{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Cobra model parser"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we can produce dfs relevant for the \"modelReaction_data_I\" INCA tools input"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This example notebook illustrates the use of a parser that prepares part the input for other BFAIR tools, the MFA tools. This will have to be done if you want to run MFA based on a metabolic model that has not been processed before. As of now, processing tools for .json and .sbml files are provided. The procedure is the same for either file type but one example each with the corresponding output is provided."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Academic license - for non-commercial use only - expires 2021-05-28\n",
      "Using license file /Users/matmat/gurobi.lic\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Determination of memory status is not supported on this \n",
      " platform, measuring for memoryleaks will never fail\n"
     ]
    }
   ],
   "source": [
    "import cobra\n",
    "import pandas as pd\n",
    "\n",
    "# BFAIR dependencies\n",
    "from BFAIR.INCA import parse_cobra_model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "model_data, reaction_data, metabolite_data = parse_cobra_model('data/FIA_MS_example/database_files/iJO1366.json', 'E. coli', '10-03-2021')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>model_id</th>\n",
       "      <th>date</th>\n",
       "      <th>model_description</th>\n",
       "      <th>model_file</th>\n",
       "      <th>file_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>10-03-2021</td>\n",
       "      <td></td>\n",
       "      <td>{\\n\"metabolites\":[\\n{\\n\"id\":\"10fthf_c\",\\n\"name...</td>\n",
       "      <td>json</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  model_id        date model_description  \\\n",
       "0  E. coli  10-03-2021                     \n",
       "\n",
       "                                          model_file file_type  \n",
       "0  {\\n\"metabolites\":[\\n{\\n\"id\":\"10fthf_c\",\\n\"name...      json  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "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>model_id</th>\n",
       "      <th>rxn_id</th>\n",
       "      <th>rxn_name</th>\n",
       "      <th>equation</th>\n",
       "      <th>subsystem</th>\n",
       "      <th>gpr</th>\n",
       "      <th>genes</th>\n",
       "      <th>reactants_stoichiometry</th>\n",
       "      <th>reactants_ids</th>\n",
       "      <th>products_stoichiometry</th>\n",
       "      <th>products_ids</th>\n",
       "      <th>lower_bound</th>\n",
       "      <th>upper_bound</th>\n",
       "      <th>objective_coefficient</th>\n",
       "      <th>flux_units</th>\n",
       "      <th>reversibility</th>\n",
       "      <th>used_</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>EX_cm_e</td>\n",
       "      <td>Chloramphenicol exchange</td>\n",
       "      <td>cm_e --&gt;</td>\n",
       "      <td>Extracellular exchange</td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-1.0]</td>\n",
       "      <td>[cm_e]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>EX_cmp_e</td>\n",
       "      <td>CMP exchange</td>\n",
       "      <td>cmp_e --&gt;</td>\n",
       "      <td>Extracellular exchange</td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-1.0]</td>\n",
       "      <td>[cmp_e]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>EX_co2_e</td>\n",
       "      <td>CO2 exchange</td>\n",
       "      <td>co2_e &lt;=&gt;</td>\n",
       "      <td>Extracellular exchange</td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-1.0]</td>\n",
       "      <td>[co2_e]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>-1000.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>EX_cobalt2_e</td>\n",
       "      <td>Co2+ exchange</td>\n",
       "      <td>cobalt2_e &lt;=&gt;</td>\n",
       "      <td>Extracellular exchange</td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-1.0]</td>\n",
       "      <td>[cobalt2_e]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>-1000.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>DM_4crsol_c</td>\n",
       "      <td>Sink needed to allow p-Cresol to leave system</td>\n",
       "      <td>4crsol_c --&gt;</td>\n",
       "      <td>Intracellular demand</td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-1.0]</td>\n",
       "      <td>[4crsol_c]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2578</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>RNDR4</td>\n",
       "      <td>Ribonucleoside-diphosphate reductase (UDP)</td>\n",
       "      <td>trdrd_c + udp_c --&gt; dudp_c + h2o_c + trdox_c</td>\n",
       "      <td>Nucleotide Salvage Pathway</td>\n",
       "      <td>((b2234 and b2235) and b3781) or ((b2234 and b...</td>\n",
       "      <td>[b2234, b3781, b2235, b2582]</td>\n",
       "      <td>[-1.0, -1.0]</td>\n",
       "      <td>[trdrd_c, udp_c]</td>\n",
       "      <td>[1.0, 1.0, 1.0]</td>\n",
       "      <td>[dudp_c, h2o_c, trdox_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2579</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>RNDR4b</td>\n",
       "      <td>Ribonucleoside-diphosphate reductase (UDP) (gl...</td>\n",
       "      <td>grxrd_c + udp_c --&gt; dudp_c + grxox_c + h2o_c</td>\n",
       "      <td>Nucleotide Salvage Pathway</td>\n",
       "      <td>(b0849 and (b2675 and b2676)) or (b1064 and (b...</td>\n",
       "      <td>[b2675, b3610, b0849, b1064, b1654, b2676]</td>\n",
       "      <td>[-1.0, -1.0]</td>\n",
       "      <td>[grxrd_c, udp_c]</td>\n",
       "      <td>[1.0, 1.0, 1.0]</td>\n",
       "      <td>[dudp_c, grxox_c, h2o_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2580</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>RNTR1c2</td>\n",
       "      <td>Ribonucleoside-triphosphate reductase (ATP) (f...</td>\n",
       "      <td>atp_c + 2.0 flxr_c + 2.0 h_c --&gt; datp_c + 2.0 ...</td>\n",
       "      <td>Nucleotide Salvage Pathway</td>\n",
       "      <td>(b0684 and b3924 and b4238 and b4237) or (b289...</td>\n",
       "      <td>[b0684, b4238, b2895, b4237, b3924]</td>\n",
       "      <td>[-1.0, -2.0, -2.0]</td>\n",
       "      <td>[atp_c, flxr_c, h_c]</td>\n",
       "      <td>[1.0, 2.0, 1.0]</td>\n",
       "      <td>[datp_c, flxso_c, h2o_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2581</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>RNTR2c2</td>\n",
       "      <td>Ribonucleoside-triphosphate reductase (GTP) (f...</td>\n",
       "      <td>2.0 flxr_c + gtp_c + 2.0 h_c --&gt; dgtp_c + 2.0 ...</td>\n",
       "      <td>Nucleotide Salvage Pathway</td>\n",
       "      <td>(b0684 and b3924 and b4238 and b4237) or (b289...</td>\n",
       "      <td>[b0684, b4238, b2895, b4237, b3924]</td>\n",
       "      <td>[-2.0, -1.0, -2.0]</td>\n",
       "      <td>[flxr_c, gtp_c, h_c]</td>\n",
       "      <td>[1.0, 2.0, 1.0]</td>\n",
       "      <td>[dgtp_c, flxso_c, h2o_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2582</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>RNTR3c2</td>\n",
       "      <td>Ribonucleoside-triphosphate reductase (CTP) (f...</td>\n",
       "      <td>ctp_c + 2.0 flxr_c + 2.0 h_c --&gt; dctp_c + 2.0 ...</td>\n",
       "      <td>Nucleotide Salvage Pathway</td>\n",
       "      <td>(b0684 and b3924 and b4238 and b4237) or (b289...</td>\n",
       "      <td>[b0684, b4238, b2895, b4237, b3924]</td>\n",
       "      <td>[-1.0, -2.0, -2.0]</td>\n",
       "      <td>[ctp_c, flxr_c, h_c]</td>\n",
       "      <td>[1.0, 2.0, 1.0]</td>\n",
       "      <td>[dctp_c, flxso_c, h2o_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2583 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     model_id        rxn_id  \\\n",
       "0     E. coli       EX_cm_e   \n",
       "1     E. coli      EX_cmp_e   \n",
       "2     E. coli      EX_co2_e   \n",
       "3     E. coli  EX_cobalt2_e   \n",
       "4     E. coli   DM_4crsol_c   \n",
       "...       ...           ...   \n",
       "2578  E. coli         RNDR4   \n",
       "2579  E. coli        RNDR4b   \n",
       "2580  E. coli       RNTR1c2   \n",
       "2581  E. coli       RNTR2c2   \n",
       "2582  E. coli       RNTR3c2   \n",
       "\n",
       "                                               rxn_name  \\\n",
       "0                              Chloramphenicol exchange   \n",
       "1                                          CMP exchange   \n",
       "2                                          CO2 exchange   \n",
       "3                                         Co2+ exchange   \n",
       "4         Sink needed to allow p-Cresol to leave system   \n",
       "...                                                 ...   \n",
       "2578         Ribonucleoside-diphosphate reductase (UDP)   \n",
       "2579  Ribonucleoside-diphosphate reductase (UDP) (gl...   \n",
       "2580  Ribonucleoside-triphosphate reductase (ATP) (f...   \n",
       "2581  Ribonucleoside-triphosphate reductase (GTP) (f...   \n",
       "2582  Ribonucleoside-triphosphate reductase (CTP) (f...   \n",
       "\n",
       "                                               equation  \\\n",
       "0                                             cm_e -->    \n",
       "1                                            cmp_e -->    \n",
       "2                                            co2_e <=>    \n",
       "3                                        cobalt2_e <=>    \n",
       "4                                         4crsol_c -->    \n",
       "...                                                 ...   \n",
       "2578       trdrd_c + udp_c --> dudp_c + h2o_c + trdox_c   \n",
       "2579       grxrd_c + udp_c --> dudp_c + grxox_c + h2o_c   \n",
       "2580  atp_c + 2.0 flxr_c + 2.0 h_c --> datp_c + 2.0 ...   \n",
       "2581  2.0 flxr_c + gtp_c + 2.0 h_c --> dgtp_c + 2.0 ...   \n",
       "2582  ctp_c + 2.0 flxr_c + 2.0 h_c --> dctp_c + 2.0 ...   \n",
       "\n",
       "                       subsystem  \\\n",
       "0         Extracellular exchange   \n",
       "1         Extracellular exchange   \n",
       "2         Extracellular exchange   \n",
       "3         Extracellular exchange   \n",
       "4           Intracellular demand   \n",
       "...                          ...   \n",
       "2578  Nucleotide Salvage Pathway   \n",
       "2579  Nucleotide Salvage Pathway   \n",
       "2580  Nucleotide Salvage Pathway   \n",
       "2581  Nucleotide Salvage Pathway   \n",
       "2582  Nucleotide Salvage Pathway   \n",
       "\n",
       "                                                    gpr  \\\n",
       "0                                                         \n",
       "1                                                         \n",
       "2                                                         \n",
       "3                                                         \n",
       "4                                                         \n",
       "...                                                 ...   \n",
       "2578  ((b2234 and b2235) and b3781) or ((b2234 and b...   \n",
       "2579  (b0849 and (b2675 and b2676)) or (b1064 and (b...   \n",
       "2580  (b0684 and b3924 and b4238 and b4237) or (b289...   \n",
       "2581  (b0684 and b3924 and b4238 and b4237) or (b289...   \n",
       "2582  (b0684 and b3924 and b4238 and b4237) or (b289...   \n",
       "\n",
       "                                           genes reactants_stoichiometry  \\\n",
       "0                                             []                  [-1.0]   \n",
       "1                                             []                  [-1.0]   \n",
       "2                                             []                  [-1.0]   \n",
       "3                                             []                  [-1.0]   \n",
       "4                                             []                  [-1.0]   \n",
       "...                                          ...                     ...   \n",
       "2578                [b2234, b3781, b2235, b2582]            [-1.0, -1.0]   \n",
       "2579  [b2675, b3610, b0849, b1064, b1654, b2676]            [-1.0, -1.0]   \n",
       "2580         [b0684, b4238, b2895, b4237, b3924]      [-1.0, -2.0, -2.0]   \n",
       "2581         [b0684, b4238, b2895, b4237, b3924]      [-2.0, -1.0, -2.0]   \n",
       "2582         [b0684, b4238, b2895, b4237, b3924]      [-1.0, -2.0, -2.0]   \n",
       "\n",
       "             reactants_ids products_stoichiometry              products_ids  \\\n",
       "0                   [cm_e]                     []                        []   \n",
       "1                  [cmp_e]                     []                        []   \n",
       "2                  [co2_e]                     []                        []   \n",
       "3              [cobalt2_e]                     []                        []   \n",
       "4               [4crsol_c]                     []                        []   \n",
       "...                    ...                    ...                       ...   \n",
       "2578      [trdrd_c, udp_c]        [1.0, 1.0, 1.0]  [dudp_c, h2o_c, trdox_c]   \n",
       "2579      [grxrd_c, udp_c]        [1.0, 1.0, 1.0]  [dudp_c, grxox_c, h2o_c]   \n",
       "2580  [atp_c, flxr_c, h_c]        [1.0, 2.0, 1.0]  [datp_c, flxso_c, h2o_c]   \n",
       "2581  [flxr_c, gtp_c, h_c]        [1.0, 2.0, 1.0]  [dgtp_c, flxso_c, h2o_c]   \n",
       "2582  [ctp_c, flxr_c, h_c]        [1.0, 2.0, 1.0]  [dctp_c, flxso_c, h2o_c]   \n",
       "\n",
       "      lower_bound  upper_bound  objective_coefficient       flux_units  \\\n",
       "0             0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "1             0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "2         -1000.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "3         -1000.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "4             0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "...           ...          ...                    ...              ...   \n",
       "2578          0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "2579          0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "2580          0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "2581          0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "2582          0.0       1000.0                    0.0  mmol*gDW-1*hr-1   \n",
       "\n",
       "      reversibility  used_  \n",
       "0             False   True  \n",
       "1             False   True  \n",
       "2              True   True  \n",
       "3              True   True  \n",
       "4             False   True  \n",
       "...             ...    ...  \n",
       "2578          False   True  \n",
       "2579          False   True  \n",
       "2580          False   True  \n",
       "2581          False   True  \n",
       "2582          False   True  \n",
       "\n",
       "[2583 rows x 17 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "reaction_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
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       "      <th>model_id</th>\n",
       "      <th>met_name</th>\n",
       "      <th>met_id</th>\n",
       "      <th>formula</th>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>10-Formyltetrahydrofolate</td>\n",
       "      <td>10fthf_c</td>\n",
       "      <td>C20H21N7O7</td>\n",
       "      <td>-2</td>\n",
       "      <td>c</td>\n",
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       "      <th>1</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)</td>\n",
       "      <td>12dgr120_c</td>\n",
       "      <td>C27H52O5</td>\n",
       "      <td>0</td>\n",
       "      <td>c</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>1,2-Diacyl-sn-glycerol (ditetradecanoyl, n-C14:0)</td>\n",
       "      <td>12dgr140_c</td>\n",
       "      <td>C31H60O5</td>\n",
       "      <td>0</td>\n",
       "      <td>c</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>1,2-Diacyl-sn-glycerol (ditetradec-7-enoyl, n-...</td>\n",
       "      <td>12dgr141_c</td>\n",
       "      <td>C31H56O5</td>\n",
       "      <td>0</td>\n",
       "      <td>c</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>1,2-Diacyl-sn-glycerol (dihexadecanoyl, n-C16:0)</td>\n",
       "      <td>12dgr160_c</td>\n",
       "      <td>C35H68O5</td>\n",
       "      <td>0</td>\n",
       "      <td>c</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>1800</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>D-Serine</td>\n",
       "      <td>ser__D_p</td>\n",
       "      <td>C3H7NO3</td>\n",
       "      <td>0</td>\n",
       "      <td>p</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1801</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>L-Serine</td>\n",
       "      <td>ser__L_p</td>\n",
       "      <td>C3H7NO3</td>\n",
       "      <td>0</td>\n",
       "      <td>p</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1802</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>Shikimate</td>\n",
       "      <td>skm_p</td>\n",
       "      <td>C7H9O5</td>\n",
       "      <td>-1</td>\n",
       "      <td>p</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
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       "    <tr>\n",
       "      <th>1803</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>Selenite</td>\n",
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       "      <td>O3Se</td>\n",
       "      <td>-2</td>\n",
       "      <td>p</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
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       "    <tr>\n",
       "      <th>1804</th>\n",
       "      <td>E. coli</td>\n",
       "      <td>Sulfur dioxide</td>\n",
       "      <td>so2_p</td>\n",
       "      <td>O2S</td>\n",
       "      <td>0</td>\n",
       "      <td>p</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1805 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     model_id                                           met_name      met_id  \\\n",
       "0     E. coli                          10-Formyltetrahydrofolate    10fthf_c   \n",
       "1     E. coli     1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)  12dgr120_c   \n",
       "2     E. coli  1,2-Diacyl-sn-glycerol (ditetradecanoyl, n-C14:0)  12dgr140_c   \n",
       "3     E. coli  1,2-Diacyl-sn-glycerol (ditetradec-7-enoyl, n-...  12dgr141_c   \n",
       "4     E. coli   1,2-Diacyl-sn-glycerol (dihexadecanoyl, n-C16:0)  12dgr160_c   \n",
       "...       ...                                                ...         ...   \n",
       "1800  E. coli                                           D-Serine    ser__D_p   \n",
       "1801  E. coli                                           L-Serine    ser__L_p   \n",
       "1802  E. coli                                          Shikimate       skm_p   \n",
       "1803  E. coli                                           Selenite      slnt_p   \n",
       "1804  E. coli                                     Sulfur dioxide       so2_p   \n",
       "\n",
       "         formula  charge compartment  bound  used_  \n",
       "0     C20H21N7O7      -2           c    0.0   True  \n",
       "1       C27H52O5       0           c    0.0   True  \n",
       "2       C31H60O5       0           c    0.0   True  \n",
       "3       C31H56O5       0           c    0.0   True  \n",
       "4       C35H68O5       0           c    0.0   True  \n",
       "...          ...     ...         ...    ...    ...  \n",
       "1800     C3H7NO3       0           p    0.0   True  \n",
       "1801     C3H7NO3       0           p    0.0   True  \n",
       "1802      C7H9O5      -1           p    0.0   True  \n",
       "1803        O3Se      -2           p    0.0   True  \n",
       "1804         O2S       0           p    0.0   True  \n",
       "\n",
       "[1805 rows x 8 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metabolite_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "'' is not a valid SBML 'SId'.\n"
     ]
    }
   ],
   "source": [
    "model_data, reaction_data, metabolite_data = parse_cobra_model('data/FIA_MS_example/database_files/wormjam-20180125.sbml', 'C. elegans', '10-03-2021')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "     model_id        date model_description  \\\n",
       "0  C. elegans  10-03-2021                     \n",
       "\n",
       "                                          model_file file_type  \n",
       "0  <?xml version='1.0' encoding='UTF-8'?>\\n<sbml ...      sbml  "
      ]
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     "execution_count": 7,
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   "source": [
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  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "      <th>0</th>\n",
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       "      <td>-1000.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
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       "      <td>True</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>ACACCT_m</td>\n",
       "      <td>acetoacetyl-CoA:acetate CoA-transferase</td>\n",
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       "      <td>WBGene00007330</td>\n",
       "      <td>[WBGene00007330]</td>\n",
       "      <td>[-1.0, -1.0]</td>\n",
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       "      <td>[1.0, 1.0]</td>\n",
       "      <td>[aacoa_m, ac_m]</td>\n",
       "      <td>-1000.0</td>\n",
       "      <td>1000.0</td>\n",
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       "      <th>2</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>1_2_1_18_RXN_m</td>\n",
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       "      <td>[WBGene00000114]</td>\n",
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       "      <td>[coa_m, msa_m, nadp_m]</td>\n",
       "      <td>[1.0, 1.0, 1.0]</td>\n",
       "      <td>[accoa_m, co2_m, nadph_m]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>ACYLCOASYN_RXN_c</td>\n",
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       "      <td>atp_c + coa_c + fatacid_c --&gt; amp_c + fataccoa...</td>\n",
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       "      <td>[atp_c, coa_c, fatacid_c]</td>\n",
       "      <td>[1.0, 1.0, 1.0]</td>\n",
       "      <td>[amp_c, fataccoa_c, ppi_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>False</td>\n",
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       "      <th>4</th>\n",
       "      <td>C. elegans</td>\n",
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       "      <td>WBGene00009218</td>\n",
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       "      <td>[1.0, 1.0, 1.0]</td>\n",
       "      <td>[amp_m, fataccoa_m, ppi_m]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>3296</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>DARDMT_n</td>\n",
       "      <td>nuclear desoxyadenosine residue N6 demethylation</td>\n",
       "      <td>akg_n + mdadnr_n + o2_n --&gt; co2_n + dadnr_n + ...</td>\n",
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       "      <td>WBGene00017304</td>\n",
       "      <td>[WBGene00017304]</td>\n",
       "      <td>[-1.0, -1.0, -1.0]</td>\n",
       "      <td>[akg_n, mdadnr_n, o2_n]</td>\n",
       "      <td>[1.0, 1.0, 1.0]</td>\n",
       "      <td>[co2_n, dadnr_n, succ_n]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3297</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>DARMT_n</td>\n",
       "      <td>nuclear desoxyadenosine residue N6 methylation</td>\n",
       "      <td>amet_n + dadnr_n --&gt; ahcys_n + mdadnr_n</td>\n",
       "      <td></td>\n",
       "      <td>WBGene00015939</td>\n",
       "      <td>[WBGene00015939]</td>\n",
       "      <td>[-1.0, -1.0]</td>\n",
       "      <td>[amet_n, dadnr_n]</td>\n",
       "      <td>[1.0, 1.0]</td>\n",
       "      <td>[ahcys_n, mdadnr_n]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3298</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>OH_Exchange_reactions_e</td>\n",
       "      <td>OH transport</td>\n",
       "      <td>oh_e --&gt;</td>\n",
       "      <td></td>\n",
       "      <td>WBGene00007388</td>\n",
       "      <td>[WBGene00007388]</td>\n",
       "      <td>[-1.0]</td>\n",
       "      <td>[oh_e]</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3299</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>BIO0020</td>\n",
       "      <td>Assembly of free fatty acids pool for biomass ...</td>\n",
       "      <td>0.0171 arach_c + 1e-05 ddca_c + 1e-05 fa16p1n7...</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-0.0171, -1e-05, -1e-05, -0.0417, -0.0616, -0...</td>\n",
       "      <td>[arach_c, ddca_c, fa16p1n7_c, hdca_c, lnlc_c, ...</td>\n",
       "      <td>[1.0]</td>\n",
       "      <td>[freefatacid_c]</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3300</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>APOACP_SYNTH</td>\n",
       "      <td>apo-ACP protein synthesis (from amino acids)</td>\n",
       "      <td>0.090226 alatrna_c + 0.06015 argtrna_c + 0.007...</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[]</td>\n",
       "      <td>[-0.090226, -0.06015, -0.007519, -0.097744, -0...</td>\n",
       "      <td>[alatrna_c, argtrna_c, asntrna_c, asptrna_c, a...</td>\n",
       "      <td>[0.324, 1.0, 2.0, 2.324, 2.324, 0.090226, 0.06...</td>\n",
       "      <td>[adp_c, apoACP_c, gdp_c, h_c, pi_c, trnaala_c,...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>mmol*gDW-1*hr-1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3301 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        model_id                   rxn_id  \\\n",
       "0     C. elegans                 ACACCT_c   \n",
       "1     C. elegans                 ACACCT_m   \n",
       "2     C. elegans           1_2_1_18_RXN_m   \n",
       "3     C. elegans         ACYLCOASYN_RXN_c   \n",
       "4     C. elegans         ACYLCOASYN_RXN_m   \n",
       "...          ...                      ...   \n",
       "3296  C. elegans                 DARDMT_n   \n",
       "3297  C. elegans                  DARMT_n   \n",
       "3298  C. elegans  OH_Exchange_reactions_e   \n",
       "3299  C. elegans                  BIO0020   \n",
       "3300  C. elegans             APOACP_SYNTH   \n",
       "\n",
       "                                               rxn_name  \\\n",
       "0               acetoacetyl-CoA:acetate CoA-transferase   \n",
       "1               acetoacetyl-CoA:acetate CoA-transferase   \n",
       "2     Malonate-semialdehyde dehydrogenase (acetylating)   \n",
       "3             2,3,4-saturated fatty acyl-CoA synthetase   \n",
       "4             2,3,4-saturated fatty acyl-CoA synthetase   \n",
       "...                                                 ...   \n",
       "3296   nuclear desoxyadenosine residue N6 demethylation   \n",
       "3297     nuclear desoxyadenosine residue N6 methylation   \n",
       "3298                                       OH transport   \n",
       "3299  Assembly of free fatty acids pool for biomass ...   \n",
       "3300       apo-ACP protein synthesis (from amino acids)   \n",
       "\n",
       "                                               equation subsystem  \\\n",
       "0                   acac_c + accoa_c <=> aacoa_c + ac_c             \n",
       "1                   acac_m + accoa_m <=> aacoa_m + ac_m             \n",
       "2     coa_m + msa_m + nadp_m --> accoa_m + co2_m + n...             \n",
       "3     atp_c + coa_c + fatacid_c --> amp_c + fataccoa...             \n",
       "4     atp_m + coa_m + fatacid_m --> amp_m + fataccoa...             \n",
       "...                                                 ...       ...   \n",
       "3296  akg_n + mdadnr_n + o2_n --> co2_n + dadnr_n + ...             \n",
       "3297            amet_n + dadnr_n --> ahcys_n + mdadnr_n             \n",
       "3298                                          oh_e -->              \n",
       "3299  0.0171 arach_c + 1e-05 ddca_c + 1e-05 fa16p1n7...             \n",
       "3300  0.090226 alatrna_c + 0.06015 argtrna_c + 0.007...             \n",
       "\n",
       "                 gpr             genes  \\\n",
       "0     WBGene00007330  [WBGene00007330]   \n",
       "1     WBGene00007330  [WBGene00007330]   \n",
       "2     WBGene00000114  [WBGene00000114]   \n",
       "3     WBGene00009218  [WBGene00009218]   \n",
       "4     WBGene00009218  [WBGene00009218]   \n",
       "...              ...               ...   \n",
       "3296  WBGene00017304  [WBGene00017304]   \n",
       "3297  WBGene00015939  [WBGene00015939]   \n",
       "3298  WBGene00007388  [WBGene00007388]   \n",
       "3299                                []   \n",
       "3300                                []   \n",
       "\n",
       "                                reactants_stoichiometry  \\\n",
       "0                                          [-1.0, -1.0]   \n",
       "1                                          [-1.0, -1.0]   \n",
       "2                                    [-1.0, -1.0, -1.0]   \n",
       "3                                    [-1.0, -1.0, -1.0]   \n",
       "4                                    [-1.0, -1.0, -1.0]   \n",
       "...                                                 ...   \n",
       "3296                                 [-1.0, -1.0, -1.0]   \n",
       "3297                                       [-1.0, -1.0]   \n",
       "3298                                             [-1.0]   \n",
       "3299  [-0.0171, -1e-05, -1e-05, -0.0417, -0.0616, -0...   \n",
       "3300  [-0.090226, -0.06015, -0.007519, -0.097744, -0...   \n",
       "\n",
       "                                          reactants_ids  \\\n",
       "0                                     [acac_c, accoa_c]   \n",
       "1                                     [acac_m, accoa_m]   \n",
       "2                                [coa_m, msa_m, nadp_m]   \n",
       "3                             [atp_c, coa_c, fatacid_c]   \n",
       "4                             [atp_m, coa_m, fatacid_m]   \n",
       "...                                                 ...   \n",
       "3296                            [akg_n, mdadnr_n, o2_n]   \n",
       "3297                                  [amet_n, dadnr_n]   \n",
       "3298                                             [oh_e]   \n",
       "3299  [arach_c, ddca_c, fa16p1n7_c, hdca_c, lnlc_c, ...   \n",
       "3300  [alatrna_c, argtrna_c, asntrna_c, asptrna_c, a...   \n",
       "\n",
       "                                 products_stoichiometry  \\\n",
       "0                                            [1.0, 1.0]   \n",
       "1                                            [1.0, 1.0]   \n",
       "2                                       [1.0, 1.0, 1.0]   \n",
       "3                                       [1.0, 1.0, 1.0]   \n",
       "4                                       [1.0, 1.0, 1.0]   \n",
       "...                                                 ...   \n",
       "3296                                    [1.0, 1.0, 1.0]   \n",
       "3297                                         [1.0, 1.0]   \n",
       "3298                                                 []   \n",
       "3299                                              [1.0]   \n",
       "3300  [0.324, 1.0, 2.0, 2.324, 2.324, 0.090226, 0.06...   \n",
       "\n",
       "                                           products_ids  lower_bound  \\\n",
       "0                                       [aacoa_c, ac_c]      -1000.0   \n",
       "1                                       [aacoa_m, ac_m]      -1000.0   \n",
       "2                             [accoa_m, co2_m, nadph_m]          0.0   \n",
       "3                            [amp_c, fataccoa_c, ppi_c]          0.0   \n",
       "4                            [amp_m, fataccoa_m, ppi_m]          0.0   \n",
       "...                                                 ...          ...   \n",
       "3296                           [co2_n, dadnr_n, succ_n]          0.0   \n",
       "3297                                [ahcys_n, mdadnr_n]          0.0   \n",
       "3298                                                 []          0.0   \n",
       "3299                                    [freefatacid_c]          0.0   \n",
       "3300  [adp_c, apoACP_c, gdp_c, h_c, pi_c, trnaala_c,...          0.0   \n",
       "\n",
       "      upper_bound  objective_coefficient       flux_units  reversibility  \\\n",
       "0          1000.0                    0.0  mmol*gDW-1*hr-1           True   \n",
       "1          1000.0                    0.0  mmol*gDW-1*hr-1           True   \n",
       "2          1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "3          1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "4          1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "...           ...                    ...              ...            ...   \n",
       "3296       1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "3297       1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "3298       1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "3299       1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "3300       1000.0                    0.0  mmol*gDW-1*hr-1          False   \n",
       "\n",
       "      used_  \n",
       "0      True  \n",
       "1      True  \n",
       "2      True  \n",
       "3      True  \n",
       "4      True  \n",
       "...     ...  \n",
       "3296   True  \n",
       "3297   True  \n",
       "3298   True  \n",
       "3299   True  \n",
       "3300   True  \n",
       "\n",
       "[3301 rows x 17 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "reaction_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "    }\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>model_id</th>\n",
       "      <th>met_name</th>\n",
       "      <th>met_id</th>\n",
       "      <th>formula</th>\n",
       "      <th>charge</th>\n",
       "      <th>compartment</th>\n",
       "      <th>bound</th>\n",
       "      <th>used_</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>((N-acetyl-D-glucosaminyl)2-(alpha-D-mannosyl)...</td>\n",
       "      <td>n2m2masn_c</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>({[(mannosyl),(phosphoethanolaminyl)]-dimannos...</td>\n",
       "      <td>mem2emgacpail_c</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>(1,4-alpha-D-glucosyl)n-glucosyl glucogenin</td>\n",
       "      <td>ggn_n</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td>nucleus</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>(1,4-alpha-D-glucosyl)n-glucosyl glucogenin</td>\n",
       "      <td>ggn_c</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>(3R)-3-hydroxymyristoyl-[acp]</td>\n",
       "      <td>3hmrsACP_c</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2388</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>uridine-5'-monophosphate(1−) residue</td>\n",
       "      <td>urir_m</td>\n",
       "      <td>C9H10N2O8P</td>\n",
       "      <td>-1</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2389</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>cytidine 5'-monophosphate(1-) residue</td>\n",
       "      <td>cytr_m</td>\n",
       "      <td>C9H11N3O7P</td>\n",
       "      <td>-1</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2390</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>cytidine 5'-monophosphate(1-) residue</td>\n",
       "      <td>cytr_c</td>\n",
       "      <td>C9H11N3O7P</td>\n",
       "      <td>-1</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2391</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td>Composite of all DNA and RNA for biomass</td>\n",
       "      <td>dnarnatotal_c</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2392</th>\n",
       "      <td>C. elegans</td>\n",
       "      <td></td>\n",
       "      <td>freefatacid_c</td>\n",
       "      <td>None</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0.0</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2393 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        model_id                                           met_name  \\\n",
       "0     C. elegans  ((N-acetyl-D-glucosaminyl)2-(alpha-D-mannosyl)...   \n",
       "1     C. elegans  ({[(mannosyl),(phosphoethanolaminyl)]-dimannos...   \n",
       "2     C. elegans        (1,4-alpha-D-glucosyl)n-glucosyl glucogenin   \n",
       "3     C. elegans        (1,4-alpha-D-glucosyl)n-glucosyl glucogenin   \n",
       "4     C. elegans                      (3R)-3-hydroxymyristoyl-[acp]   \n",
       "...          ...                                                ...   \n",
       "2388  C. elegans               uridine-5'-monophosphate(1−) residue   \n",
       "2389  C. elegans              cytidine 5'-monophosphate(1-) residue   \n",
       "2390  C. elegans              cytidine 5'-monophosphate(1-) residue   \n",
       "2391  C. elegans           Composite of all DNA and RNA for biomass   \n",
       "2392  C. elegans                                                      \n",
       "\n",
       "               met_id     formula  charge    compartment  bound  used_  \n",
       "0          n2m2masn_c        None       0        cytosol    0.0   True  \n",
       "1     mem2emgacpail_c        None       0        cytosol    0.0   True  \n",
       "2               ggn_n        None       0        nucleus    0.0   True  \n",
       "3               ggn_c        None       0        cytosol    0.0   True  \n",
       "4          3hmrsACP_c        None       0        cytosol    0.0   True  \n",
       "...               ...         ...     ...            ...    ...    ...  \n",
       "2388           urir_m  C9H10N2O8P      -1  mitochondrion    0.0   True  \n",
       "2389           cytr_m  C9H11N3O7P      -1  mitochondrion    0.0   True  \n",
       "2390           cytr_c  C9H11N3O7P      -1        cytosol    0.0   True  \n",
       "2391    dnarnatotal_c        None       0        cytosol    0.0   True  \n",
       "2392    freefatacid_c        None       0                   0.0   True  \n",
       "\n",
       "[2393 rows x 8 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metabolite_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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