
       " '108_constants_parentheses_coupling_brs',\n",
       " '102_chalepin_binding_ggapdh_inhibitor',\n",
       " '101_cotton_effect_negative_configuration',\n",
       " '33_ch3_veratryl_rel_nt',\n",
       " '139_h3_me_21_22',\n",
       " '4_cell_cells_cancer_human',\n",
       " '24_merck_mm_detector_performed',\n",
       " '28_dd_br_16_11',\n",
       " '64_artigo_química_mail_universidade',\n",
       " '71_pathway_mep_pathways_ipp',\n",
       " '67_mass_kovat_indexes_massas',\n",
       " '126_lc_voltage_esi_shimadzu',\n",
       " '62_comet_dna_damage_caseargrewiin',\n",
       " '93_catl_competitive_inhibitors_catv',\n",
       " '103_hex_lactam_allergic_anti',\n",
       " '111_iryanthera_used_bark_infections',\n",
       " '22_oils_essential_oil_grandella',\n",
       " '49_oil_viscous_arome_inf',\n",
       " '80_separation_phase_solvent_grade',\n",
       " '40_wood_allyl_trunk_hydroxy',\n",
       " '65_wood_kg_trunk_manaus',\n",
       " '82_23_19_27_26',\n",
       " '15_species_brazil_word_index',\n",
       " '130_glucose_enrichment_13c_incorporation',\n",
       " '46_sílica_gradiente_fração_coluna',\n",
       " '56_gallic_gallates_gsh_hemolysis',\n",
       " '55_pergamon_printed_9422_pp',\n",
       " '59_england_pergamon_printed_press',\n",
       " '138_cashew_apple_bt_antitumor',\n",
       " '95_mica_cep_vanderlan_maria',\n",
       " '74_plates_mtt_added_well',\n",
       " '3_de_ants_os_para',\n",
       " '112_extraction_casearins_casearin_sonication',\n",
       " '134_views_any_francis_content',\n",
       " '78_9422_britain_great_0031',\n",
       " '88_been_contain_isolated_have',\n",
       " '91_prop_conditions_static_midodrine',\n",
       " '87_hz_me_ch_cme',\n",
       " '123_meo_oh_ome_me',\n",
       " '141_soln_aq_separated_residue',\n",
       " '45_hydroxyl_the_centrolobol_group',\n",
       " '20_medium_containing_culture_erlenmeyer']"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[node for node in G.nodes() if G.nodes[node]['group'] == 'topic']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['3,4-dihydroxybenzoic acid geranyl ester',\n",
       " 'p-hydroxybenzoic acid-geranyl ester',\n",
       " 'astilbin; Rel-(2R, 3R)-dihydroquercetin-3-O-±-L-rhamnoside',\n",
       " '7′-multijuguinone',\n",
       " '12′-hydroxy-7′-multijuguinone',\n",
       " '(Z)-piplartine; 8(Z)-N-(12,13, 14-trimethoxycinnamoyl)- 3-pyridin-2-one',\n",
       " '(E)-piplartine',\n",
       " '8,9-dihydropiplartine; N-(12,13,14-trimethoxydihydrocinnamoyl)-Δ3-pyridin-2-one',\n",
       " 'Piperine',\n",
       " '10,11-dihydropiperine; Δα,β-dihydropiperine',\n",
       " '4,5-dihydropiperlonguminine; Piperlonguminine',\n",
       " 'Pellitorine',\n",
       " '4,5-dihydropiperyline',\n",
       " '(3Z,5Z)-N-isobutyl-8-(30,40-methylenedioxy-phenyl)-heptadienamide',\n",
       " \"N-[3-(6'-methoxy-3',4'-methy-lenedioxyphenyl)-2(Z)-propenoyl]pyrrolidine\",\n",
       " 'Fagaramide',\n",
       " 'Methyl (E)-6,7,8-trimethoxycinnamate',\n",
       " 'Piperyline, N-[10-(13,14-methylenedioxyphenyl)-7(E),9(E)-pentadienoyl]-pyrrolidine',\n",
       " 'Tetrahydropiperyline, N-[10-(13,14-methylenedioxyphenyl)-pentanoyl]-pyrrolidine',\n",
       " 'N-[10-(13,14-methylenedioxyphenyl)-7(E),9(Z)-pentadienoyl]-pyrrolidine',\n",
       " 'Arboreumine',\n",
       " 'N-[10- (13,14-methylenedioxyphenyl)-7(E)-pentaenoyl]-pyrrolidine',\n",
       " 'Methyl 6,7,8-trimethoxydihydrocinnamate',\n",
       " 'Clusifoliol',\n",
       " '2-Episesalatin',\n",
       " 'Sesartemin',\n",
       " \"Isoswertisin-4'-methyl-ether-2''α-L-rhamnoside\",\n",
       " \"Isoswertisin-2''α1-L-rhamnoside\",\n",
       " 'Methyl (3R,4R,5R)-3-{[(2E)-3-(3,4-dihydroxyphenyl)-2-propenoyl]oxy}-1,4,5-trihydroxycyclohexanecarboxylate',\n",
       " 'Methyl (3R,4R,5R)-3-{[(2Z)-3-(3,4-dihydroxyphenyl)-2-propenoyl]oxy}-1,4,5-trihydroxycyclohexanecarboxylate',\n",
       " 'Nitensidine D',\n",
       " 'Nitensidine E',\n",
       " 'Kaempferol-3-O-rutinoside',\n",
       " 'Kaempferol-3-O-α-L-rhamnopyranosyl-(1→6)-β-D-galactopyranoside',\n",
       " 'Quercetin-3-O-α-L-rhamnopyranosyl-(1→6)-β-D-galactopyranoside',\n",
       " '6-Hydroxy-rutin',\n",
       " 'Kaempferol-3-O-D-galactopyranoside',\n",
       " 'Kaempferol-3-O-D-glucopyranoside',\n",
       " 'Kaempferol-3-O-α-L-rhamnopyranosyl-(1-6)-α-L-rhamnopyranosyl-(1-4)-β-D-glucopyranoside',\n",
       " 'Catechin, Ent-catechin',\n",
       " 'Procyanidin B-3',\n",
       " 'Casearin X; (1R*,3S*,5S*,6aR*,7S*,8S*,10R*,10aR*)-1-(Acetyloxy)-3,5,6,6a,7,8,9,10-octahydro-10-hydroxy-7,8-dimethyl-7-[(2Z)-3-methylpenta-2,4-dien-1-yl]naphtho[1,8a-c]furan-3,5-diyl Dibutanoate',\n",
       " 'Casearin L; (1R*,3S*,5S*,6aR*,7R*,8R*,9S*,10S*,10aR*)-1,10-Bis(acetyloxy)-3,5,6,6a,7,8,9,10-octahydro-9-hydroxy-5-methoxy-7,8-dimethyl-7-[(2Z)-3-methylpenta-2,4-dien-1-yl]naphtho[1,8a-c]-furan-3-yl Butanoate',\n",
       " 'Casearin O; (1R*,3S*,5S*,6aR*,7R*,8R*,9S*,10S*,10aR*)-1,10-Bis(acetyloxy)-5-methoxy-7,8-dimethyl-7-[(2Z)-3-methylpenta-2,4-dien-1-yl]-3,5,6,6a,7,8,9,10-octahydronaphtho[1,8a-c]furan-3,9-diyl Dibutanoate',\n",
       " '(-)-Hardwickiic acid',\n",
       " 'Casearin D; (1R*,3S*,5S*,6aR*,7R*,8R*,9S*,10S*,10aR*)-1-(Acetyloxy)-3,5,6,6a,7,8,9,10-octahydro-5,10-dihydroxy-7,8-dimethyl-7-[(2Z)-3-methylpenta-2,4-dien-1-yl]naphtho[1,8a-c]furan-3,9-diyl Dibutanoate',\n",
       " 'Casearin X Dialdehyde; (2R*,4aS*,5S*,7R*,8R*,8aS*)-4,4a-Diformyl-1,2,4a,5,6,7,8,8a-octahydro-5-hydroxy-7,8-dimethyl-8-[(2Z)-3-methylpenta-2,4-dien-1-yl]naphthalen-2-yl Butanoate',\n",
       " 'Caseargrewiin F; (1R*,3S*,5S*,6aR*,7S*,8R*,10R*,10aR*)-1,3-Bis(acetyloxy)-3,5,6,6a,7,8,9,10-octahydro-10-hydroxy-7,8-dimethyl-7-[(2Z)-3-methylpenta-2,4-dien-1-yl]naphtho[1,8a-c]furan-5-yl Butanoate',\n",
       " 'Kaempferitrin',\n",
       " \"Pterogynoside; Kaempferol-3-O-(3''-O-4'''-methylgallate-α-L-rhamnoside)\",\n",
       " 'Kaempferol',\n",
       " 'Afzelin, 3-O-α-rhamnosyl kaempferol',\n",
       " 'Caseobliquin A',\n",
       " 'Rel-6β-hydroxyzuelanin-2β-benzoate',\n",
       " 'Rel-2α-hydroxyzuelanin-6β-benzoate',\n",
       " '2β-Hydroxyzuelanin-6β-cinnamate',\n",
       " 'Quercetin',\n",
       " 'Quercitrin, 3-O-α-rhamnosylquercetin',\n",
       " 'Syringic acid',\n",
       " '2,4,6-trimethoxybenzoic acid',\n",
       " '5-hydroxymethyl- 2-furancarboxaldehyde; 5-hydroxymethyl-2-furfuraldehyde',\n",
       " 'arjunolic acid',\n",
       " '20-hydroxyecdysone; polypodine A',\n",
       " 'polypodine B',\n",
       " 'stachysterone',\n",
       " 'shidasterone',\n",
       " 'ellagic acid 4-O-α-L-rhamnopyranoside; eschweilenol C',\n",
       " 'Isoorientin',\n",
       " 'schaftoside',\n",
       " 'carlinoside',\n",
       " '4-Nerolidilcatechol',\n",
       " 'Taraxerol acetate',\n",
       " \"Rel-(7R,8S,7'S,8'S)-4-hydroxy-4',5'-methylenedioxy-3,5,3'-trimethoxy-7,7'-epoxylignan\",\n",
       " \"Rel-(7R,8S,7'S,8'S)-4',5'-methylenedioxy-3,4,5,3'-tetramethoxy-7,7'-epoxylignan\",\n",
       " \"Rel-(7R,8S,7'S,8'S)-4'-hydroxy-3,4,5,3',5'-pentamethoxy-7,7'-epoxylignan\",\n",
       " \"Rel-(7R,8S,7'S,8'S)-4,5,4',5'-dimethylenedioxy-3,3'-dimethoxy-7,7'-epoxylignan\",\n",
       " \"Rel-(7R,8S,7'S,8'S)-9-hydroxy-4',5'-methylenedioxy-3,4,5,3'-tetramethoxy-7,7'-epoxylignan\",\n",
       " 'Pristimerin; 20α-3-hydroxy-2-oxo-24-nor-friedela-1-10,3,5,7-tetraen-carboxylic acid-29-methylester',\n",
       " 'Pimara-7,15-dien-3β-ol',\n",
       " 'Dimethyl terephthalate',\n",
       " '(22E,24R)-ergosta-4,6,8(14),22-tetraen-3-one',\n",
       " '8-hydroxy-6-methoxy-3-methylisocoumarin',\n",
       " 'Ergosterol peroxide',\n",
       " '5α-carboxystrictosidine',\n",
       " 'Turbinatine',\n",
       " '3,4-dehydro-strictosidine',\n",
       " '3,4-dehydrostrictosidine acid',\n",
       " 'Strictosidine acid',\n",
       " 'Cordifoline',\n",
       " 'Deoxycordifoline',\n",
       " 'Harman-3-carboxylic acid',\n",
       " '7-Methoxydiderroside',\n",
       " \"6'-Acetyl-β-D-glucopyranosyldiderroside\",\n",
       " 'Secoxyloganin',\n",
       " 'Diderroside',\n",
       " '6β-hydroxy-7-epigardoside methyl ester',\n",
       " '3β-O-[α-L-rhamnopyranosyl-(1→2)-O-β-D-glucopyranosyl-(1→2)-O-β-D-glucopyranosyl]-28-O-β-D-glucopyranoside pomolate',\n",
       " 'Ixoside',\n",
       " '3,4,5-trimethoxyphenyl 1-O-β-D-apiofuranosyl-(1→6)-O-β-D-glucopyranoside',\n",
       " \"Nitensoside A; Sorbifolin 6-O-α-rhamnopyranosyl(1'''→6'')-β-glucopyranoside\",\n",
       " \"Nitensoside B; Pedalitin 6-O-α-rhamnopyranosyl(1'''→6'')-β-glucopyranoside\",\n",
       " 'Sorbifolin',\n",
       " 'Sorbifolin 6-O-β-glucopyranoside',\n",
       " 'Pedalitin',\n",
       " 'Pedalin, pedalitin 6-O-β -glucopyranoside',\n",
       " '3-O-β-D-(6’-methyl)-glucopyranosyl-28-O-β-D-glucopyranosyl-oleanate',\n",
       " 'Oleanolic acid 3-sophoroside',\n",
       " '6α-acetoxymanoyl oxide',\n",
       " '6α-malonyloxymanoyl oxide',\n",
       " '6α-malonyloxy-n-butyl ester manoyl oxide',\n",
       " 'Ferulic acid',\n",
       " 'α-Gardiol',\n",
       " 'β-Gardiol',\n",
       " 'Sinapic acid',\n",
       " 'Quercetin 3-O-sophoroside',\n",
       " 'Chlorogenic acid',\n",
       " '3,4,5-Trimethoxyphenyl-1-O-β-D-(5-O-syringoyl)-apiofuranosyl-(1→6)-β-D-glucopyranoside',\n",
       " 'Gallic acid; 3,4,5-trihydroxybenzoic acid',\n",
       " 'Methyl gallate',\n",
       " 'n-Propyl gallate',\n",
       " 'Lauryl gallate',\n",
       " 'taxifolin',\n",
       " 'Ourateacatechin',\n",
       " '(-)-Epigallocatechin',\n",
       " 'Proanthocyanidin',\n",
       " 'Kaempferol 3-O-α-L-rhamnopyranosyl (1→6)-O-[β -D-glucopyranosyl (1→3)-O-α-L-rhamnopyranosyl-(1→2)]-O-β -D-glucopyranosyl',\n",
       " 'Quercetin 3-O-α-L-rhamnopyranosyl (1→6)-O-[β -D-glucopyranosyl (1→3)-O-α-L-rhamnopyranosyl-(1→2)]-O-β -D-glucopyranosyl',\n",
       " '6-methoxyeugenin',\n",
       " '9-hydroxyeugenin',\n",
       " 'Austdiol',\n",
       " 'Austdiol diacetate',\n",
       " 'Mycoleptone A tetraacetate',\n",
       " 'Mycoleptone B',\n",
       " 'Eugenitin',\n",
       " 'Mycoleptone A',\n",
       " '(2S)-2-methyl-8-(3\"-methylbut-2\"-enyl)-2-(4\\'-methylpent-3\\'-enyl)-2H-chromene-6-carboxylic acid',\n",
       " \"Gaudichaudianic acid; (2S)-2-methyl-2-(4'methyl-3'-pentenyl)-8-(3''-methyl-2-butenyl)- 2H-1-benzopyran-6-carboxylic acid\",\n",
       " '2,2-dimethyl-2H-chromene-6-carboxylic acid',\n",
       " \"(2S)-8-Isopentyl-2-methyl-2-(4'-methylpentyl)chroman-6-carboxylic acid\",\n",
       " '(2S)-Methyl-2-methyl-8-(3\"-methylbut-2\"-enyl)-2-(4\\'-methylpent-3\\'-enyl)-2H-chromene-6-carboxylate',\n",
       " \"(2S)-Methyl-8-isopentyl-2-methyl-2-(4'-methylpentyl)chroman-6-carboxylate\",\n",
       " 'Methyl-2,2-dimethylchroman-6-carboxylate',\n",
       " 'Methyl-8-hydroxy-2,2-dimethylchroman-6-carboxylate',\n",
       " \"Methyl-2,2-dimethyl-8-(3'-methylbut-2'-enyl)chroman-6-carboxylate\",\n",
       " 'Methyl-8-(ethanoyloxy)-2,2-dimethyl-2H-chromene-6-carboxylate',\n",
       " 'Methyl-8-hydroxy-2,2-dimethyl-2H-chromene-6-carboxylate',\n",
       " \"4-Methoxy-3-(3',7'-dimethylocta-2'-E-6'-dienyl)benzoic acid\",\n",
       " \"3-(3',7 '-dimethyl-2',6 '-octadienyl)-4-methoxy-benzoic acid\",\n",
       " '(+)-11α-Hydroxyerythravine',\n",
       " '(+)-Erythravine',\n",
       " '(+)-α-Hydroxyerysotrine',\n",
       " '(-)-3-O-acetyl-spectaline',\n",
       " \"2-(R)-Methyl-6-(S)-(tetradecyl-13'-one)-3(R)-O-tert-butyldimethylsilyl-piperidine\",\n",
       " \"7,4'-Dimethoxyflavone\",\n",
       " 'Fasciculiferin',\n",
       " 'Tithonine',\n",
       " 'Farnisine',\n",
       " \"7,4'-Dihydroxyflavone\",\n",
       " 'Sargachromenol',\n",
       " 'Sargaquinoic acid',\n",
       " \"Juruenolic acid; 2-(4'-Methylpentenyl-3)-10-oxoundecan-2,6-dienoic acid\",\n",
       " '17-(3,4-Methylenedioxyphenyl)-heptadecanoic acid',\n",
       " '19´-(3,4-Methylenedioxyphenyl)-nonadecanoic acid',\n",
       " '21´-(3,4-Methylenedioxyphenyl)-henicosanoic acid',\n",
       " '(+)-Guaiacin',\n",
       " 'Heveaflavone',\n",
       " 'Amentoflavone 7”,4”’-dimethyl ether',\n",
       " 'Podocarpusflavone A',\n",
       " 'Amentoflavone',\n",
       " '(+)-3-O-feruloylcassine',\n",
       " 'Sinapyl 4-O-β-D-glucopyranoside alcohol',\n",
       " 'Sinapyl 4-O-β-D-glucopyranoside aldehyde',\n",
       " 'N-acetylnonaine',\n",
       " 'Liriodenine',\n",
       " '3β-hydroxy-stigmast-5-en-7-one; 24-β-7-oxositosterol',\n",
       " 'Syringaldehyde',\n",
       " 'Platydesmine',\n",
       " 'Rel-(+)-(7S,9R,10S)-3,9,12-trihydroxycalamenene',\n",
       " 'Rel. (+)-(7S,10S) 3,12-dihydroxycalamenene',\n",
       " '3,12-Dihydroxycadalene',\n",
       " '3,11,12-Trihydroxycadalene',\n",
       " 'Casearin S',\n",
       " 'Casearin T',\n",
       " '(-)-Epigallocatechin-3-O-gallate',\n",
       " \"2,4-Dihydroxy-6-[(1'E,3'E)-penta-1', 3'-dienyl]-benzaldehyde\",\n",
       " 'Periconicin B',\n",
       " '(-) Cis-4-hydroxy-6-deoxyscytalone',\n",
       " '(4R)-4,8-dihydroxy-α-tetralone',\n",
       " 'Salacin',\n",
       " 'Maytenin, Tingenone',\n",
       " '20α-Hydroxymaytenin; 20-hydroxy-20-epi-tingenone',\n",
       " 'Netzahualcoyene',\n",
       " 'Egonol',\n",
       " 'Homoegonol',\n",
       " '(±)-Syringaresinol',\n",
       " '2-oxo-piperol B; (7S*, 8R*, 1R*, 3R*)-3,4,5-trimethoxy-3,7-cyclo-8,1-neolig-8-ene-2,4(3H)-dione',\n",
       " 'Piperol B',\n",
       " 'Burchellin',\n",
       " '2-Hexyl-3-methyl-butanodioic acid',\n",
       " 'Cytochalasin D',\n",
       " 'Griseofulvin',\n",
       " 'α-L-xylopyranosyl-(4\"→20)-(3-O-β-D-glucopyranosyl)-1\\'-O-E-caffeoyl-β-D-glucopyranoside',\n",
       " '1,6-di-O-caffeoyl-β-D-glucopyranoside',\n",
       " '1-O-(E)-caffeoyl-β-D-glucopyranoside',\n",
       " '1-O-(E)-feruloyl-β-D-glucopyranoside',\n",
       " 'Ethyl 2,4-dihydroxy-5,6-dimethylbenzoate',\n",
       " 'Phomopsilactone',\n",
       " '2-hydroxyphenylacetic acid',\n",
       " '7-Methyl-sargachromenol; 2,7,8-Trimethyl-2-[(3-E,7-Z)-4,12-dimethyl-8-carboxyl-3,7,11-tridecatrienyl]-3-chromen-6-ol, β-caroteno',\n",
       " 'Epi-guaiacin',\n",
       " 'Verrucosin',\n",
       " 'Nectandrin B',\n",
       " \"4-Hydroxy-(3',7'-dimethyl-1'-oxo-octa-2'-E-6'-dienyl)benzoic acid\",\n",
       " \"4-Hydroxy-3-(3',7'-dimethyl-3'-hydroxy-1'-oxo-6'-octenyl)benzoic acid\",\n",
       " \"1,4-Dihydroxy-2-(3',7'-dimethyl-1'-oxo-2'-E-6'-octadienyl)benzene\",\n",
       " \"Isosakuranetin; 5,7-dihydroxy-4'-methoxyflavanone\",\n",
       " \"Sakuranetin; 5,4'-dihydroxy-7-methoxyflavanone\",\n",
       " '2-Methyl-5-methoxy-benzopyran-4-one',\n",
       " \"(2'S)-2-(propan-2'-ol)-5-hydroxy-benzopyran-4-one\",\n",
       " '3-O-β-D-quinovopyranosyl quinovic acid',\n",
       " '3-O-β-D-quinovopyranosyl cincholic acid',\n",
       " '28-O-β-D-glucopyranosyl quinovic acid',\n",
       " 'Trans-3’-methylsulphonylallyl trans-cinnamate',\n",
       " 'Galioside',\n",
       " 'Galioside aglicone',\n",
       " 'Apodanthoside',\n",
       " '11-O-trans-feruloylteucrein',\n",
       " 'Teucrein',\n",
       " \"4-Hydroxy-(3',7'-dimethyl-1'-oxo-octa-2'-Z-6'-dienyl)benzoic acid\",\n",
       " '3,4,5-Trimethoxydihydrocinnamic acid',\n",
       " \"Aduncumene; Methyl 2-methoxy-5-(3'-methyl-1'-oxo-2'-butenyl)benzoate\",\n",
       " \"2',6'-Dihydroxy-4'-methoxydihydrochalcone\",\n",
       " 'Piperaduncine B',\n",
       " \"Methyl 4-hydroxy-3-(3'-methyl-2'-butenyl)benzoate\",\n",
       " \"Methyl 4-hydroxy-3-(3'-methyl-2'-hydroxy-3'-butenyl)benzoate\",\n",
       " \"Hostmaniene; 4-Hydroxy-3-(2',3'-dihydroxy-3'-methylbutyl)benzoate\",\n",
       " 'Methyl 2,2-dimethyl-1-oxo-2H-1-benzopyran-6-carboxylate',\n",
       " \"4-Hydroxy-3-(3',7'-dimethylocta-2'-E-6'-dienyl)benzoic acid\",\n",
       " \"Methyl taboganate; Methyl 4-hydroxy-3-(3'-methyl-1'-oxo-2'-butenyl)benzoate\",\n",
       " 'Chlorogenic acid methyl ester, Methyl (1S,3R,4R,5R)-3-{[(2E)-3-(3,4-dihydroxyphenyl)-2-propenoyl]oxy}-1,4,5-trihydroxycyclohexanecarboxylate',\n",
       " \"2-(2'-O-trans-caffeoyl)-C-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone\",\n",
       " \"2-(2'-O-trans-cinnamoyl)-C-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone\",\n",
       " \"2-(2'-O-transcoumaroyl)-C-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone\",\n",
       " 'Mangiferin',\n",
       " \"2-(2'-O-benzoyl)-C-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone\",\n",
       " 'Muraxanthone',\n",
       " '22β-hydroxypristimerin',\n",
       " 'Cognatine',\n",
       " 'Netzahualcoyonol',\n",
       " 'Netzahualcoyondiol',\n",
       " '2α,3α-Dihydroxy-urs-12-en-28-oic acid',\n",
       " 'Stearic acid 4-pentoyloxyphenethyl ester',\n",
       " 'Dipropyl disulphide',\n",
       " 'Dibenzyl sulphide',\n",
       " 'Dibenzyl disulphide',\n",
       " 'Dibenzyl trisulphide',\n",
       " 'Dibenzyl tetrasulphide',\n",
       " 'Benzylhydroxymethyl sulphide',\n",
       " 'Di(benzyltrithio) methane',\n",
       " \"5-(3'' -Hydroxypropyl)-7-methoxy-2-(3',4' -methyl-enedioxyphenyl)benzofuran\",\n",
       " \"5-[3''-(β-D-glucopyranosyloxy)propyl]-7-methoxy-2-(3',4'-methylenedioxyphenyl)benzofuran\",\n",
       " \"5-[3''-(β-D-glucopyranosyloxy)propyl]-7-methoxy-2-(3',4'-dimethoxyphenyl)benzofuran\",\n",
       " 'Di-hydrodehydrodiconiferyl alcohol',\n",
       " 'Nitensidine A',\n",
       " 'Nitensidine B',\n",
       " 'Nitensidine C',\n",
       " 'N-1,N-2,N-3-Triisopentenylguanidine',\n",
       " \"N-[7-(3',4'-methylenedioxyphenyl)-2(Z),4(Z)-heptadienoyl]pyrrolidine\",\n",
       " 'Viburgenin',\n",
       " 'Plumericin',\n",
       " 'Isoplumericin',\n",
       " '(-)-Spectalinine',\n",
       " 'Canavaline',\n",
       " 'Leptophyllin A',\n",
       " 'Chaetoglobosin B',\n",
       " '2-Methyl-4-hydroxy-butyl caffeoate',\n",
       " 'β-photogedunin',\n",
       " 'Aphidicolin',\n",
       " \"Acteoside; [β-3,4-dihydroxyphenyl)-ethyl]-(3'-O-α-L-rhamnopyranosyl)-(4'-O-cafeoyl)-β-D-glycopyranoside, verbascoside\",\n",
       " 'Luteolin; 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one',\n",
       " \"2',5-dihydroxy-3-methoxy-8-dimethylallyl-6, 7-(2' ',2''-dimethylpyrano)-dihydroflavonol\",\n",
       " '(3R,4R)-3,4-Dihydro-4,6-dihydroxy-3-methyl-1-oxo-1H-isochromene-5-carboxylic acid',\n",
       " '(R)-7-Hydroxymellein',\n",
       " '(3R,4R)-4,7-Dihydroxymellein',\n",
       " 'Leiokinine A',\n",
       " 'Leptomerine',\n",
       " 'Kokusaginine',\n",
       " 'Maculosidine',\n",
       " 'Skimmianine',\n",
       " '3-Acetyl aleuritolic acid',\n",
       " '19,20-Epoxycytochalasin D',\n",
       " '19,20-Epoxycytochalasin C',\n",
       " '19,20-Epoxycytochalasin N',\n",
       " '19,20-Epoxycytochalasin Q',\n",
       " '19,20-Epoxycytochalasin R',\n",
       " 'Chalepin',\n",
       " 'Isopropyl gallate',\n",
       " 'n-Butyl gallate',\n",
       " 'Isobutyl gallate',\n",
       " 'n-Pentyl gallate',\n",
       " '3,4,5-Triacetoxybenzoic acid',\n",
       " 'p-Coumaric acid',\n",
       " 'Casearupestrin A',\n",
       " 'Casearupestrin B',\n",
       " 'Casearupestrin C',\n",
       " 'Casearupestrin D',\n",
       " '2,7-Di-O-acetylcasearupestrin A',\n",
       " '2,6-di-O-acetylcasearupestrin D',\n",
       " 'Isopimpinellin',\n",
       " 'Xanthyletin',\n",
       " 'Orcinol',\n",
       " 'Cyclo-(L-Pro-L-Val)',\n",
       " 'Uracil',\n",
       " '4-Hydroxymellein',\n",
       " '8-methoxymellein',\n",
       " '5-hydroxymellein',\n",
       " 'β-caryophyllene, trans-caryophyllene',\n",
       " 'cyclo (L)-Pro-Gly',\n",
       " '1,2-dihydro- 3β-hydroxy-7-deacetoxy-7-oxogedunin',\n",
       " 'Photogedunin',\n",
       " \"3,4-dimethyl-2-(4'-hydroxy-3',5'-dimethoxyphenyl)-5-methoxy-tetrahydrofuran\",\n",
       " '1-[3-(3,7-dimethylocta-2,6-dien-1-yl)-2,4,6- trihydroxyphenyl]-3-(4-hydroxyphenyl)propan-1-one',\n",
       " '1- (5,7-dihydroxy-2,2-dimethylchroman-6-yl)-3-(2,2-dimethylchroman- 6-yl)propan-1-one',\n",
       " '1-(5,7-dihydroxy-2,2-dimethylchroman- 6-yl)-3-[4-hydroxy-3-(3-methylbut-2-en-1-yl)- phenyl]propan-1-one',\n",
       " '1-(5,7-dihydroxy-2,2-dimethylchroman-6-yl)-3-(1,1,4a-trimethyl-2,3,4,4a,9a-hexahydro-1H-xanthen-7-yl)propan-1-one',\n",
       " 'urauchimycin A',\n",
       " 'urauchimycin B',\n",
       " \"7-Hydroxy-4',6-dimethoxyisoflavone; Afrormosin; Afromosin\",\n",
       " 'germacrene D',\n",
       " 'Tagitinin C',\n",
       " '1-methoxy-3-hydroxy-3,10b-4,5a-diepoxy-8b-isobutyroyloxygermacr-11(13)-en-6a,12-olide',\n",
       " 'Anhydrofusarubin',\n",
       " 'Beauvericin',\n",
       " 'ω-fenil alcanoic acid',\n",
       " 'Alkenoic acid',\n",
       " '1,3,5-trihydroxy-4-methoxy-10-methyl- 2,8-bis(3-methylbut-2-enyl)acridin-9(10H)-one',\n",
       " '1,3,5-trihydroxy- 2,8-bis(3-methylbut-2-enyl)-10-methyl-9-acridone',\n",
       " 'Glycocitrine-IV',\n",
       " 'Glycocitrine-I',\n",
       " 'Citrusinine-II',\n",
       " 'Citrusinine-I',\n",
       " '5-hydroxynoracronycine; Atalaphyllidine',\n",
       " 'Pyranofoline',\n",
       " '3,4-dihydro-3,5,8-trihydroxy-6-methoxy-2,2,7-trimethyl-2Hpyrano[ 2,3-a]acridin-12(7H)-one',\n",
       " '11β-acetoxyobacunone',\n",
       " 'cryptomeridiol',\n",
       " 'Hispidol A',\n",
       " 'Piscidinol A',\n",
       " 'Pentaol',\n",
       " 'Nilocetin',\n",
       " 'Iso-odoratol',\n",
       " '3,11-dioxoolean-12-en-28- onic acid',\n",
       " 'Oleanonic acid',\n",
       " 'citrusinine-I',\n",
       " 'atalaphyllinine',\n",
       " 'des-N-methylnoracronycine',\n",
       " '5-hydroxy-N-methylseverifoline',\n",
       " '24-methylenecycloartan-3b-ol',\n",
       " '24-methylene-3,22-dihydroxycholesterol',\n",
       " '5,7-dimethoxy-2,2-dimethyl-2H-1-benzopyran-6-propanoate',\n",
       " '5,7-dimethoxy-2,2-dimethyl-2H-1-benzopyran-6-propanoic acid',\n",
       " '2-butyl-D-fructofuranoside',\n",
       " '3-Oxoursolic acid',\n",
       " '2-phenyl-4H-chromen-4-one',\n",
       " 'Haplotusine',\n",
       " 'β-Sitosterol benzoate',\n",
       " '5-hydroxyflavone',\n",
       " 'Cabraleadiol',\n",
       " 'Ocotillone',\n",
       " 'Odoratone',\n",
       " 'Odoratol',\n",
       " '22-hydroxytirucalla-7,24-diene-2,3-dione',\n",
       " 'Acetonide of odoratol',\n",
       " 'Gedunin',\n",
       " '6α-acetoxy-14β,15β-epoxyazadirone',\n",
       " 'toonacilin',\n",
       " 'Citibrasine',\n",
       " '2,3-dihydro-4,9-dihydroxy-2-(2-hydroxy-propan-2-yl)- 11-methoxy-10-methylfuro[3,2-b]acridin-5(10H)-one',\n",
       " 'bis-5-hydroxyacronycine',\n",
       " \"Myrsinoic acid A, 3-Geranyl-4-hydroxy-5-(3'',3''-dimethylallyl)benzoic acid\",\n",
       " '4-metoxi-6-[2-(metilamino)fenil]- 2H-piran-2-ona',\n",
       " 'Methyl angolensate',\n",
       " 'limonexic acid',\n",
       " 'Ricinine',\n",
       " 'p-hydroxybenzoic acid',\n",
       " '2α,3α-dihydroxyolean-12- en-28-oic acid',\n",
       " '2α,3α,19α- trihydroxyurs-12-en-28-oic acid',\n",
       " 'Chrysoeriol',\n",
       " 'acacetin',\n",
       " '3-O-methylquercetin',\n",
       " '3,3-O-dimethylquercetin',\n",
       " '3,7,4-O-trimethylkaempferol',\n",
       " 'penduletin 4-O-methyl ether',\n",
       " 'Methacrylic acid',\n",
       " \"3',4',5',3,5,7,8-heptamethoxyflavone\",\n",
       " \"3,5,6,7,3',4',5'-heptamethoxyflavonol\",\n",
       " 'amorphispironone',\n",
       " 'scillascillin',\n",
       " 'α-eudesmol',\n",
       " 'guaiol',\n",
       " 'Hinesol',\n",
       " 'γ-eudesmol',\n",
       " \"2'-hydroxy-3,4,4'-trimethoxy-5',6'-(2'',2''-dimethylpyrano)-chalcone\",\n",
       " \"3',4'-methylenedioxy-5,7-dimethoxyflavone\",\n",
       " \"3',4'-methylenedioxy-5,6,7- trimethoxyflavone\",\n",
       " \"3',4'-methylenedioxy-5,5',6,7-tetramethoxyflavone\",\n",
       " \"3',4',5',5,7,8-hexamethoxyflavone\",\n",
       " \"8-hydroxy-3,5,7,3',4',5'-hexamethoxyflavonol\",\n",
       " \"3',4',5',5,7-pentamethoxyflavone\",\n",
       " 'neoisoastilbin',\n",
       " '21α,25-dimethylmelianodiol',\n",
       " '21β,25-dimethylmelianodiol',\n",
       " '3,21-Di-epi-feroniellide B',\n",
       " '7-hydroxy-3- (11-dimethylallyl)-8-methoxycoumarin',\n",
       " 'fumiquinozoline F',\n",
       " '[8]-gingerol',\n",
       " '[10]-gingerol',\n",
       " '2-n-nonyl-4-quinolone',\n",
       " '1-methyl-2-n-nonyl-4-quinolone',\n",
       " '(−)-Grandisin',\n",
       " '(3-(2-(4-hydroxyphenyl)-2-oxoethyl)-5,6-dihydropyridin- 2(1H)-one)',\n",
       " 'fraxinellone',\n",
       " 'fraxinellonone',\n",
       " 'epoxy-fraxinellone',\n",
       " 'Picramnioside F',\n",
       " 'Mayoside C',\n",
       " '2-n-Propylquinoline',\n",
       " '2-n-Pentylquinoline',\n",
       " \"2-(1'-pentenyl)-Quinoline\",\n",
       " \"2-(3',4'-methylenedioxyphenylethyl)-Quinoline\",\n",
       " 'Cuspanine; 1-hydroxy-2,3,5,6-tetramethoxy-9-acridone',\n",
       " 'Cusculine; 1,2,3,5,6-pentamethoxy-9-acridone',\n",
       " '5-pentadecylresorcinol',\n",
       " '6-pentadecylsalicylic acid',\n",
       " '2-methyl-5-pentadecylresorcinol',\n",
       " '5-[8(Z)-pentadecenyl]resorcinol',\n",
       " '2-methyl-5-[8(Z)-pentadecenyl]resorcinol',\n",
       " '2-methyl-5-[8(Z),11(Z)-pentadecadienyl]resorcinol',\n",
       " '2-methyl-5-[8(Z),11(Z),14-pentadecatrienyl]resorcinol',\n",
       " '5-[8(Z),11(Z),14-pentadecatrienyl]resorcinol',\n",
       " '5-[8(Z),11(Z)-pentadecadienyl]resorcinol',\n",
       " '6-[8(Z)-pentadecenyl]salicylic acid',\n",
       " '6-[8(Z),11(Z),14-pentadecatrienyl]salicylic acid',\n",
       " '6-[ 8(Z),11(Z) -pentadecadienyl] salicylic acid',\n",
       " 'Piperovatine']"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[node for node in G.nodes() if G.nodes[node]['group'] == 'name']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "nx.write_gpickle(G, \"{}hin03-05.gpickle\".format(path))"
   ]
  }
 ],
 "metadata": {
  "interpreter": {
   "hash": "fb93546e6995fdb0878df83f1978a6e198dddb57421150bbcbdd2209f86aef4c"
  },
  "kernelspec": {
   "display_name": "Python 3.8.13 ('biotopic')",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
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   "nbconvert_exporter": "python",
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